Durable Rust Resistance in Wheat Phase IIwheatrust.cornell.edu/documents/DRRW_II_21Feb10 Final-sans.pdf · Project Name: Durable Rust Resistance in Wheat Organization Name: Cornell

Durable Rust Resistance in Wheat Phase II

Proposal February 21, 2010

Submitted to the Bill and Melinda Gates Foundation

By the Office of International Programs College of Agriculture and Life Sciences, Cornell University

Contact Dr. Ronnie Coffman

International Programs, College of Agriculture and Life Sciences 252 Emerson Hall, Cornell University

Ithaca, NY 14853-7801 (USA) Telephone: (607) 255-3035 Fax: (607) 255-6683

E-mail: [email protected] REDACTED COPY: CONFIDENTIAL BUDGET INFORMATION REMOVED

Table of Contents

Summary Information ................................................................................................................... 1

Charitable Purpose ........................................................................................................................ 2

Project Description ........................................................................................................................ 2

Narrative ....................................................................................................................................... 2

Appendix A: Logframe Table...................................................................................................... 22

Appendix B: Budget [not available]

Appendix C: Detailed Description of Proposed Work ............................................................... 88

Objective 21: Improved testing, multiplication, and adoption of replacement varieties ..... 89

Objective 22: Increased levels of global investments and coordination in stem rust research and development .................................................................................................... 107

Objective 23: Stem rust populations tracked and monitored .............................................. 148

Objective 24: World-class stem rust response phenotyping facilities in East Africa ......... 193

Objective 25: Durably resistant, high yielding wheat varieties .......................................... 223

Objective 26: High breeding value wheat lines with two or more marker-selectable stem rust resistance genes .................................................................................................... 258

Objective 27: Optimized wheat improvement system in Ethiopia ..................................... 314

Objective 28: Project management, communication, and coordination ............................. 326

Appendix D: Milestones ............................................................................................................. 360

Appendix E: Impact Metrics....................................................................................................... 409

Grant Proposal – Summary Information Project Name: Durable Rust Resistance in Wheat Organization Name: Cornell University

Institutional Official authorized to submit and accept grants on behalf of the organization: Prefix First name Linda Surname Brainard Suffix Title Grant and Contract Officer II Telephone 607-255-7123

Fax 607-255-5058 Address

123 Day Hall Ithaca, NY 14853

E-mail [email protected] Web site Project Director/Primary Contact: Prefix First name Ronnie Surname Coffman Suffix Title Director Telephone 607-255-3505

Fax 607-255-6683 Address

252 Emerson Hall Ithaca, NY 14853

E-mail [email protected] Web site

U.S. Tax Status: Not for profit – tax exempt Geographic Location(s) of project: North America, Africa, Asia, Australia, Denmark

Amount Requested From Foundation ($USD):

Project Duration (months): 60

Estimated Total Cost of Project ($USD):

Organization’s total revenue for most recent audited financial year ($USD):

1


Charitable Purpose To reduce systematically the world's vulnerability to stem rust diseases of wheat through an international collaboration unprecedented in scale and scope.

Project Description The ability of the world's farmers to meet current and future demand for wheat is threatened by the highly virulent stem rust population emerging from East Africa. This project will mitigate that threat through coordinated pathogen surveillance activities, and breeding initiatives. Together, these efforts will replace susceptible varieties in farmer’s fields with seed of durably resistant varieties, created by accelerated multilateral plant breeding, and delivered through optimized developing country seed sectors.

Background and Rationale Stem Rust: Historical Perspective

Stem rust is the most feared disease of wheat. Stem rust spores arriving as late as one month before harvest can turn a previously healthy crop into a tangled mass of stems, which produces little to no grain. Moderately infected fields can produce as many as 1011 spores/hectare, which are picked up by wind currents, resulting in the movement of astronomical numbers of rust spores hundreds or thousands of kilometers to infect other regions. In the 1953 pandemic in North America, rust spores produced in fields in Kansas were deposited across 100,000 km2 of wheat 1,000 km north in North Dakota and Minnesota at a rate of over eight million spores per hectare. The result was the loss of 40% of North America’s spring wheat crop. Although individual fields can be annihilated, average yield losses on a regional basis under epidemic conditions are commonly 10%. A loss of this magnitude is enough to have disastrous humanitarian effects on wheat producing countries in the developing world, as well as substantial secondary impacts on the entire global economy. Pandemics have been noted throughout history, with significant events occurring in South Asia, China, Central Asia, East and Central Europe, North America and elsewhere in the past 130 years. The last major continental pandemic was that described above in North America. The episode triggered international collaboration that helped lay the groundwork for the development of the wheat varieties of the Green Revolution. Although stem rust epidemics have occurred since 1955, they were localized (e.g. 1973 and 1974 in Australia and the SE United States, respectively; and 1992 in Ethiopia). This 40-year period when stem rust was quiescent was a result of genetic resistance. Ug99

In 1998 a Ugandan crop scientist, Dr. William Wagoire, collected samples of a stem rust variant that appeared to be virulent on the previously undefeated and widely used major gene Sr31. Subsequent bioassays demonstrated that the Uganda isolate represented a unique pathotype (or race), which had a unique and potentially dangerous virulence pattern. In scientific terms, this race is designated TTKSK, but it is widely known by the colloquial name given the isolate: Ug99 (“Ug” for Uganda; “99” for the year its discovery was published). By 2004 Ug99 had colonized wheat fields of both Kenya and Ethiopia. An expert panel report, Sounding the Alarm on Global Stem Rust, issued May 29, 2005, declared Ug99 to be a threat to world wheat production (see www.globalrust.org). The report predicted that Ug99 would migrate across the Red Sea to Yemen, then to the Middle East, and subsequently to Central and South Asia. The predicted

2


immediate path of Ug99 to South Asia covers a region that produces 19 percent of the world’s wheat (ca. 117 million tons) and has a population of one billion people. It is likely that either wind currents or inadvertent human transport will eventually carry Ug99 to North Africa, Europe, West Asia, China, Australia, and the Americas.

Collaborative research between early 2005 and 2007 established that Ug99 defeats virtually every race-specific resistance gene used in commercial varieties grown throughout the world. Ug99 defeats more of the 50+ known major resistance genes than any previously known stem rust lineage. In 2006, researchers discovered a variant of Ug99 in Kenya (TTKST) that defeats the widely used stem rust gene Sr24. This even more dangerous race will follow the same path that Ug99 is predicted to follow. Over 90 percent of the world’s commercial wheat varieties are susceptible to the new variant, including almost all the wheat on the predicted path between East Africa and South Asia. Without swift intervention, stem rust will re-establish itself as a devastating cause of lost production in vast tracts of wheat in the developing world. In January 2007, it was confirmed that Ug99 had migrated from eastern Africa and was infecting wheat in Yemen in the Arabian Peninsula. Scientists are convinced that the Ug99 lineage will reach the Middle East in the immediate future. More recently, Ug99 was found in Iran. A summary of the status and prospects of this threat was recently published (Singh et al., 2008). Potential Impact of Ug99 on the World’s Poor

Wheat represents approximately 30% of the world’s production of grain crops. The FAO predicts that 598 million tons of wheat will be harvested this year on 220 million hectares of land. Nearly half of that production will be harvested in developing countries. On average, each person in the world consumes 68.2 kilograms of wheat each year. That equates to about 630 calories per day per person, or 1/2 to 1/3 of the minimal energy requirements of most adults. In North Africa, West and Central Asia, wheat provides more calories than all other grains combined. The Middle East and North African countries consume over 150% of their own wheat production and are heavily dependent on imports. In Sub-Saharan Africa wheat is the number one urban food staple.

Once Ug99 and its derivatives have established themselves in North Africa, the Middle East, and South Asia, annual losses could reach US$3 billion in a given year. The effects on rural livelihoods and geopolitical stability would be incalculable. Large populations of poor wheat- farming families would be seriously affected and few have alternative livelihoods. The impact on landless laborers dependent on agricultural jobs would also be severe, and one could anticipate an increase in the rural-urban migration of landless laborers and small farmers. Moreover, such large production losses would have significant implications for national economic growth rates in seriously affected countries and could even affect global wheat markets.

Durable Rust Resistance in Wheat - Phase II In early 2008, the Bill & and Melinda Gates Foundation awarded a three year grant, “Durable Rust Resistance in Wheat” (DRRW), to a consortium of institutions led by Cornell University. Details of that project’s work plan, and the Year 1 and Year 2 progress reports can be found at www.wheatrust.cornell.edu. This is a proposal for DRRW Phase II, a five-year continuation of DRRW Phase I, where year 1 of Phase II is coincident with year 3 of Phase I.

A significant addition to the Phase II proposal is Objective 21; Improved testing, multiplication, and adoption of replacement varieties. The majority of outputs of Phase I have contributed to the rapid development of locally adapted and acceptable replacement varieties resistant to prevailing

3


stem rust races in the targeted countries threatened by Ug99. The Project’s goals, however, will be realized only when farmers are planting seed of durably resistant and agronomicly improved varieties. Although the belief that “good varieties sell themselves” may be true, variety turnover in most developing countries is very slow, and the preponderance of a single variety over a long period of time is common in large wheat growing areas. Both of these features suggest that the systems that link the outputs of breeding programs with resource poor farmers are not inherently configured for the kind of response that is required to replace current susceptible varieties in a short period of time when under the threat of an epiphytotic. Objective 21 identifies the components of a ‘seed system’, and proposes coordination of multilateral interventions to improve the delivery of resistant varieties to resource poor farmers.

Another significant feature of the Phase II proposal is an integrated Gender Strategy embedded in the Activities of the Objectives (Activities 22.a.1; 25.d.1; 26.e.1, 26.e.2; 28.d.1). We acknowledge in Phase II the need to address gender equity at both the level of professional development of women wheat scientists, as well as a moral imperative to ensure food security at the household level in developing countries. We also recognize the need for a comprehensive review and appraisal of gene deployment strategies that improve the durability of deployed resistance genes or gene combinations. This is reflected in the greater emphasis on minor gene adult plant resistance (APR) and combinations of major genes where APR is not yet attainable. The “type” of resistance, and the number of genes in a given cultivar is one consideration in gene deployment to improve durability. Mixtures (blends), coordinated deployment of varieties or genes to avoid uniformity and disrupt the pathosystem, and an array of other approaches are in need of consideration. Promoting international discourse and requisite research on questions relevant to rational gene deployment strategies remains part of our portfolio and will be the subject of an upcoming DRRW Gap Analysis (an annual activity in Objective 22) In addition, we have established project-wide metrics that will aid us in monitoring the delivery of outputs and measure their impact.

Objectives (including Milestones) Appendix A contains the logframes for the eight Objectives of the Phase II proposal, numbered 21 through 28. The first digit in the identifier of each Objective is a “2,” to distinguish from Phase I Objectives. Where relevant, the relationship between a Phase II Objective and the corresponding Phase I Objective(s) are noted in the summaries below. For Phase II, we introduced “Component” as a new element in the organization of Objectives. Components are nested within Objectives and are labeled “a,” “b,” etc. Sequentially numbered Activities are then nested within Components. Outputs and Outcomes are associated with specific Activities. For Phase II, Project Milestones are equated with the Activity Outputs (with target delivery dates) and are included as Appendix D. Project Impact Metrics are attached as Appendix E.

Objective 21: Improved testing, multiplication and adoption of replacement varieties. Replacing the world’s deployed wheat varieties in the face of Ug99 will require vast sums of money, well beyond the scope of this project. This Objective is aimed at coordinating that investment, from multiple donors, which should support the provision of rust resistant wheat varieties in the short-term, but also ensure the development of sustainable national wheat seed systems that allow more rapid turnover of wheat varieties in the future. Spillover effects from

4


reviewing and modifying regulatory requirements that promote more efficient replacement of wheat cultivars will be of benefit to introducing other crops and technologies, thus mitigating food production and food security issues. An efficient and rational regulatory environment is also desirable for private sector engagement. Thus, it is important to work through current national seed systems. The goal is to mobilize and resource the major national players in each country in terms of varietal testing, seed production and seed delivery to ensure that rust resistant wheat varieties are available to all farmers. This goal dictates the choice of partners in each country. As a result of our planning and analysis during Phase I, we now define a seed system to include the following areas: variety testing, pre-release seed multiplication, regulatory framework, Breeder and similar source seed multiplication, commercial seed production, and variety promotion and popularization. During Phase II, DRRW will make modest, targeted investments aimed at relieving constraints to rapid adoption of improved varieties in two at-risk countries. Cornell will also continue active engagement in this arena in other countries with the goal of catalyzing the emergence of high performance seed sectors in all Ug99 threatened countries.

Transnational Coordination: With representation from the various donor projects anticipated, a committee will be formed to provide guidance and coordination (Activity 21.a.1). Such a committee already exists to coordinate the USAID Famine Seed Project but is not currently active. Leadership (committee chair) will come from an individual employed by one or more of the seed projects. DRRW will be represented an Associate Director/Plant Breeder and will serve as a secretariat for the committee, organizing meetings and facilitating communications.

Kenya and Ethiopia: Though relatively small in area, Kenya’s wheat crop is a critical target because it is a major breeding ground for new stem rust variants such as Ug99, and it is a major source of inoculum. Development of a seed system that replaces extant Kenya varieties with durably resistant varieties will suppress the pathosystem, addressing both of those issues. Activity 21.b.1supports increasing the number and precision of multi-location trials by both the breeding program (KARI-Njoro) and the National Performance Trials managed by the Kenya Plant Health Inspection Service (KEPHIS) that provide data for national release decisions. Activities 21.b.2 and 21.b.3 address the timing and efficiencies of Breeder Seed production by KARI. Preliminary agreement among key actors was reached on procedural and regulatory issues affecting these issues during Phase I. Activity 21.b.2 seeks formalization and implementation of collaborative strategies enabling pre-release purification and multiplication of KEPHIS endorsed Breeder Seed of KARI candidate lines. If implemented, the agreements between KARI and KEPHIS will enable availability of Breeder Seed at the time of commercial release as opposed to 1-2 years later. Activity 2.b.3 likewise seeks to rationalize KEHPIS/KARI policies and strategies in a manner that will enable KARI to produce more efficiently subsequent generations of Breeder Seed.

Activities 21.b.4 and 21.b.5 address opportunities to enhance communication among all stakeholders throughout the wheat improvement value chain, from flour millers to the Kenya Seed Company and back to KARI plant breeders. Many of Ethiopia’s resource-poor farmers depend on wheat as a source of subsistence and as a cash crop. Wheat breeding and Breeder Seed production is done by the Ethiopian Institute of Agricultural Research (EIAR), as well as by regional research institutes. The Crop Variety Register lists 41 bread wheat varieties “under production,” 28 of which have been released since 1998, but five varieties account for more than 90% (and one variety for more than half) of seed

5


production. Multiple in-country consultations with Ethiopia seed system actors repeatedly identified shortage of Breeder Seed and Pre-Basic Seed as the most critical limiting factor to the availability of Certified Seed. Dissemination and popularization strategies are by no means sufficient, but those steps are moot if the system is unable to provide Breeder and other source seed in sufficient quantity to meet downstream needs. Accordingly, the single activity (21.c.1) focuses on investments aimed at increasing EIAR’s capacity to generate Breeder and Pre-Basic Seed. Financial commitments include irrigation for main- and off-season seed production, field equipment and seed processing equipment to increase timeliness or efficiencies of field work and post harvest seed conditioning, a seed quality lab to evaluate and monitor seed lots going into production, and operational costs for seed production. In-service training for staff engaged in all aspects of seed production, processing, and quality testing is to be provided, as is training in maintenance of field and laboratory equipment.

Objective 22: Increased levels of global investments and coordination in stem rust research and development.

The overarching goal of Objective 22 will be to increase global funding for wheat improvement and rust research, and to improve coordination among donors, research institutions, and development agencies working in wheat improvement and rust research. In Objective 2 of DRRW Phase I, the primary vehicle for advocacy was in large measure driven by the launch and implementation of the project itself. The official announcement of the Project in April 2008 was widely reported, as was the DRRW-managed 2009 BGRI Technical Workshop. Tangible outcomes that we believe were related to the emergence of the DRRW project include the US $5.2M USAID famine seed project, earmark of US $1.5M for rust research to the USDA-ARS budget in the FY09 Omnibus bill, and the multi-national Delhi Declaration on Wheat Stem Rust Ug99 issued November 8, 2009. Agriculture and Agri-Food Canada’s wheat rust research program recently received an impressive $13.3 M CDN of support from Canada’s new Agricultural Policy Framework, “Growing Forward.” Opportunities are being pursued with several government agencies in Europe and Asia, as well as multilateral organizations, which should result in significant complementarities to Phase II resources. DDRW senior staff have availed themselves for media interviews and are constantly seeking opportunities to promote wheat rust investments on an ad hoc basis.

For Phase II, we believe that more resources can be mobilized for wheat rust and wheat improvement research and development through proactive advocacy. Effective advocacy will be achieved through a comprehensive strategy that unites the research collaboration-enhancing activities of the BGRI and targeted media and policymaker outreach that will keep “sounding the alarm” about wheat rust and food security. Accordingly, this Objective proposes a strategic partnership (in Components 22.b and 22.d) between DRRW management and Burness Communications (http://www.burnesscommunications.com/). We expect that the activities in this Objective will build a foundation to help the rust research community inform and inspire political and scientific leaders. We hope these leaders will choose courses of action, based on an understanding of the global implications of their policies.

BGRI Secretariat: Activities in support of the BGRI (Activity 22.a.1), continuing from Phase I, will include providing quarterly updates on wheat rust research and development activities and news items to the BGRI community worldwide, engaging the BGRI Executive Committee and other members actively in advocacy and fundraising, holding the annual BGRI workshop and

6


supporting meetings and ongoing communications of the BGRI Executive Committee, and enabling strategic investments (in non-DRRW workshops to get a rust-related session on the agenda for instance) for leveraged advocacy. New activities include the establishment of two awards that aim to help foster women wheat breeders (Activity 22.a.2). The first award, the Jeanie Borlaug Laube Women in Triticum (WIT) Award, honors early career women wheat breeders and scientists, and supports their participation at the annual BGRI Technical Workshop and a short course at CIMMYT-Obregon. The second award, the WIT Mentor Award, honors both men and women who are recognized as outstanding mentors of women wheat scientists or who have strengthened their research programs with gender-focused activities. Media: Media communications will be a new activity in the DRRW Phase II proposal and will be largely implemented by Burness Communications, with leadership from the DRRW Management Unit (Components 22.b and 22.d). Activity 22.b.1 will include promoting media coverage of the rust problem and the need for sustained support for rust research through key message development, press releases, media training, and media monitoring.

Advocacy: Face-to-face meetings to advocate for financial support, or improved coordination and cooperation among institutions and countries will be essential to meeting our overall advocacy objectives. Visits to donor nation embassies by DRRW Management and/or BGRI Executive Committee members to obtain funds to support research aimed at combating the wheat rusts will be supported (Activity 22.c.1). Policymakers are key allies in the global effort to understand and manage the wheat rust problem, and they need information specifically targeted to them that addresses their priorities (Activity 22.d.1). Activities in this component will develop communications materials for policymakers and donors, and develop an annual gap analysis to identify shortfalls in funding and collaboration in rust research and wheat improvement (Activity 22.d.2).

The Internet is fast becoming the global hub for all information, with many knowledge resources being accessible via the web. The DRRW project will continue to harness this “communications revolution” to provide critical information for BGRI members, rust researchers, policymakers, donors, and the public by maintaining and augmenting a catalogue of wheat improvement and rust research projects, institutions and people (Activity 22.e.1); and maintaining a user-friendly BGRI website (Activity 22.e.2).

Objective 23: Stem rust populations monitored, tracked and characterized Knowledge of the distribution and incidence of the stem rust disease (surveillance) and of races of the stem rust pathogen (race analysis and tracking), and the potential impact of these races on local wheat germplasm, are all fundamental to the formulation and adoption of appropriate national and international policies, investments, and strategies in plant protection, plant breeding and in seed systems. A global decline in the incidence of stem rust over the past 40 years, attributable at least in part to resistance breeding and the widespread deployment of the resistance gene Sr31, led to many countries abandoning stem rust surveillance and an alarming reduction in the global skill base in rust race analysis and general rust pathology. These deficiencies were addressed in Objective 3 of DRRW Phase I, in which limited and targeted stem rust pathogen characterization was undertaken at three ARIs, the establishment of capacity for in-country stem rust race analysis in Kenya and Ethiopia was initiated, and a Global Cereal Rust Monitoring System (GCRMS) with standardized protocols for surveillance and handing of rust isolates was established.

7


This Objective (23) is the only Phase II objective targeting the actual causal agent of stem rust, Puccinia graminis f. sp. tritici, and is the only initiative attempting to document and understand global variability in this pathogen. The information generated on the distribution of stem rust races, including TTKSK and other Ug99 variants, and the incidence and distribution of evolving stem rust variants, will be important in underpinning pre-breeding (Objective 26), breeding (Objective 25), and the release and post-release management of wheat germplasm (Objective 21). It will also provide guidance to the stem rust phenotyping activities planned under Objective 24, and will be instrumental in advocacy efforts under Objective 22.

Global Cereal Rust Monitoring System (GCRMS): The International Focal Point (IFP) at FAO will be responsible for overall coordination and delivery of the proposed outputs of Component “a.” The IFP will supervise technical staff working on database and tool development. Officially nominated National Focal Points will be responsible for data compilation, quality control and information dissemination at the country level. An overall scheme on operational aspects, including information flows, was provided in the DRRW Phase I proposal, and we have revised this significantly for Phase II based on lessons learned (Appendix C, Supplement 23.2 Global Cereal Rust Monitoring System, information and rust sample flow).

Activity 23.a.1 will maintain and enhance the functional information platform and core databases for tracking and monitoring rust populations by a) expanding, enhancing and maintaining the core databases that underpin the GCRMS, which includes the routine import and maintenance of field survey data, trap nursery summary information, race analysis summary information and potentially the future inclusion of trap plot data, b) facilitating efficient data management by the development of automated or semi-automated procedures for data import into the centralized core database, c) routine updating and maintenance of secondary data, including climatic and environmental data, and d) developing customized analytical tools that facilitate easy integration of the core and secondary data sets in a meaningful way. To enhance the core rust pathogen information described in Activity 23.a.1 complementary national or sub-national information relating to wheat production, agro-ecologies, varietal composition and performance are important in allowing assessments of rust incidence and threat. Existing information platforms developed by CIMMYT, namely; the International Wheat Information System (IWIS) and the Wheat Atlas will be enhanced and integrated into the GCRMS (Activity 23.a.2). Using IWIS as an underlying data management platform for wheat variety and performance data, the Wheat Atlas component will extract relevant variety summary information and provide an intuitive user interface to a host of additional wheat sector data at the country level. This data rich electronic atlas of country-level wheat data will be integrated in a seamless manner with the updated rust surveillance and pathogen monitoring information derived from Activity 23.a.1.

Under Activity 23.a.3 information dissemination on surveillance and monitoring of rust populations will be strengthened by a) routine delivery of information products derived from the GCRMS to targeted user groups and b) core information products comprising web-based situational updates, bulletins and web mapping tools. Delivery of summarized race analysis and trap nursery data will be important components. The activities described above are designed to convert the current emerging monitoring system into a fully operational system, delivering accurate and timely information to inform decision-making and provide for the timely response to any threat posed by virulent races of stem rust.

8


In the second Phase, the missing link in an effective GCRMS will be implemented—a global reference center for stem rust isolates. The DRRW is leveraging investments by Aarhus University to establish a global reference center for stem rust (Activity 23.a.4). DRRW funds will contribute training activities in the area of stem rust race analysis for national programs scientists. This advocacy success will lead to a Global Rust Reference Center (GRRC) that will:

• Accept stem rust samples year round from any National Surveillance effort. • Be collected in a global reference collection of stem rust isolates. • Train national program pathologists in standard surveillance and race typing protocols.

The GRRC will allow for a fully functional global stem rust monitoring system. Surveillance: In most of the countries affected or at immediate risk of TTKSK and its variants, stem rust has appeared in warm areas. Many current stem rust genotypes used in trap nurseries have a vernalization requirement or photoperiod sensitivity that precludes final disease assessment of stem rust infections (on stems). Although several laboratories use the North American (NA) differential set, most use a combination of NA, Stakman and other tester genotypes and therefore the number and type of differential genotypes and Sr-genes varies. Because of differences among, and occasional impurity of, differential sets, interpretation of surveillance data among countries is difficult. To eliminate these problems, ICARDA will undertake central seed multiplication and seed dissemination of wheat genotypes for use as trap plots (Activity 23.b.1). This will be achieved by:

• Collecting current genotypes used in trap plots. A stem rust race analysis set and stem rust monogenic lines were obtained from Dr. Jin (USDA, CDL-Minnesota) and Dr. Fetch (AAFC), respectively, in 2008.

• Large-scale seed increase of differential genotypes at ICARDA where both spring and winter type and/or day-length sensitive Sr-genotypes can be grown.

• Distribution of seed following clearance by ICARDA’s seed health lab. Once adequate quantities of pure seed are available, current and future stem rust trap nurseries will be revised and a new set of Sr-genotypes comprising the most important Sr-genes in spring type and or day-length insensitive backgrounds, selected mega commercial cultivars, and known sources of APR gene/s will be selected by the team to be used as an international trap nursery. The International Stem Rust Trap Nursery (ISRTN) will be provided to rust labs and NARS. Seed Health Certificates will be issued by ICARDA’s seed health lab to enable seed import. The nursery will be sown in two 1-meter rows in rust-prone areas in each country and field scoring will be undertaken using a modified Cobb scale. Key Sr-genes and/ or commercial cultivars grown in regions carrying the key Sr-genes (Sr31, Sr24, Sr36 and Sr38) will be planted as large breeding plots (4 X 4-meter rows) in research stations every year. Geo-referenced information of these locations will be mapped and virulence patterns will be monitored every year at each location. Virulence frequencies will be determined over the years, within and across locations.

Activity 23.b.2 will train young scientists in the field of rust surveillance, field-based pathogenicity surveys (“trap nurseries”), and data management. This will involve: a) Training of field surveyors to use survey protocols, rust sampling, disease data collection, and Global Positioning System (GPS) information; b) Conducting traveling rust-survey workshops; c) Expanding existing networks of national surveillance teams to cover priority countries in Africa, Asia and the Middle East at-risk of virulent races of stem rust; d) Identifying National Focal

9


Points in all new countries incorporated into the network; and e) Providing technical support and capacity building to at least 10 countries in the network on an annual basis.

Because rust epidemics can develop rapidly, and high rust levels can threaten neighboring regions, immediate response and expert assessment is required. Contingency funds are therefore included to provide some flexibility in engaging a consultant(s) should concerns arise about rust outbreaks in any country not under surveillance (Activity 23.b.3).

Pathogen characterization: Seedling based assays conducted in plant growth facilities remain the only way to determine the pathogenicity spectra of rust isolates. Some of the most useful information in guiding resistance breeding activities that came from Phase I surveillance and tracking activities was from the race analysis work conducted by AAFC, USDA, University of the Free State (South Africa) and the Seed & Plant Improvement Institute (Iran). In Phase II, Drs. Jin and Fetch will continue to provide technical backstopping for countries undertaking race analysis (i.e. verification of putatively new races), and undertake limited and strategically targeted race analysis for countries that do not have this capacity (Activity 23.c.1).

Quarantine restrictions regarding the exchange of viable rust isolates between countries have hampered efforts to gain insight into the diversity of stem rust races in many countries. While AAFC and USDA will continue to offer limited race analysis that is constrained by seasonality, it will be vital in Phase II to develop in-country race analysis capability, both in terms of skills and infrastructure (Activity 23.c.2). Skills in race analysis and operational infrastructure exist in India, Iran, Ethiopia and Turkey, and funds are available in some projects being managed by FAO for additional infrastructure upgrades. Resources for training in race analysis and infrastructure in Kenya and Ethiopia are allocated under Objective 24 in the Phase II proposal. Allocations of limited funding to allow Turkey and India to undertake race analyses are included. The most efficient and likely sustainable way of establishing in-country race analysis capability in countries other than these will be to identify and to train key personnel in race analysis. The training needed will be of at least three months duration and should take place at some combination of AAFC, University of The Free State, University of Sydney, the USDA Cereal Disease Laboratory, or at Aarhus University’s Global Reference Center (Activity 23.a.4). Notwithstanding the importance of detailed in-country race analyses, the most pressing challenge is to resolve the current distribution of TTKSK and Ug99 variants. Because of the difficulties and time required to establish in-country capacity in race analysis in all at-risk countries, efforts to obtain preliminary baseline information on the incidence of stem rust plus the virulence of isolates for the key resistance genes Sr24, Sr31 and Sr36 initiated in Phase I will continue. This will be achieved by low resolution surveys in each country involving collection of rust samples, inoculation of duplicate “Quicksets” with the bulk, and marker analysis using host tissue from all plants on which stem rust is found. Molecular marker assays conducted in Australia will use diagnostic markers for important rust resistance genes, including Sr24, Sr31, and Sr36.

The increase and distribution of pure seed for trap plots proposed to be undertaken by ICARDA will therefore be extended to include seed of differential genotypes used for race determination. The genotypes to be used and distributed will be based on discussions initiated at Obregon in March 2009 and being coordinated by Dr. Fetch. Dr. Nazari, using pure seed sources, will then initiate seed increases and distribution to countries undertaking race analysis.

10


Preliminary surveys of barberry conducted in Kenya (Jin), Uzbekistan and Turkey (Park) have established the existence of aecial infections by a form of the stem rust pathogen Puccinia graminis. While it is not clear if some or all of these infections are actually due to the form of P. graminis that infects wheat (P. graminis f. sp. tritici), it nonetheless demonstrates clearly that barberry continues to play a role in the life cycle of P. graminis, although likely minor, in at least some regions. Activity 23.c.3 will involve more extensive surveys of barberry in eastern Africa and possibly neighboring regions, and analyses of any aecial infections found at the USDA Cereal Disease Laboratory to establish what f. spp. are present, and if P. graminis f. sp. tritici is found, what races are present. Protocols to extract DNA from dead rust urediospores and permits to allow importation were previously developed at University of Sydney. The SSR fingerprint of “Ug99” and other races within this lineage provide a means of distinguishing stem rust isolates that do not belong to the “Ug99” lineage. Published SSR markers and new SSR markers developed by USyd will be used to fingerprint international collections of the stem rust pathogen (Activity 23.c.4). This will apply to situations where concern exists about the potential presence of a member of the “Ug99” lineage, and also more broadly to isolates of both bread wheat and durum wheat from different regions to gain a better understanding of global genetic variability in this pathogen. Recent sequencing of P. graminis f. sp. tritici genome provides an important new resource for understanding the evolution and diversity of this pathogen (USDA, Broad Institute). In addition, several isolates of P. graminis f. sp. tritici including Ug99 and 3 members of this lineage have been sequenced using Next-Generation technologies (Illumina) resulting in a PgtSNP database of over 1 million loci. These results are being used to develop a rapid diagnostic assay (real-time PCR) for the identification Ug99 and members of this lineage (USDA). In Activity 23.c.5 Next-Generation sequencing of representative isolates from around the world will be used to expand the current Pgt SNP database allowing the development of rapid molecular diagnostic tools for the identification of the major races lineages worldwide, as well as, new emerging race groups.

Host characterization: Knowing the distribution and nature of stem rust races is of fundamental importance in guiding pre-breeding and breeding for resistance. This information is also important in the post-release management of stem rust, but its value is significantly lower in the absence of knowledge of the stem rust resistance genes present in wheat varieties under cultivation. Combined knowledge of race distribution and of the resistance status of cultivars allows risk assessments and also informs the threat of new races to production of current varieties in any given geography. To better understand geographical distribution of rust resistance genes in the major wheat-growing areas, Activity 23.d.1 will involve collecting and multiplying seed of commercial cultivars grown in countries affected or at risk of “Ug99” (representative commercial cultivars are available through ICARDA seed collection and, in 2008, the 10 most currently grown cultivars in CWANA countries were obtained and planted for large-scale seed increase at quarantine isolation areas at ICARDA). Race determinations of cereal rust pathogens can only be conducted in seedling tests under controlled growth conditions. Field-based trap plots provide useful information on the presence of specific virulences in a region. Both approaches are entirely dependent on host genotypes carrying target resistance genes. Unfortunately, many genotypes used as differentials in wheat rust work carry multiple resistance genes, often leading to confusion and incorrect virulence

11


determinations. Work over the past 20 years at USyd led to the identification of the Australian wheat cultivar “Avocet” as a useful background genotype into which single genes conferring resistance to stripe rust have been backcrossed. The Avocet NIL series has been deployed internationally as trap plots and have been used by some laboratories as differential genotypes for seedling race analyses. Similar but incomplete sets of NILs exist for stem rust, produced in Canada (LMPG series), Australia (W2691 series), and the USA (ISr series). Activity 23.d.2 will involve compiling, verifying and preserving all current stem rust NIL stocks and the production of a new NIL set for stem rust using an awnless version of Avocet lacking Sr5 and Sr26 and carrying Lr46/Yr29 alone or in combination with Lr34/Yr18. Coordinating Surveillance Activities: Funds are requested to allow the Objective Leader to convene regular meetings of the Surveillance Advisory Panel via teleconference, to interact face-to-face with all participants within Objective 23, and also for periodic interaction with Leaders of other Objectives, to ensure the works progresses smoothly and that it is in line with the overall goal of the Phase II proposal (Activity 23.e.1).

The Surveillance Advisory Panel will provide quality assurance of surveillance data; facilitate surveillance activities (sample acquisitions, requests for race analysis by a third party, capacity building/ support, data sharing); support national program activities; raise awareness of significant developments and provide advice (to be channeled through FAO); manage interactions with rust surveillance activities funded outside the Phase II proposal, to ensure complementarities and to prevent duplication; decide on the composition of trap nurseries – annual review and input from other objective leaders; and provide guidance to the Objective Leader (R. Park) in managing inter-objective coordination (e.g. using surveillance data to inform breeding, pre-breeding and seed systems strategies). Objective 24: World-class stem rust response phenotyping facilities in East Africa.

Kenya and Ethiopia continue to be the only places in the world where the Ug99 lineage can be used year round in support of the mission-critical pre-breeding and breeding components of this Project. In collaboration with Objective 25 (Breeding), germplasm will be evaluated with the goal of developing varieties having adult plant resistance (APR) or pyramided combinations of major genes. The discovery of new sources of resistance in both domestic and wild relatives of wheat, in conjunction with Objective 26 (Pre-Breeding) activities, will increase the diversity of genes available to breeding programs. The precise phenotypic evaluation of plants for APR, in the field and in tunnel houses, is central to the DRRW project and is a necessary complement to the activities of Objectives 25 and 26. The development of world-class screening facilities in the center of origin of Ug99 and other threatening pathotypes of stem rust is critical to our ability to evaluate germplasm for new sources of resistance, to incorporate them in breeding programs, and deploy them as durably resistant varieties. The activities in this objective serve not only the global wheat community, but also have a direct benefit to East African wheat growers, producers and consumers. Activity 25.b.3, Kenya breeding, and Activity 27.a.3, Ethiopia durum and bread wheat breeding programs are direct beneficiaries of this Objective. Phenotyping in Kenya and Ethiopia: The proposed work is an expansion of the phenotyping work of DRRW Phase I Objective 4 undertaken at the Kenya Agricultural Research Institute (KARI) Njoro Research Center by Dr. R. Wanyera and P. Njau, and the Ethiopian Institute of Agriculture Research (EIAR) with Dr. B. Girma. The Activities in this Objective will increase the capacity to phenotype germplasm for reaction to stem rust race Ug99. Specifically, and in

12


concert with Phase I, bread wheat germplasm will be screened in Kenya and durum wheat in Ethiopia (Activities 24.a.1 and 24.b.1, respectively). The data generated will be collated and shared with collaborators, major stakeholders, and the international community. Governance of the data and germplasm is determined by a Germplasm Access Agreement presented to each collaborator, and by the standard Material Transfer Agreement (sMTA). Activities 24.a.2 and 24.b.2 are new to Phase II and complement Objective 26 (Pre-Breeding) by providing high quality phenotypic data and mapping information on germplasm containing new sources of resistance (about 3000 genotypes/year). The phenotypic data will be generated both for seedlings in controlled greenhouses and on adult plants in semi-controlled tunnel houses. The coordinated screening of seedling and adult plants will distinguish between two types of resistance—major gene resistance (seedling or hypersensitive response genes) and minor gene (adult-plant) resistance. The outcomes of these activities will include the identification and mapping of novel sources of durable stem rust resistance (with Objective 26) that will be made available to breeders to deploy in breeding programs (with Objective 25). Using the same approach, resistance will be characterized and confirmed in both bread wheat (Activity 24.a.3) and durum wheat (Activity 24.b.3) varieties being considered for release in at-risk countries. The genetic basis of resistance of candidate and released varieties will inform national and international resistance management strategies that foster sustainable wheat production.

Underlying all of these activities (24.a.1, 24.a.2, 24a.3, 24.b.1, 24.b.2, and 24.b.3) is the need to maintain and multiply pure isolates and regularly monitor stem rust races in the field. Activities 24.a.4 and 24.b.4 will ensure proper management of the pathogen and field epiphytotics. These activities will also support national pathogen surveillance and race analysis in conjunction with Objective 23, but with a specific commitment to East Africa. Regular monitoring of the temporal-spatial occurrence of TTKSK and other extant Ug99 variants, and the evolution of this or other lineages, will inform appropriate use of inocula in screening nurseries and the development of subsequent breeding and gene deployment strategies. Activity 24.b.6 explicitly seeks to redress our lack of knowledge of the nature of stem rust on tetraploid wheat species and varieties in Ethiopia, thus enabling more effective screening of durum and other tetraploid species at Debre Zeit. Activities 24.a.6 and 24.b.7 will support expansion of seed health units within KARI and EIAR to work with national quarantine systems to preclude the import or export of seed borne disease and stem rust spores into and out of Kenya and Ethiopia.

In Activities 24.a.7 and 24.b.8, a set of training events, exchange visits and participation at international fora by KARI and EIAR scientists are proposed. Exchange visits by scientists from KARI and EIAR staff to advanced cereal rust laboratories will foster information exchange, technology sharing and research skill development in rust pathology. CIMMYT will provide training in field skills in the areas of data recording and database management, recognition and screening of rust pathogens, selection, resistance breeding and seed health management.

During Phase I, modest screening facilities were established in Kenya with KARI-Njoro, and in Ethiopia at Debre Zeit, for phenotypic evaluation of germplasm for resistance to Ug99. At this juncture, it is necessary to strengthen these facilities for adequate phenotyping and the long-term sustainability of these important screening nursery operations (Activities 25.a.8 and 25.b.9).

13


Objective 25: Durably resistant, high yielding wheat varieties. The work described here continues and expands the Durable Rust Resistant Wheat (DRRW) Phase I wheat breeding activities. The overarching goal is to provide National Programs in at-risk countries with a continually improved and diverse array of situation-appropriate candidate varieties that combine Ug99 resistance with attributes required for rapid uptake by small-scale farmers. For spring bread wheat (Activity 25.a.1 and 25.a.2) and spring durum wheat (Activity 25.b.1), CIMMYT’s long standing two generations per year Mexico-based “shuttle” breeding system continues to be augmented with selection at the East Africa phenotyping sites (see Objective 24) to produce candidate replacement varieties. Durum breeding, now more directly focused in Ethiopia, provides continued benefits to India and other at-risk countries producing durum wheat. The durum work described here will involve close collaboration with in-country breeding supported in Objective 27. Minor gene based “adult plant resistance” is the primary means of delivering durable resistance in spring bread wheat, while combinations of two independent major genes is the near-term stem rust resistance solution for durum wheat varieties. Candidate replacement varieties derived from all International Center breeding activities are distributed to national programs through CIMMYT’s international testing network.

The past years have demonstrated a pressing need to expose National Program scientists to techniques not only in stem rust pathology and resistance breeding, but also in the design, execution, and analysis of multi-location performance trials. In Activity 25.d.1, we describe a suite of training events to address this need. We also propose to invest in the wheat component of ICIS (International Crop Information System, http://www.icis.cgiar.org/icis/index.php/ICIS, in order to reach the long-sought goal of a user-friendly common platform that will facilitate information management and sharing aspects of field nursery, yield trial, pedigree, and molecular marker data.

New to Phase II is to combine Whole Family Training and Participatory Variety Selection to collect data on wheat traits desired by all members of the wheat producing unit (both men and women). In Activity 25.c.1 this approach will be implemented in coordination with in-country gender specialists during farmer field days in India and Ethiopia.

Collectively, these activities and associated investments address nearly 50 million hectares of wheat in developing countries that are threatened by Ug99 and its derivatives, and provide the initial foundation for a new era of cooperative, global wheat improvement. Objective 26: High breeding value wheat lines with two or more marker-selectable stem rust resistance genes Objective 26 rationalizes Phase I Objectives 6, 7, and 8 into a single Objective. Refinement and expansion of promising, high-priority Phase I activities will direct future research and germplasm development. Continued focus on discovery, introgression, and characterization of new HR and APR genes will strengthen the pipeline of useful genes available in wheat breeding programs and enable strategic deployment of gene combinations. Alien-derived genes on reduced chromosome segments will be moved into elite genetic backgrounds, while newly discovered genes on large alien chromosome segments will be manipulated to recover small translocations. Development of DNA diagnostic markers for effective management of HR and APR genes is needed for global wheat breeding programs and will continue to be a central focus. Systemic emphasis on delivery of high breeding-value lines with desirable gene combinations together with diagnostic markers will ensure translation of research efforts into breeding

14


products. The emphasis of resistance gene combinations (minor with minor, major with major, or minor with major) reflects a cultivar-level gene deployment strategy aimed at minimizing exposure and defeat of our cadre of resistance genes. While we will employ modern molecular genetics, cytogenetics, and germplasm development techniques in the activities proposed, we are optimistic and aware of potential contributions from rapid advances in genomics and molecular biology. High resolution genetic mapping and diagnostic marker development for HR and APR genes in Phase II will enable cloning and follow-up manipulation of these loci in the medium to long term. Thus, genetic resources and information developed during this project will help drive future molecular breeding and biotechnology solutions in wheat improvement. Gene discovery, postulation, and phenotypic support of genetic mapping and germplasm development: Seedling screening of stem rust resistance is an integral component of the global effort to combat stem rust (Activity 26.a.1). Programs led by Yue Jin & Matt Rouse (USDA-ARS Cereal Disease Lab), Brian Steffenson (Univ. of Minnesota), Jacob Manisterski (ICCI, Tel Aviv University), Zak Pretorius (Free State Univ.), and Harbans Bariana (Sydney Univ.–PBI): 1) provide phenotypic data for genetic mapping of HR genes having effective levels of resistance to Ug99 and other highly virulent and evolving races, 2) postulate genes based on multi-pathotype responses and infection types, 3) enable APR resistance breeding by accounting for HR genes, 4) discover new resistance genes by screening collections in primary, secondary and tertiary gene pools, 5) assist in selection of resistant lines resulting from wild relative introgression, parent building, and breeding efforts, and 6) provide critical input on development of new segregating populations for mapping/inheritance studies. Each program is also committed to training the next generation of leaders in this artful, exacting field.

A major bottleneck in discovery and genetic mapping of durable rust resistance loci is the lack of knowledge, methodology and expertise to perform routine precision APR phenotyping in controlled or semi-controlled environments (greenhouses, hoop/tunnel houses, plant growth rooms). Precision APR screening will be required to fully dissect APR loci by minimizing environmental variation (or even interference) and controlling important variables during inoculation, infection, and disease development that quantitatively alter resistance responses (Activity 26.a.2). Zak Pretorius is poised to focus his program to develop this priority area. Complimentary controlled screening and validation of APR resistance phenotypes will be undertaken through research efforts lead by a representative from the Ethiopian Institute of Agricultural Research, Sridhar Bhavani (CIMMYT, Njoro Kenya), and Brian Steffenson (University of Minnesota). In addition to refining and documenting techniques and quantitative measures required for stem rust APR precision phenotypic evaluation, these programs will speed gene discovery, APR genetic mapping and germplasm development efforts. Population development and introgression of new sources of resistance: Activity 26.b.1 is focused on the development of mapping populations, allelic tests or other inheritance studies, and transfer of resistance genes from new, primary gene pool-derived sources of HR and APR (from Phase I or Activities 26.a.1, 2) to adapted genetic backgrounds; these resources are necessary to characterize additional useful, marker-selectable, resistance genes. High-priority populations will be used for genetic mapping in 26.c.1, based on consultation with Yue Jin, Harbans Bariana, Ravi Singh, and Jim Anderson.

Although alien-derived chromosome segments have provided massive global contributions to on-farm wheat production (such as T1BL.1RS, T1AL.1RS, and T1BL·1BS-3Ae#1L), the historic pace of exploitation of traits from alien donors has been dismal. While previously constrained by

15


the laborious and highly technical nature of the required cytogenetic techniques, advances in DNA marker technology and application have created a paradigm shift concerning transfer of desirable traits from alien species. Enhanced efforts to introgress broadly effective resistance genes from existing cytogenetic stocks and secondary and tertiary gene pool accessions will provide even greater diversity of stem rust resistance. In Activity 26.b.2, amphiploids, chromosome addition, and/or translocation lines will be produced by crossing spring wheat and durum lines with desirable donors identified during Phase I and through Phase II activities (26.a.1, 2). Cytogenetic stocks produced by Eitan Millet (ICCI), Mike Pumphrey (USDA-ARS), and Ian Dundas (University of Adelaide) with new resistance genes from Aegilops. bicornis, Ae. longissima, Ae. sharonensis, Ae. speltoides, Haynaldia villosa, and Thinopyrum species will provide additional raw material for longer-term germplasm enhancement activities (26.b.3). Transfer of potentially new HR and APR genes discovered in Ae. tauschii is a medium-term strategy due to “normal” homologous recombination of chromosomes. Populations will be developed from promising wild relative accessions in each species to study inheritance/allelism of resistance and enable genetic mapping as part of Activity 26.c.1. High-priority populations will be used for genetic mapping in 26.c.1, based on consultation with Yue Jin, Harbans Bariana, Ravi Singh, and Jim Anderson. Wheat-alien chromosome lines, translocation lines, and partial amphiploids with resistance to multiple stem rust races including Ug99 were recently indentified from Ae. caudata, Ae. geniculata, Ae. sharonensis, Ae. searsii, Ae. speltoides, H. villosa, Th. intermedium, Th. junceum, and Th. ponticum by Steve Xu, Ian Dundas, Eitan Millet, and Mike Pumphrey. With Avtivity 26.b.3 cytogenetic manipulation of these stocks to produce translocation lines useful in wheat breeding programs has been initiated, but will require continued efforts to derive useful germplasm. Resistance genes in stocks produced as part of Activity 26.b.2 will provide more targets requiring this effort. Mapping, validation, and delivery of marker-selectable resistance genes: Research focused on mapping and fine-mapping of loci with effective resistance genes in existing populations segregating for HR genes, recombinant inbred line or double haploid APR populations, and additional APR and HR populations either being developed or that will be developed by project collaborators (Activities 26.b.1,2 and 26.c.2) will enable identification of diagnostic markers required to pyramid and manipulate both HR and APR genes (Activity 26.c.1). The increased emphasis on precision APR phenotyping (Activity 26.a.2 and Objective 24) will accelerate characterization and validation of APR markers. As loci contributing to APR are identified, phenotypic effects, epistatic interactions, and consistency need to be validated/determined in different genetic backgrounds. Under Activity 26.c.2 this reliability information provides wheat breeders a means to prioritize target loci in forward breeding efforts. Suitable validation materials (backcross, near-isogenic lines, or near isogenic-populations) contrasting for APR loci in appropriate elite genetic backgrounds will be developed and tested in East African screening nurseries and in precision APR phenotyping experiments as part of Activity 26.a.2. Development of mutant resources for APR donors is a complimentary validation strategy that may also aid in identification of diagnostic DNA markers and eventual cloning of APR genes; large mutant populations will be developed and characterized for two or more high-priority donors. The delivery of high-breeding value wheat lines, each with two marker-selectable stem rust resistance genes, to breeding programs will be enhanced in Phase II by the expertise of

16


CIMMYT’s David Bonnett and Susanne Dreisigacker (Activity 26.c.3). Improved communication, integration, and delivery to breeding programs will ensure adoption of Objective 26 outputs. Gene deployment strategies can be more effectively addressed due to centralized pyramiding efforts and useful markers that will be refined in the CIMMYT genotyping laboratory for routine use in their Global Wheat Program (Breeding Objective). Collection, preservation and distribution of genetic resources and information: Valuable genetic stocks, mapping populations, and high value breeding lines produced by Objective 26 efforts will be stored at dual locations (Activity 26.d.1). The USDA-ARS National Small Grains Germplasm Research Facility and CIMMYT gene banks will preserve and distribute mapping populations and other stable germplasm. For genetic stocks requiring cytogenetic expertise for maintenance (amphiploids, partial amphiploids, addition lines, etc.), the Wheat Genetic and Genomic Resources Center at Kansas State University and the Tottori Alien Chromosome Bank of Wheat have agreed to preserve and distribute materials. These centers have long-term missions to maintain and share genetic resources with the wheat genetics community.

Jorge Dubcovsky will proactively incorporate the genetic mapping, marker information, protocols and germplasm developed in the project into the scope of the wheat marker-assisted selection website (http://maswheat.ucdavis.edu/) developed and maintained by his group at UC Davis (Activity 26.d.2). This user-driven site is frequented by wheat geneticists across the globe (~4500 hits per month) to access information on genes that have supporting DNA marker information. Relevant information categories will include gene-specific marker information, detailed protocols, donor germplasm available, contact information for germplasm distribution, and contact information for research labs with expertise on specific markers or genes. Dubcovsky’s group will also coordinate enhanced germplasm distribution. Evaluation of Genomic Selection Models in Breeding for APR: Led by Mark Sorrells of Cornell, Activity 26.e.1 will explore improved efficiencies to breeding for durable rust resistance by employing Genomic Selection (GS) in a recurrent selection scheme to simultaneously select for stem rust APR in spring bread wheat germplasm characterized for high agronomic performance. GS is a new selection methodology that is specifically developed to improve genetic gain in selection for quantitative traits. There is an added benefit in that it can reduce the burden and expense associated with phenotyping large populations for traits of low heritability. Given the polygenic nature of APR, the difficulty of phenotypically evaluating resistance to multiple pathogens and races, and the immediate need for durable rust resistance, GS is a strategy that offers considerable appeal. Activity 26.e.2 addresses the hypothesis that by shifting some wheat breeding activities from field intensive phenotypic evaluations to genotypic intensive lab work, as enabled by GS, plant breeders may experience less work-life conflict. Lowering professional barriers such as season-long field activities that include travel away from family, may result in increased recruitment of scientists to this profession. Women considering a career in plant breeding will especially benefit from decreased work-life conflict.

Molecular Genetics of Rust Resistance Near the Sr9 Locus: Led by Matthew Rouse of the USDA-ARS-CDL, Activity 26.f.1 is based on recent data that indicate the presence of a Ug99 resistance locus linked or allelic with the Sr9 locus (resistance genes temporarily designated as SrWeb and SrGabo56). Several stem rust alleles are present at the Sr9 locus, which is also known to be allelic with stripe rust resistance genes Yr5 and Yr7. Scientists at the USDA-ARS, Pullman, WA are conducting studies in order to clone Yr5. The availability of markers and sequence information at the Yr5 locus will enable the development of markers potentially tightly linked

17


with Sr9 and SrGabo56 in available mapping populations. In order to test for the allelism of SrGabo56 and Sr9, populations for testing allelism have been derived. Screening of these populations with both stem rust and molecular markers can determine whether or not SrGabo56 is and allele of Sr9.

The unique phenotypic diversity at the Sr9 locus makes this an appealing candidate for cloning. Understanding the variation responsible for five Sr9 alleles, Yr5, Yr7, and SrGabo56 will uniquely enhance our understanding of the molecular mechanisms of resistance and race-specificity and could provide base knowledge for long-term projects including the development of new resistance alleles and for the deployment of durable resistance. The marker information available from the mapping of Sr9a, SrWeb, SrGabo56, and Yr5, the sequence information available from the Yr5 mapping project, and the plant populations currently available make the molecular dissection of resistance at this locus feasible.

Objective 27: Optimized wheat improvement system in Ethiopia. Ethiopia is at once home to a large number of wheat-dependent farmers and consumers, and one of the few countries already colonized by Ug99. It is also the likely jumping off point for migration of Ug99 either to west-central Asia, or South Asia. For these reasons, Cornell embraces the notion that an Ethiopia-specific Objective aimed at supporting Ethiopia per se, is logical for both local (Ethiopia’s population) and global reasons. Overall coordination of EIAR DRRW activities is also supported. Coordination: Under Activity 27.a.1 the EIAR wheat breeding programs for bread wheat and durum wheat will be coordinated with contributions from plant pathology, agro-industrial stakeholders, seed production stakeholders, and collaborations with many international and regional programs. Wheat-based research centers in Ethiopia will contribute to the evaluation and selection of varieties to be considered as candidates for commercial release. Staffing positions will be identified and responsibilities outlined in contribution to an efficient program that delivers genetic progress on yield performance and protection against endemic pathogens. Progress will be evaluated twice annually. Bread and Durum Wheat Breeding Programs: Both bread wheat and durum wheat breeding programs will involve a two cycle per year evaluation and selection program (Activities 27.a.2 and 27.a.3). Agronomic, pathologic and end-use objectives will be prioritized, and introductions from international nurseries will be evaluated and selected with these priorities in mind. Various sets of germplasm at different stages of development will be distributed for evaluation at a number of wheat research centers, with this information contributing to decisions leading to promotion of breeding lines and variety release. An array of key breeding lines will be genotyped, and along with phenotypic data collected from the research centers, will inform the crossing programs.

Training: Activity 27.a.3 will advance the human resource capacity for wheat research in Ethiopia. Research skills of technical staff will be enhanced with training opportunities in applied field research, including nursery management, data collection, and data entry and compilation. EIAR scientists will have training opportunities through exchange visits with ARIs and sister institutions, as well as longer-term training through visits to ARIs. A needed skill base in routine preventative maintenance and minor equipment/engine repair will ensure that equipment and capital investments are secured and contributing to program efficiencies.

18


Facilities: Equipment investments at EIAR, including continued investments in irrigation capacities that enable two cycle/year breeding programs, will maximize genetic progress (Activity 27.a.5). Needed renovations and equipment for laboratories, greenhouses, seed cold storage facilities that were begun in Phase I will need additional investment in the following Phase II. These investments will contribute to efficient breeding programs and allow the necessary delivery of genetic progress that will contribute to improved varieties that will result in a contribution to food security for Ethiopia. Objective 28: Project management, communication and coordination

Management and coordination will be similar to Phase I of the Durable Rust Resistance in Wheat Project with refinements based on lessons learned. Phase II will be administered by the DRRW Project Management Unit (PMU) of the Office of International Programs in the College of Agriculture and Life Sciences (IP/CALS) at Cornell University in Ithaca, New York. IP/CALS has extensive experience with donor-funded projects and has its own Project Management Office. IP/CALS’s long and successful donor-funded project experience will ensure timely satisfaction of all BMGF reporting requirements. Efficient, transparent project management is essential to achieving the DRRW project goals. The DRRW project has dedicated staff for this purpose, and it also draws on the institutional and human resources of IP/CALS and the Cornell community in the design and implementation of its project management mechanisms. This Objective has four components: project management (Component 28.a), communications (Component 28.b), global access (Component 28.c), and gender opportunity enhancement (Component 28.d). Activities and key outputs of these components are described in detail in the work plan section of this narrative. Project Management: Project management component activities include the financial, administrative, legal and IT services necessary to administer the DRRW project (Activity 28.a.1), and all financial and technical reporting to the BMGF (Activity 28.a.2). Communication will be fostered between the PMU and the scientific Objective Team Leaders, project milestones and cross-objective impact will be measured (Activity 28.a.3). The PMU will also engage regularly with the External Program Advisory Committee (EPAC; Activity 28.a.4). Equipment and IT support will assist the PMU in Activity 28.a.5. Internal supplies fall under Activity 28.a.6.

Communications: This component includes the development of outreach materials to inform of events and progress of the DRRW project (Activity 28.b.1), and the development of web resources to support learning, communication and collaboration within the DRRW project and in the larger wheat rust community (Activity 28.b.2).

Global Access: Global access component activities include the development and management of the DRRW project’s Global Access Strategy and an annual review of “project level workflows,” to ensure that innovations and information produced by the DRRW scientific objectives are being efficiently implemented within the DRRW project. (Activity 28.c.1).

Gender Opportunities Enhancement: Activities in this component include the management of the Objective-specific gender initiatives as well as to identify opportunities to enhance gender parity through contingency gender funds. (Activities 28.d.1).

19


The Director of IP/CALS, Dr. Ronnie Coffman, will serve as the Principal Investigator (PI) and Director for the project and supervise the coordinating staff. PMU staff contributes to both Objective 22 (Advocacy) and to Objective 28 (Project Management) as evidenced in the budget. Special Initiatives: Two special initiatives are proposed for development in conjunction with the BMGF Program Officer if the grant is funded. The first Special Initiative (Activity 28.e.1.), “Stem Rust Isolate Sequencing Initiative,” aims to fund the collection, molecular characterization and sequencing of a global population of Puccinia graminis (Pgt) isolates. By understanding the epidemiology and population structure of Pgt, we can better understand from what circumstances Ug99 evolved and what the next Ug99 might evolve to look like in the future.

The second Special Initiative (Activity 28.e.2.), “Gene Deployment Initiative,” will fund four talented post-docs in four high-profile, productive labs to identify and stack sets of three or more major genes that are otherwise not released as single genes. This strategy will be central to the responsible deployment of major genes in CIMMYT APR germplasm and will ensure the longevity of materials developed and released by the project.

Potential Risks

All Objectives: • Climate/weather disrupting testing, seed multiplication, etc. • Germplasm exchange restricted by host governments. • Civil unrest restricts access to or damages critical facilities. Objective 21: Seed • Economics of seed production; unreliable government funding of critical operations. • Political and policy uncertainties, and resistance to paradigm shifts required by distinct

government and private agencies. • Replacement varieties dominate large landscapes rendering them vulnerable to other threats. Objective 22: Advocacy • Failure to capture the full potential of the BGRI because of rivalries or lack of commitment

by key members. • Global economic conditions preclude investments. Objective 23: Tracking Pathogens • Countries don’t embrace the Global Cereal Rust Monitoring System, leaving areas not

monitored, or data not shared. • In-country race analysis capacity not developed, North American capacity is shut down, or

both. • Seed exchange is limited by quarantine regulations and seed for trap nursery and race

analysis work cannot reach critical actors. • Lack of in-country coordinated surveillance/response leads to false reports undermining

credibility; or misses emerging threats. Objective 24: Critical Facilities

20


• International screening nurseries at Debre-Zeit, Ethiopia, and Njoro, Kenya are the source of inoculum triggering epidemics or new races [NOTE: we categorically reject these risks under current circumstances where stem rust is wide spread].

• Inoculation fails to trigger infection and a screening season is lost. • Irrigation systems fail and off-season crops fail. • Inadvertent human transmission of Ug99 lineage rust to other countries. Objective 25: Breeding • Objective 24 cannot deliver critical data and seed. • Public awareness of APR’s partial resistance retards acceptance. • Cultural factors disallow Whole Family Participatory Variety Selection to be effective. Objective 26: Pre-Breeding • Minor genes conferring APR are not readily mapped. • HR genes are defeated individually. • Aggressiveness or virulence to APR emerges. • Community sharing of resources is restricted. • Breeders don’t use outputs Objective 27: Ethiopia • Departure of key EIAR personnel. • Acquisition of equipment is delayed. Objective 28: Management • Sub-contractor reluctance/inability to adequately track and report encumbering background

technologies, or project-funded value-added technologies. • Inefficiencies in coordination within the project or between the project and other actors due

to insufficient commitment to transparency and inclusiveness. • Resistance to gender equity measures by male-dominated science community. • Globalrust.org Knowledge Bank falls short of expectations because of inherent resistance to

web collaborative environment or other factors.

Organizational Capacity and Management Plan The Cornell University DRRW management has successfully implemented Phase I, with many lessons learned. Programmatic (science/technology) management has strengthened as willing Objective leaders were identified. Management details are found in Appendix C, Objective 28.

References Cited Singh R.P., Hodson D.P., Huerta-Espino J., Jin Y., Njau P., Wanyera R., Herrera-Foessel S.A.,

Ward R.W. (2008) Will stem rust destroy the world's wheat crop?, Advances in Agronomy, Vol 98. pp. 271-309.

21

Appendix A: Logframe Table / Durable Rust Resistance in Wheat Phase II

Appendix A: Logframe Table

22

Appendix A: Logframe Table Objective 21 / Durable Rust Resistance in Wheat Phase II

Objective 21: Improved testing, multiplication and adoption of replacement varieties

Component Activity Activity Outputs (completion date) Activity Outcomes

Primary responsible scientist/ inst.

21.a. Trans-national coordin-ation

21.a.1. Explore, and establish as necessary, the development of an international committee to evaluate, coordinate, and recommend improvements and investments in seed systems.

Representation from the following would be anticipated:

• Selected NARS • CG centers • FAO • Private sector • Donor agencies • Legal/Regula-

tory policy

Determine the need for developing a seed systems and policy committee, to be established under the umbrella of the Borlaug Global Rust Initiative, which does not duplicate other international efforts. (Jun 2011)

Develop consensus objectives, establish goals and associated budgets. (Dec 2011)

Investments in equipment and training which lead to improvement in the precision of performance trails, providing greater discrimination among a cohort of entries and focusing seed multiplication resources on developing the most promising varieties. (Dec 2012)

Development of efficient regulatory systems which do not impede breeding progress, but do enhance the speed with which improved varieties and new technologies are able to enter the marketplace. (Jun 2011, recurring annually)

Encourage regulations and policies that enable the development of private sector investments. (Jun 2011, recurring annually)

Five Years A seed systems and policy committee is formed and has established objectives, goals and timelines for execution and accomplishment.

Performance, diversity, and acceptability of new stem rust resistant varieties entering seed multiplication are the product of farmer input through participatory variety selection. Capacity and security of Nucleus and Breeder Seed production enables earlier entry of new, farmer endorsed varieties into Foundation Seed production.

Ten Years Seed systems & policy committee has engaged national and international actors and demonstrated progress in interventions leading to efficient seed systems and development of nascent private sector engagement.

Efficiency of seed system performance is enhanced by a regulatory framework where

G. Cisar, Cornell

23




constraints to variety release are eliminated.

Commercial and extension seed production actors are able to access adequate supplies of Foundation Seed early in the commercialization process.

Commercial seed availability to small-holder farmers is optimized.

Fifteen Years Vulnerability of the world’s wheat crop to stem rust is systematically diminished through adoption of improved, diversely resistant varieties that meet farmer requirements including yield stability, acceptable end-use quality, and improved productivity.

Engagement with national regulatory agencies in improvements to seed systems has spillover effects applicable to multiple crops and emerging (transgenic, etc.) technologies.

Encouragement of private sector investments in seed systems leads to multiple genetically diverse varieties in the marketplace, resulting in improved stability of production

24




and the opportunity to develop economic investments in wheat and other crops. This will support an agriculturally diverse and ecologically sustainable environment, leading to improved genetic durability for all crop species in a given agro ecology.

21.b. Kenya.

21.b.1. Improve the capability of KARI and KEPHIS to generate reliable data with improved accuracy from replicated trials (KARI) and National Performance Trials (KEPHIS).

KARI plants International Wheat Information System (IWIS) designed Advanced Yield Trials (AYT) at 8 locations (up from 3 in 2008). Each location has single site, and multi-year analyses conducted in time to inform selection decisions prior to planting of the next season. >75% of data sets enable statistically significant discrimination between the top yielding line and the mean of all lines. (Dec 2010, recurring annually).

KEPHIS plants 5-8 additional locations (or at least 2 sites per location) of the NPT for yield and agronomic evaluation, and in collaboration with KARI, evaluates NPT entries in the KARI Njoro stem rust screening nursery. (Jun 2011 onward).

Five Years Kenya wheat seed supply chain is able to identify higher yielding and stem rust resistant wheat varieties with greater precision.

Ten and Fifteen Years Kenya national wheat yield trends are matching or superior to analogous environments in other countries.

KARI

KEPHIS

CIMMYT (IWIS imple-mentation)

CGA

21.b.2.

Identify and implement collaborative strategies enabling pre-release purification/multipli-cation and availability of KEPHIS endorsed Breeder Seed of KARI candidate lines at the time of approval for Official Release.

KARI and KEPHIS seek agreement on modalities and logistics by which the following anticipatory steps can occur concurrently with descriptor development, DUS assessment, and final stage of National Performance Trials (Apr 2011):

• First round of ear-row purification, • Ear-row derived plot grow-out/purification, and • Follow-on bulking of Breeder Seed

Dedicated and irrigation-enabled land (two hectares) available for ear-row purification of candidate varieties at KARI-Njoro

Five Years Released varieties that can protect Kenya from stem rust, thus reducing cost of production and increased food safety through reduced use of fungicides, reach farmers two years earlier than with system in place in 2008.

One-quarter of Kenya’s wheat

KARI

KEPHIS

25




(Apr 2011)

One or more hectares of seed production concurrent with NPT of each KARI line in 2nd year of NPT; the harvest of which KEPHIS endorses as eligible to be considered Breeder Seed, contingent on KEPHIS inspection; enabling availability of three tons of putative Breeder Seed of each candidate after 2nd year NPT. (Dec 2011, recurring annually; contingent on agreement of first output for this activity)

area, both in small and large scale farm sectors, is planted to wheat varieties that yield 10% greater than the weighted average of varieties planted in 2008, and also have resistance to local races of stem rust.

Ten Years As above, but 80% of area and similar yield trend.

Fifteen Years As above but 95% of area and similar yield trend.

21.b.3.

Identify and implement streamlined approaches to Breeder Seed production subsequent to initial production.

The current three stage ear-row, ear-row derived plot, and follow-on bulk method is employed less often without loss of purity of Breeder Seed lots. (Nov 2012, recurring annually)

Five, Ten and Fifteen Years Rates of genetic gain are not compromised by inefficient Breeder Seed production.

KEPHIS

KARI

21.b.4.

Promote awareness of new Ug99 resistant varieties and/or lines that are candidates for release as varieties.

4-8 Field Days jointly planned and executed by Ministry of Agriculture (MoA), KARI, Cereal Growers Association (CGA), and the Kenya Seed Company (KSC). (Aug 2011, recurring annually)

Five Years 100 % of Kenya’s large scale farmers; and 50% of small scale farmers are aware of current stem rust resistant varieties

Ten and Fifteen Years As above, but 90% of small-scale farmers are aware.

KARI

MoA

CGA

KSC

26




21.b. 5.

Maximize efficiencies and effectiveness of Certified wheat seed supply chain from Pre-Basic Seed to farm and industry/consumer use.

Key representatives of milling/processing, growers (CGA+), MoA Extension, KSC, KEPHIS, and KARI jointly visit key AYT and NPT sites; and actively engage in communication on current and future wheat varieties. (Nov 2011, recurring annually)

Annual production of Breeder Seed by KARI matches KSC needs, (Nov 2011, recurring annually)

Certified Seed production by KSC of stem rust resistant and otherwise improved lines meets producer and consumer demands, (Jun 2011, recurring annually)

Mutual awareness of milling, flour, and processing properties of wheat grain (including characteristics of new varieties) enhanced through a workshop involving flour millers, KARI and other key stakeholders (Mar 2011).

Five Years Rate of variety turn over in farmer’s fields is commensurate with demonstrated superiority of new varieties.

Ten and Fifteen Years Multiple varieties with superior agronomic performance and diverse genetic resistance to stem rust are common in the marketplace.

The private sector becomes increasingly engaged in the wheat seed enterprise.

One of the putative origins of virulent pathotypes of stem rust is no longer contributing to the development of a pathotype that can threaten global wheat production.

MoA

KEHPIS

KARI

KSC

CGA

21.c. Ethiopia (details under dis-cussion, funding through Phase I)

21.c.1 Increase capacity, stability, and quality of Breeder and Pre-Basic Seed production.

Off-season irrigation capacity is created or enhanced for Breeder and Pre-Basic Seed production at Kulumsa, Debre-Zeit, Melkassa, and Werer. (Dec 2011)

Planting and harvest methods and equipment are upgraded to reduce labor costs and ensure timely completion of field work. (Dec 2011)

Seed processing equipment is upgraded at key Centers. (Apr 2012)

Five, Ten and Fifteen Years Breeder Seed availability does not limit adoption/production of stem rust resistant varieties. Breeder Seed availability does not limit adoption/production of stem rust resistant varieties.

Main- and off-season multiplication of candidate

EIAR

27




Seed quality laboratories are upgraded, equipped, and staffed at key Centers. (Apr 2012)

Key staff responsible for seed quality testing, equipment maintenance, field management and post-harvest seed handling are provided in-service training. (Sept 2012)

varieties, enabled by improved irrigation capacity, is a routine practice.

A robust and comprehensive national wheat breeding program, coupled with an equally robust and comprehensive seed system, begins to contribute to alleviating the persistent food insecurity problems that have plagued Ethiopia.

Ten and Fifteen Years The delivery and popularization of an array of durably and diversely resistant varieties emanating from the EIAR breeding programs is a seamless and unbroken continuum, efficiently linked with rapid seed multiplication, variety registration and extension activities (ten years and beyond).

Seed quality and seed health of varieties in commerce allow increased realization of the genetic potential of varieties, resulting in improved national wheat production (ten years and beyond).

28


Objective 22: Increased levels of global investments and coordination in stem rust research and development

Component Activity Activity Outputs (completion dates) Activity Outcomes

Primary responsible scientist / Inst

22.a. BGRI.

22.a.1. Act as an effective Secretariat to the BGRI, enabling communication and providing support for the activities of this body.

BGRI members and stakeholder communities receive quarterly updates on rust research and news (information drawn from other relevant activities, media reports, etc). (Mar, Jun, Sep, Dec 2011, recurring annually)

BGRI Executive Committee (ExCo) and other key members proactively engaged in advocacy and fundraising. (Feb 2011, recurring annually)

Annual BGRI technical workshop held; regular ongoing communications arranged among ExCo members. (May and Jun 2011, recurring annually)

Strategic investments outside the purview of the BGRI have been made, and have, as a result, enabled leveraged advocacy. (Sep 2011, recurring annually)

Five years A sustainable platform of advocacy for wheat rust research, plant breeding, and development activities has been implemented and maintained.

Members of the BGRI Executive Committee and regular members are actively engaged and working toward raising funds for wheat rust research and development projects, with evidence of increased funding reaching wheat rust R&D projects.

Ten years Significant scientific advances in stem rust research have been made that would not have been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project

New high-yielding varieties that can withstand newly emerging pathotypes are being developed and adopted under a rational gene deployment strategy.

Poverty and hunger have been reduced in vulnerable regions, as better varieties of wheat are introduced that offer better yields and yield stability that comes with improved resistance.

Cornell

29




Fifteen years Significant scientific advances in stem rust research have been made that would not have been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project.



22.a.2. Foster professional development of women wheat breeders through the BGRI

A Gender Equity luncheon is held at Annual BGRI Technical Workshop, sensitizing the BGRI participants to gender issues in agricultural development (Jun 2010)

BGRI establishes the annual Jeanie Borlaug Women in Triticum (WIT) award (2010, recurring annually)

Three WIT award recipients are chosen annually (2010 & recurring annually)

The Women in Triticum Mentor Award is established by the BGRI (Jun 2010)

One Women in Triticum Mentor Award is granted annually (2011, recurring annually)

Five years BGRI participants are sensitized to gender parity issues.

More female researchers participate in BGRI activities.

More female researchers participate in training at CIMMYT-Obregon

Ten years More women wheat breeders are employed by national programs, universities and International Agricultural Research Centers.

Cornell

30




Fifteen years Gender parity improves in the field of wheat breeding and genetics.

22.b. Media activities for reaching key audiences.

22.b.1. Promote media coverage of the rust problem and need for sustained support for rust research through key message development, press releases, media training, and media monitoring.

Clear and concise messages developed with input from the stem rust research community (Sep 2011, recurring annually)

Advocacy and communications strategy operates in real-time via ongoing strategic discussion regarding advocacy and media. (Feb 2011, recurring annually)

Two press releases developed in collaboration with Project managers (topics based on review of presentations, peer-reviewed papers, gap analysis, etc. to determine news value and in light of advocacy objectives) translated into relevant languages (Arabic, French, Farsi, etc.), and stories published in key outlets in target countries. (May 2011 and Nov 2011, recurring annually around BGRI workshop and other relevant events)

Desk side meetings with journalists arranged for key spokespeople, organized around four trips a year (these meetings will take place during trips made as part of meeting other objectives). (Sep 2011, recurring annually)

Electronic and hard copy report compiled for each media outreach effort, with a summary of the coverage and original clippings for key donors and policy makers, and DRRW internal files. (Sept 2011, recurring annually)

Five years Regular, comprehensive media exposure to the problem of wheat stem rust is achieved, keeping the problem and the need for action in front of policymakers.

Ten years Significant scientific advances in stem rust research have been made that would not have been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project.



Fifteen years Significant scientific advances in stem rust research have been made that would not have been possible without the advocacy efforts of the BGRI and

Cornell

31




the scientific objectives of the DRRW project.



22.c. Targeted fundraising.

22.c.1. Visits to donor nation embassies in nations vulnerable to stem rust.

Funds obtained from donor nation officials to support local research and other activities aimed at combating stem rust. (Jun 2011, recurring annually)

Five years Greater economic resources have been devoted to rust research, breeding and development.



Poverty and hunger have been reduced in vulnerable regions, as better varieties of wheat are introduced that offer better yields and yield stability that comes

Cornell

32




with improved resistance.



Poverty and hunger have been reduced in vulnerable regions, as better varieties of wheat are introduced that offer better yields and yield stability that comes with improved resistance

22.d. Advocacy activities for reaching key audiences.

22.d.1. Promote awareness and action by policy makers and donors to address stem rust in a coordinated way and to support stem rust research and wheat improvement.

Five high-level meetings arranged between critical players and relevant government officials (Sep 2013)

Results of media outreach packaged and disseminated to promote further awareness. (Oct 2011, recurring annually)

Print and electronic materials available in relevant languages to support advocates in their outreach efforts. (Oct 2011, recurring annually)

Five years Greater economic resources have been devoted to rust research, breeding and development


New high-yielding varieties that can withstand newly emerging pathotypes

Cornell

33




are being developed and adopted under a rational gene deployment strategy.





22.d.2. Conduct annual gap analysis to identify shortfalls in funding and opportunities

Gap analysis report finalized and approved (and reviewed for news value, as described under media activities). (Sep 2011, recurring annually


Ten years Significant scientific advances in stem rust research have been made that

Cornell

34




for investment in rust research and wheat improvement, and disseminate results.

would not have been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project.






35




22.e. Web-based activities in support of advocacy, fundraising and collaboration.

22.e.1. Maintain and augment a catalogue of wheat improvement and rust research projects and associated information.

Online resource maintained and in use to support Advocacy activities. (Feb 2010)


Ten years Significant scientific advances in stem rust research made that would not have been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project.




New high-yielding varieties that can withstand newly emerging pathotypes are being developed and adopted under a rational gene deployment strategy. Poverty and hunger have been reduced

Cornell

36




in vulnerable regions, as better varieties of wheat are introduced that offer better yields and yield stability that comes with improved resistance

22.e.2. Maintain content of BGRI website.

BGRI website content is maintained with input/interaction from rust community; content reviewed regularly for news value. (Feb 2011, recurring annually)

BGRI website will be viewed as a major source of wheat rust knowledge (Dec 2012)





Fifteen years Significant scientific advances in stem rust research have been made that would not have been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW

Cornell

37




project.



38


Objective 23: Stem rust populations tracked and monitored

Component Activities Activity Outputs (completion dates) Activity Outcomes

Primary responsible scientist/ inst

23.a. Global Cereal Rust Monitoring System (GCRMS)

23.a.1. Maintain and enhance the functional information platform and core databases for tracking and monitoring stem rust populations.

Core data bases populated with quality controlled rust survey data from at least 10 countries per year. (Sep 2011, recurring annually)

Automated / semi-automated data import tools and routines. (Sep 2012)

Customized analytical tools developed. (Sep 2013)

Five Years Accessible, up-to-date information on stem rust incidence and populations in 10 priority countries.

Ten Years Accessible, up-to-date information on stem rust incidence and populations in 30 priority countries.

Fifteen Years The GCRMS is the primary source of information relating to stem rust incidence and populations globally.

D. Hodson, FAO

23.a.2. Spatial data platform.

The Wheat Atlas internet-based data hub populated, with NARs data inputs and validation. (Jun 2012)

Five Years Data exchange through user oriented web portals rapidly affects policies that favor wheat economic productivity for small-holder farmers in developing nations.

Fifteen Years International efforts to mitigate and eliminate the effects to small-holder farmers against wheat stem rust are no longer limited by lack of ready access to germplasm, data, seed and knowledge

P. Kosina, CIMMYT, Mexico

39




23.a.3. Deliver timely and accurate information on stem rust populations via an expanded GCRMS.

A range of targeted information updates for stem rust available on a regular basis (i.e. web situation updates, bulletins, race frequency summaries, trap nursery summaries). (Sep 2011, recurring annually)

Five Years GCRMS information used routinely by national partners to guide decisions regarding control and management of stem rust in at least 10 countries.

Ten Years GCRMS information used routinely by national partners to guide decisions regarding control and management of stem rust in at least 30 countries.

Fifteen Years GCRMS information used routinely by national partners to guide decisions regarding control and management of stem rust globally.

D. Hodson, FAO

23.a.4. Leverage establish-ment of a Global Rust Reference Center (GRRC) by supporting race analysis and training

GRRC is established with significant investments from Denmark. (Sep 2013)

National Program Pathologists from at-risk countries are trained in pathotype (race) analysis. (Sep 2014, recurring annually)

Five Years GRRC is operating. Stem rust samples are received and analyzed in a timely and regular manner. After 5 years, GRRC operating costs are expected to be a regularized activity of the FAO.

Ten Years A new generation of rust pathologists from National Programs are trained in rust surveillance and pathotype (race) analysis.

The GCRMS includes regular high quality international race information generated by GRRC.

M. Hovmoller, Aarhus U

40




23.b. Surveillance.

23.b.1. Trap plot network support.

Pure and adequate seed of genotypes used in trap plots maintained and stored. (Sep 2011, recurring annually)

Seed distributed to all countries participating in trap plots nurseries. (Sep 2012, recurring annually)

Five, Ten and Fifteen Years Trap plot nurseries used in global rust surveillance comprise or include standard reference genotypes.

K. Nazari, ICARDA

23.b.2. Expand and enhance national capacity to undertake rust surveillance.

National survey teams established and contributing annually to national and global cereal rust monitoring systems in at least 10 countries. (Sep 2011, recurring annually)

Technical backstopping provided to national focal points and/or survey teams in at least 10 countries per year (Sep 2011, recurring annually)

Stem rust surveillance in regions of strategic importance but not covered by core activities. (Sep 2011, recurring annually)

Five Years An effective network of surveillance teams for stem rust is supported in 10 priority countries and contributing to the GCRMS annually.

Knowledge of stem rust distribution and incidence and principal races present in non-target regions of strategic importance if stem rust becomes a problem.

Ten Years An effective network of surveillance teams for stem rust operating in 30 priority countries and contributing to the GCRMS annually.

Fifteen Years National agricultural program systems are undertaking routine annual stem rust monitoring.

K. Nazari, ICARDA

23.c. Pathogen characterization.

23.c.1. Stem rust race analysis backstop-ping ARIs.

Selected key stem rust samples or isolates are race typed by ARIs. (Sep 2011, recurring annually)

Five Years Knowledge of stem rust races present in regions of strategic importance.

Y. Jin, USDA

T. Fetch, AAFC

41




23.c.2. Stem rust race analysis in country.

Pure and adequate seed of genotypes used as differentials maintained, stored and distributed. (Sep 2011, recurring annually)

National rust laboratories in at least 5 countries equipped to undertake race analysis (Quick sets and/or full race analysis). (Sep 2012, recurring annually)

Five Years Routine standardized annual stem rust race surveys established in at least 5 developing countries, and data are incorporated into GCRMS.

Ten Years Routine standardized annual stem rust race surveys established in at least 10 developing countries, and data are incorporated into GCRMS.

Fifteen Years Routine standardized annual stem rust race surveys are conducted in countries representing all major wheat growing regions, with data incorporated into GCRMS.

K. Nazari, ICARDA

R. Park, U Syd

23.c.3.

Targeted surveillance of barberry for stem rust.

Preliminary surveys of barberry conducted in Kenya (Jin), Uzbekistan and Turkey (Park) have established the existence of aecial infections by a form of the stem rust pathogen Puccinia graminis. (Nov 2011, recurring 2012 and 2013)

Five Years Role of barberry in the evolution of Ug99 and variants is more understood.

Ten Years Ug99 and other stem rust races are better controlled due to enhanced knowledge of relationships with the alternative host in East Africa and other at-risk countries.

Fifteen Years stem rust is better controlled due to understanding of the alternate host, barberry.

Y. Jin, USDA

23.c.4.

Stem rust fingerprint-

International consensus on a core panel of informative SSR markers for fingerprinting stem rust isolates. (Sep 2012, recurring annually)

Five Years Insight into the global genetic diversity of the wheat stem rust pathogen is obtained.

R. Park, U Syd

42




ing. Selected key stem rust isolates fingerprinted with SSR markers. (Sep 2011, recurring annually).

23c.5. Stem rust molecular diagnostics.

Up to 20 key stem rust isolates sequenced to a depth of about 20X. (Sep 2011, recurring annually)

Five Years The current stem rust SNP database is expanded, allowing the development of rapid molecular diagnostic tools for the identification of the major races groups/lineages worldwide.

L. Szabo, USDA

23.d. Host charac-terization.

23.d.1. Host R gene determin-ation.

R gene determinations in global wheat germplasm, at least 50 cultivars per year. (Sep 2010, recurring annually).

On request, marker genotyping for key R genes of host tissue from stem rusted crops. (Sep 2011, recurring annually)

Information on R genes present in cultivars incorporated into Wheat Atlas. (Sep 2011, recurring annually)

Five Years R genes in wheat genotypes from at risk countries are known.

Ten Years Detailed understanding of stem rust R genes in all major wheat genotypes.

Fifteen Years Geographic distribution and graphical representation of R genes in relation to stem rust race distribution in GCRMS so to moni-tor risk of R gene breakdown (Activity 23.a).

R. Park, USyd

K. Nazari, ICARDA

P. Kosina / CIMMYT Mexico

23.d.2. Genetic stock development.

Up to 35 cataloged stem rust resistance backcrossed into a common genetic background. (Sep 2011, recurring annually)

Five Years Homozygous NILs (BC5) developed, increased and distributed to at least 10 countries.

Ten Years Utility of NILs as greenhouse differential genotypes and field trap plot genotypes assessed in all major wheat growing regions.

R. Park, U Syd

43




Fifteen Years A single core set of NILs is used internationally for both greenhouse seedling virulence assays and field trap plots.

23.e. Coordination.

23.e.1. Objective 23.

Objective 23 outputs harmonized. (Sep 2011, recurring annually)

Intra- and inter-objective (DRRW) harmonization. (Sep 2011, recurring annually)

Five Years Successful completion of all Objective components and activities and integration of all outputs with overall project.

R. Park, U Syd

Objective 23 Advisory Panel

44


Objective 24: World-class stem rust response phenotyping facilities in East Africa


Primary responsible scientist /Inst.

24.a. Kenya Phenotyping.

24.a.1. Common wheat stem rust phenotyping of breeding germplasm and research materials in the field screening nursery at Njoro, Kenya (KARI).

Main season nurseries planned, seed imported and planted, and resulting material phenotyped (Oct. 2011, recurring annually).

Main season data recorded, data and/or seed returned to collaborators and shared where appropriate and as governed by the Germplasm Acquisition Agreement (GAA). (Nov 2011, recurring annually).

Off-season nurseries planned, seed imported and planted, and resulting material phenotyped (April 2012, recurring annually).

Off-season data recorded, data and/or seed returned to collaborators and shared where appropriate and as governed by the GAA. (Jun 2012, recurring annually).

Five Years Frequency of APR in IARC and NARS advanced breeding lines increased, and resistance response enhanced from MR/MS to R/MR (Joint with Objective 25).

APR candidate bread wheat varieties for east Africa in advanced stage of release (joint with Objectives 21 and 25).

QTL for APR in bread wheat identified (joint with Objective 26)

Ten Years 90% Kenyan and 70% of Ethiopian bread wheat areas are planted to predominantly APR varieties (joint with Objectives 21 and 25).

APR bread wheat varieties are planted to >10% of central and south Asia bread wheat areas (joint with Objectives 21 and 25).

APR candidate bread wheat varieties for China’s at-risk areas are in advanced stage of release (joint with Objectives 21 and 25).

Diagnostic markers for bread wheat APR genes are employed by IARC and NARS breeders (joint with Objective 26).

P. Njau, KARI

S. Bhavani, CIMMYT, Kenya

45




Fifteen Years >50% of at-risk areas of CWANA, S. Asia and China planted to improved APR bread wheat varieties.

Cultivated resistant varieties ensure both global food security, and increased production.

24.a.2.

Seedling and adult plant phenotyping of bread wheat in greenhouse and tunnel house in support of gene mapping and novelty studies (joint with Objective 26) at Njoro Kenya (KARI).

Greenhouse and tunnel house screening planned and seed imported (Feb2011, recurring annually); material screened (Oct 2011, recurring annually).

Accurate seedling (greenhouse) and adult reaction (tunnel house) phenotype data generated and returned to collaborators and shared where appropriate (Nov 2011, recurring annually).

Five Years Novel sources of durable stem rust resistance identified, genetically characterized and mapped (joint with Objective 26 and CIMMYT Generation Challenge Program).

Novel sources of resistance available to breeders are deployed in breeding programs (joint with Objective 25 and 26).

Ten Years Deployed cultivars are durably resistant to Ug99 and other evolving stem rust variants (joint with Objective 25).

Fifteen Years Cereal cropping systems for resource poor growers in at-risk countries are stabilized and small-holder economies have improved by 10%.

P. Njau, KARI


46




24.a.3. Confirm-ation and initial char-acterization of resistance in bread wheat germ-plasm at Njoro, Ken-ya (KARI) for varieties under re-lease consid-eration in at-risk countries.

Field resistance of candidate or released varieties is re-evaluated in greenhouse for seedling reaction (Dec 2011, recurring annually) and tunnel house for adult response (Jun 2011, recurring annually) to confirm resistance and initiate resistance gene postulation work (Nov 2011, recurring annually).

DNA of confirmed resistances shared with Objective 26 to enable marker based determination of genetic basis of resistance (Dec 2011, recurring annually).

Five Years Genetic basis of resistance of released and candidate varieties is used to inform national and international resistance management strategies that enhance overall sustainability of wheat production.

Frequency of single major gene based resistance in released varieties is reduced.

Ten Years Stability of production gains is not threatened by stem rust.

Fifteen Years As above


P. Njau, KARI

24.a.4. Collection, character-ization, and maintenance of stem rust cultures, and moni-toring of field races of stem rust in the screen-ing nursery (KARI-Njoro).

Relevant cultures purified and maintained. (Feb 2011, recurring annually)

Effective epiphytotics of stem rust on screening materials maintained in field and tunnel house (Apr and Nov 2011, recurring annually)

Predominant virulent pathotypes in the screening nurseries are serially collected throughout the season and race typed to aid interpretation and validation of phenotypic data recorded during each screening cycle. Frequency and predominance of pathotypes recorded and reported to collaborators. (May 2011 and Nov 2011, recurring annually)

Five Years Changes in virulences/races during a given screening season are detected and used to enhance value of field data by informing decisions on inoculations and interpretation of data.

Ten Years Long-term database informs understanding of the biology and evolution of the stem rust population in East Africa.


P. Njau, KARI


47




24.a.5. National pathogen surveillance and race analysis in Kenya.

Rust surveys during wheat growing seasons conducted and samples collected (methods conforming to Objective 23, 2011 onwards).

Race analysis conducted at KARI-Njoro/AAFC on collected samples and virulence patterns of races in Kenya determined (Dec 2011, recurring annually).

Five Years Regular monitoring of frequency and evolution of Ug99 lineage will assist in developing anticipatory breeding and gene deployment strategies.

Ten Years Enhanced knowledge of pathogen migration and distribution will facilitate decision and adoption of appropriate national, regional and international policies, investments, and strategies in plant protection, wheat breeding and seed systems.

P. Njau, KARI


24.a.6. Establish-ment of a Seed Health unit, including standard protocols to be implement-ed for seed exchange in comple-mentation with national regulatory authorities.

Seed health unit operational (Apr 2011).

Seed health management protocols established and communicated (Jun 2011).

Staff trained in seed health (Aug 2011)

Seed health quarantine protocols implemented, including enforcement. (Sep 2011, recurring for each seed import/export shipment).

Five Years KARI strengthened seed health protocols preclude import or export of seed borne disease and stem rust spores

Ten Years As above.

Fifteen Years As above.

P. Njau, KARI


48




24.a.7. In-service learning/ training opportun-ities for KARI and national skill develop-ment.

Scientists trained in the area of cereal rust genetics, race surveillance, and race analysis, screening and rust pathology techniques by visiting scientists and by CIMMYT IFP. (Sep 2011, 2012, 2013).

Three staff trained (one per year) at CIMMYT in the area of field management, screening, data collection, data management, and methodologies related to rust resistance evaluation, selection and breeding (Aug 2011, 2012, 2013). KARI scientists attend and participate in international conferences (relevant time/conferences in, 2011, 2012, 2013).

One national Post-graduate student trained per year in area of plant pathology, breeding and genetics (summer semester 2011, recurring yearly).

Five Years Scientists and staff at critical facilities in Kenya conduct high caliber international cereal rust research.

KARI scientists are active collaborators in international rust research/breeding projects.

Ten Years As above.

P. Njau, KARI


24.a.8. Strategic investments to enhance the precision and capacity to generate reliable and accurate stem rust phenotypic data.

Fifteen hectares of land and excellent research facilities are available for national and international rust screening activities (Oct 2011).

Greenhouse capable of high throughput rust resistance seedling assays becomes available (Jun 2011)

Tunnel house capable of generating reliable and repeatable phenotypic data is available (Apr 2011). Seed health unit operational (Apr 2011)

Five Years Fully operational screening facilities in Kenya are a robust and vibrant component of an ongoing global wheat improvement effort to minimize stem rust epidemics

Ten Years As above


P. Njau, KARI


49




24.b. Ethiopia Phenotyping.

24.b.1. Durum wheat stem rust phenotyping of breeding germplasm and research materials in the field screening nursery at Debre-Zeit, Ethiopia (EIAR).

Main season nurseries planned, seed imported and planted, and resulting material phenotyped (Jun 2011, recurring annually).

Main season data recorded, data and/or seed returned to collaborators and shared where appropriate and as governed by the Germplasm Acquisition Agreement (GAA) (Nov 2011, recurring annually).

Off season nurseries planned, seed imported and planted, and resulting material phenotyped (Nov 2011, recurring annually).

Off-season data recorded, data and/or seed returned to collaborators and shared where appropriate and as governed by the GAA (Apr 2011, recurring annually).


APR candidate durum wheat varieties for east Africa in advanced stage of release (joint with Objectives 21 and 25).

QTL for APR genes in durum wheat identified (joint with Objective 26)

Ten Years 30% of Ethiopia’s durum (tetraploid) area is planted to resistant varieties (joint with Objectives 21 and 25).

APR durum wheat varieties are planted to >10% global wheat areas (joint with Objectives 21 and 25).

Diagnostic markers for durum wheat APR genes are employed by IARC and NARS breeders (joint with Objective 26).

Fifteen Years >50% of at-risk areas of global durum planted to improved APR durum wheat varieties.

Cultivated resistant varieties ensure both global food security, and increased production leading to economic security.

Bedada G., EIAR


50




24.b.2. Seedling and adult plant phenotyping of durum wheat in greenhouse and tunnel house in support of gene map-ping and novelty studies (joint with Objective 26) at Debre-Zeit, Ethiopia (EIAR).

Greenhouse and tunnel house screening planned and seed imported. (Feb 2011, recurring annually)

Material screened. (Oct 2011, recurring annually)

Accurate seedling (greenhouse) and adult reaction (tunnel house) phenotype data generated and returned to collaborators and shared where appropriate. (Nov 2011, recurring annually)


Novel sources of resistance available to breeders and deployed in breeding programs (joint with Objective 25 and 26).



Bedada G., EIAR


51




24.b.3. Confirm-ation and initial char-acterization of resistance in durum wheat germ-plasm at Debre-Zeit, Ethiopia (EIAR) for varieties under re-lease consid-eration in at-risk countries.

Field resistance of candidate or released varieties is re-evaluated in greenhouse for seedling reaction (Dec 2011, recurring annually);

and tunnel house for adult response (Jun 2011, recurring annually); to confirm resistance and initiate resistance gene postulation work (Nov 2011, recurring annually).



Frequency of single major gene based resistance in released varieties released is reduced.



Bedada G., EIAR


24.b.4. Collection, characteri-zation and maintenance of stem rust cultures and monitoring of field races in the screening nursery (EIAR Debre-Zeit and Ambo).


Effective epiphytotics of stem rust on screening materials maintained in field and tunnel house (Mar 2011, recurring annually).

Predominant virulent pathotypes in the screening nurseries field are serially collected throughout the season and race typed to aid interpretation and validation of phenotypic data recorded during each screening cycle. Frequency and predominance of pathotypes recorded and reported to collaborators. (May and Dec 2011, recurring annually)




Bedada G., EIAR


52




24.b.5. National pathogen surveillance and race analysis in Ethiopia. (EIAR-Ambo)

Rust surveys during wheat growing seasons are conducted and samples collected (methods conforming to Objective 23). (Sep 2011, recurring annually).

Race analysis conducted by EIAR-Ambo on collected samples and virulence patterns of races in Ethiopia determined. (Dec 2011, recurring annually)



Bedada G., EIAR


24.b.6. Charac-terize the nature and distribution of the stem rust popu-lation in Ethiopia’s durum/ tetraploid wheat crop through surveys and established trap nurseries. (EIAR-Ambo)

Rust samples systematically collected from farmer fields and trap nurseries of durum wheat (Sep 2011, recurring annually)

Distribution of stem rust virulences and races determined (Jun 2011, recurring annually).

Five Years Durum stem rust evaluation is more effective in identifying diverse and durable resistances using enhanced knowledge of stem rust virulences/races in Ethiopia.

Ten Years As above.


Bedada G., EIAR


53




24.b.7. Establish-ment of a Seed health unit, including standard protocols to be imple-mented for seed ex-change in comple-mentation with national regulatory authorities.

Seed health unit operational and complementing role of national quarantine authorities (Apr 2011).

Seed health management protocols established and communicated in consultation with national quarantine authorities. (Jun 2011).

Staff trained in seed health issues and protocols (Aug 2011)


Five Years EIAR strengthened seed health protocols preclude import or export of seed borne disease and stem rust spores

Ten Years As above.


Bedada Girma / EIAR


24.b.8. In-service learning/ training opportun-ities for EIAR and national skill devel-opment.

Three scientists trained (one per year) at international cereal rust labs in the area of cereal rust genetics, race surveillance, race analysis, screening and rust pathology techniques (Jul 2011, Jul 2012, Jul 2013).

Three staff trained (one per year) at CIMMYT in the area of field management, screening, data collection and methodologies related to rust resistance evaluation, selection and breeding (Aug 2011, Aug 2012, Aug 2013)

Five Years Scientists and staff at critical facilities in Ethiopia conduct high caliber international cereal rust research.

EIAR scientists are active collaborators in international rust research/breeding projects.

Ten Years As above.

Bedada Girma / EIAR


54




EIAR scientists attend and participate in international conferences (relevant time/conferences in Sep 2011, Sep 2012, Sep 2013).

National technical staff trained by two local training events relevant to field and greenhouse rust screening (Apr 2011, Apr 2012).

24.b.9. Strategic investments to enhance the precision and capacity to generate reliable and accurate stem rust phenotypic data.

Seven hectares of land and excellent research facilities are available for national and international rust screening activities (Oct 2010).


Tunnel house capable of generating reliable and repeatable phenotypic data is available (Apr 2011)

Seed health unit is operational (Apr 2011)

Five Years Fully operational screening facilities in Ethiopia are a robust and vibrant component of an ongoing global wheat improvement effort to minimize stem rust epidemics.

Ten Years As above.


Bedada Girma / EIAR


55


Objective 25: Durably resistant, high yielding wheat varieties



25.a. Bread wheat.

25.a.1. Spring bread wheat varieties with Ug99 resistance for irrigated and higher production environ-ments of Africa, Middle East, West, Central and South Asia

Between 30–50 high yielding, rust resistant potential replacement varieties tested annually in replicated yield trials in various countries at more than 50 field sites (Oct 2011, recurring annually)

Between 100–150 additional high yielding, multiple rust resistant lines distributed annually for evaluation and selection as small plots at more than 100 sites worldwide (Oct 2011, recurring annually)

About 10 new multiple rust resistant varieties with >5% higher yield potential than current cultivars released officially in various countries (Dec 2014)

Application of appropriate breeding methodology and use of germplasm with durable resistance promoted for NARS breeding programs (Dec 2010, recurring annually)

Strong partnerships built for the fast release and promotion of new stem rust resistant cultivars (Feb 2013)

Five years Bread wheat varieties with Ug99 resistance and >5% higher yields are planted as follows (joint with Objective 21): • Kenya (50% of wheat area), • Ethiopia (20% of wheat area), • India (5% of wheat area), • Pakistan (10% of spring wheat area), • Egypt (20% of wheat area), • Afghanistan (20% of spring wheat

area) • Iran (40% of spring wheat area) • Nepal (10% of wheat area) • Bangladesh (10% of wheat area) • Mexico (10% of wheat area) • Other spring wheat growing countries

(1-5% of the wheat area) Enough seed availability in target countries to replace >80% wheat area as necessary from Ug99 migration.

Higher proportions of CIMMYT, ICARDA and National Programs’ breeding materials contain diverse Ug99 resistant parents ensuring a longer-term sustainability of wheat improvement research related to Ug99 resistance.

Ten Years Between 40-80% spring wheat area in above and other countries replaced by Ug99 resistant varieties that enhance wheat production through increased yield

R. Singh, CIMMYT, Mexico

56




potential.

Several diverse 2nd generation of wheat varieties that have a high level of APR or protected by at least two effective major genes and with >10% high yield potential than current varieties released in various countries and occupy 5-40% spring wheat area.

Ug99 threat mitigated through the wide cultivation of resistant varieties and production enhanced due to their higher yielding capacity.

Fifteen Years 80% spring wheat area in majority of countries sown to Ug99 resistant varieties that enhance wheat productivity by about 10%.

Several diverse 3rd generation of wheat varieties that have a high level of APR or protected by at least two effective major genes and with >15% high yield potential than current varieties released in various countries and occupy 5-40% spring wheat area.

More wheat available to meet the increasing demand.

25.a.2.

Spring bread wheat varieties with Ug99

15–20 lines sent every year to NARS coming from rainfed international trials and screening nurseries with good yield potential, tolerance to drought and resistance to yellow rust, leaf rust and

Five Years Bread wheat varieties with Ug99 resistance and >5% higher yields are planted as follows (joint with Objective 21). • Afghanistan (5% of spring wheat area)

Y. Manes, CIMMYT, Mexico

57




resistance for drought-stressed and low production environ-ments of Africa, Middle East, West, Central and South Asia..

Ug99 stem rust (Oct 2011, recurring annually)

At least 50 lines sent to NARS with good yield potential, tolerance to drought, resistance to yellow rust, leaf rust and Ug99 stem rust (Mar 2011), recurring annually)

3–4 stem rust resistant varieties selected for release by NARS (Dec 2014)

• Ethiopia (10% of wheat area) • India, (1% of wheat area) • Iran (5% of spring wheat area) • Kenya (5% of wheat area) • Mexico (5% of wheat area) • Morocco (1% of spring wheat area) • Nepal (1% of wheat area) • Pakistan (1% of wheat area) • South Africa (1% of spring wheat area) • Syria (5% of wheat area) • Tunisia (5% of wheat area) • Turkey (1% of spring wheat area)


Ten Years Enough seed availability in target countries to replace >40% wheat area as necessary from Ug99 migration.

Several diverse new wheat varieties that have a high level of APR or protected by at least two effective major genes and with >10% high yield potential than current varieties released in rainfed areas of various countries and occupy 5-40% spring wheat area.

Fifteen Years Between 40-60% rainfed spring wheat area

58




in above and other countries replaced by Ug99 resistant varieties that enhance wheat production through increased yield potential and drought tolerance.


25.b. Africa and South Asia

25.b.1. Durum wheat varieties for Ethiopia, South Asia, and North Africa with resistance to Ug99 and its derivatives.

Approximately 50 high yielding, stem rust resistant durum lines distributed worldwide in CIMMYT screening nurseries. (Mar 2012)

20–30 stem rust resistant durum varieties with >5% higher yield than current varieties distributed worldwide for yield/adaptation testing by NARS. (Mar 2014)

2–3 stem rust resistant candidates varieties for release in Ethiopia. (Dec 2014)

Five Years Durum wheat varieties with Ug99 resistance and >5% higher yields are planted as follows (joint with Objective 21) • Ethiopia (1% durum wheat area) • India (1% durum wheat area).

Ten Years Durum wheat varieties with Ug99 resistance and >5% higher yields are planted as follows (joint with Objective 21). • Ethiopia (20% durum wheat area) • India (20% durum wheat area) • Morocco (20% durum wheat area) • Algeria (5% durum wheat area) • Tunisia (20% durum wheat area) • Syria (20% durum wheat area) • Turkey (20% durum wheat area)

K. Ammar, CIMMYT, Mexico

59




• Azerbaijan (20% durum wheat area)

Enough seed availability in target countries to replace >50% durum wheat area as necessary from Ug99 migration.


Fifteen Years >60% durum wheat area in above and other countries replaced by Ug99 resistant varieties that enhance wheat production through increased yield potential.

Several diverse 2nd generation of durum wheat varieties that have a high level of APR or protected by at least two effective major genes and with >10% high yield potential than current varieties released in various countries and occupy 5-40% durum wheat area.

25.b.2.

Kenyan wheat improve-ment for East Africa and South-Asia.

Strengthen research capacity in wheat improvement through close collaboration with wheat scientists in Kenya. (Oct 2011, recurring annually)

Assist the Kenyan Njoro ARI in building research infrastructure. (Oct 2011, recurring annually)

Liaise with multiple partners for germplasm and data exchange. (Oct 2011, recurring annually)

Five Years Scientists and staff at critical facilities in Kenya possess skill sets enabling quality assured data collection and management.

Ten Years The critical facilities are fully sustainable, actively contributing to improving food security in their respective countries and

P. Njau, KARI


60




regions while continuing to contribute to global wheat improvement efforts.

Kenya has an efficient variety development and replacement system benefiting all wheat growers. Losses due to stem rust are minimal. Education of small and large farmers for optimum management of APR protected varieties is accomplished.

The process and outcomes of this project have positive effects on gender issues in development

Fifteen Years International efforts to mitigate and eliminate the effects to small-holder famers against wheat stem rust are no longer limited by lack of ready access to germplasm, data, seed and knowledge.

25.b.3. South Asia hub for Ug99 wheat improve-ment

Strengthen research capacity in wheat improvement through close collaboration with wheat scientists in South Asia. (Jan 2011, recurring annually)

Assist South Asia (Afghanistan, Bangladesh, India and Nepal) national programs in identifying and promoting new improved wheat cultivars with genetic protection to rust and other pathogens, including cultivars for the newly opened irrigated areas. (Jan 2011, recurring annually)

Liaise with multiple partners for germplasm and data exchange. (Jan 2011, recurring annually)

Five Years Scientists and staff at critical facilities in South Asia possess skill sets enabling quality assured data collection and management with engagement in ICIS implementation.

Ten Years The critical facilities are fully sustainable, actively contributing to improving food security in their respective countries and regions while continuing to contribute to global wheat improvement efforts.

South Asian NARS have an efficient

Sathguru

Cornell

61




variety development and replacement system benefiting all wheat growers. Losses due to stem rust are minimal.

The process and outcomes of this project have positive effects on gender issues in development.

Fifteen Years International efforts to mitigate and eliminate the effects to small holder famers against wheat stem rust are no longer limited by lack of ready access to germplasm, data, seed and knowledge.

25.c. Whole Family Variety Selection

25.c.1. Foster the engagement of the entire household in participa-tory variety selection through “Family variety selection” in India and Ethiopia.

All organizing partners from NGOs, national programs, and DRRW project are convened to plan Whole Family Variety Selection approach and implementation. Realistic targets are agreed upon including: • What data to be collected at Family Field

Days is determined; • A strong mission statement is drafted for this

project component; • MoUs are agreed upon. (Sep 2011)

Whole Family Variety Selection is implemented in two countries (by Sep 2012)

Results of Whole Family Variety Selection are shared with DRRW breeders. (Sep 2013, recurring annually)

Five Years Whole Family Participatory Variety Selection is implemented in 2 countries. Desired end-use quality traits identified.

Ten Years Whole Family Participatory Variety Selection becomes standard practice (replacing gender segregated variety selection)

Genetic variation and heritability of desired traits investigated and informs breeding programs.

Fifteen Years Breeders breeding for qualities important for entire wheat producing family unit.

Increased food of desired quality in the household.

S. Davidson, Cornell

62




Women’s household labor input lessened.

25.d. Strength-ened national program capacity

25.d.1. Foster a new generation of wheat pathologists and breeders in contemp-orary wheat improve-ment with emphasis on durable adult plant resistance to stem rust.

A cadre of young research technicians and scientists (40) trained, enabling uniform reporting of global wheat rust surveillance data and knowledge. (Aug 2013)

Senior scientists (24-30) trained at CIMMYT and ICARDA on wheat pathology/breeding, particularly on the use of minor gene resistance in pathology research and variety development. (Oct 2014)

IWIS3 (an ICIS application) implemented across all Objective 25 DRRW partners, enabling better sharing of germplasm phenotypic data and information, and deployment of molecular breeding platform tools to enable more robust application of marker assisted selection. (Dec 2012)

Five Years New generation of wheat scientists engaged in short-term and long-term wheat improvement research needed for meeting future wheat demands.

Data quality is assured, and data management tools are in place and used beyond the aims of the project.

Ten Years The project’s partners have fully sustainable operations, actively contributing to improving food security in their respective countries and regions while continuing to contribute to global wheat improvement efforts.


P. Wenzel and P. Kosina, CIMMYT, Mexico

63


Objective 26: High breeding value wheat lines with two or more marker-selectable stem rust resistant genes


Primary Responsible Scientist/inst.

26.a. Gene discovery, postulation, and phenotypic support of genetic mapping and germplasm develop-ment.

26.a.1. Seedling stem rust screening of wild relatives of cultivated wheats, introgres-sion lines, mapping populations, and high breeding value lines.

Identification of Ug99 resistant Triticum/Aegilops spp., Haynaldia villosa, Secale cereale (and derived triticales) accessions, and Thinopyrum spp.-derived amphiploids with potentially new sources of seedling resistance based on multipathotype analysis; 2000 entries tested per year. (Mar 2011, recurring annually)

Identification of Ug99 resistant rye (Secale cereale and derived triticales) accessions and introgression lines with new sources of seedling resistance based on multipathotype analysis: 100 entries per year. (Dec 2011, recurring annually)

Identification of Ug99 resistant Sitopsis accessions (Ae. bicornis, Ae. longissima, Ae. sharonensis, and Ae. speltoides) and Ae. variabilis, Ae. kotschyi and Ae. geniculata with potentially new sources of seedling resistance: • 300 entries tested per year at TAU (Dec 2010,

recurring annually);

• up to 300 entries tested per year at UMN. (Mar 2011, recurring annually)

Seedling phenotypic data for genetic mapping and selection of introgression lines and breeding parents: • 500-1000 entries tested per year at UMN (Mar

2011, recurring annually); • 300 entries tested per year at Free State (Dec

2010, recurring annually);

• 500 entries tested per year at UMN (Mar 2011, recurring annually)

Five Years Seedling resistant accessions provided to both funded and unfunded collaborators for population development, genetic mapping, and germplasm enhancement of new sources of Ug99 resistance. Genetic mapping studies (with populations from both funded and unfunded partners) reveal chromosomal location of new resistance genes.

Ten Years Elite breeding lines with new sources of Ug99 resistance in variety development programs. Enhanced diversity of stem rust resistance available in wheat breeding.

Fifteen Years Durable rust resistance strategically deployed based on combinations of major genes and/or APR genes.

Y. Jin, USDA-ARS CDL

Z. Pretorius, Free State U

B. Steffenson, U Minn

J. Manisterski, ICCI Tel Aviv U

M, Rouse, USDA-ARS CDL

64




Seedling Phenotyping of Mapping Populations; Pheotyping T. monococcum populations (Mar 2012)

• Einkorn/ PI 272557

26.a.2. Controlled APR screening of seedling-susceptible wild relatives, landraces, mapping populations, and high breeding value lines.

Ug99 resistant Triticeae accessions identified with potentially new sources of adult plant resistance, validation of adult-plant resistance QTL, and confirmation of high-value breeding lines: 100 lines tested per year in greenhouse APR screens with 5 replicates (~500 data points). (Dec 2010, recurring annually)

Adult-plant phenotypic data for QTL mapping. 300 lines tested per year with 5 replicates (~1500 data points). (Dec 2010, recurring annually)

Adult-plant phenotypic data for QTL mapping, validation of adult-plant resistance QTL, and confirmation of high-value breeding lines. 200 lines tested per year with 4 replicates in BL-3 facility. (~800 data points). (Mar 2011)

Tetraploid wheat accessions with potentially new sources of APR; APR phenotypic data for genetic mapping, validation of APR QTL, and confirmation of high-value breeding lines in controlled screen-house. (Dec 2010, recurring annually)

Methods for quantitative infection and measurement of APR are determined, standardized and communicated to the rust community. (Dec 2011)

Five Years APR accessions provided to both funded and unfunded collaborators for population development, genetic mapping, and germplasm enhancement of new sources of Ug99 resistance. Genetic mapping studies reveal chromosomal location of APR loc

Ten Years Elite breeding lines with new sources of APR in variety development programs. Enhanced diversity of stem rust resistance available in wheat breeding.

Fifteen Years Durable rust resistance deployed based on combinations of new major and APR genes.

Z. Pretorius, Free State U.

B. Steffenson. U Minn

A. Badebo, EIAR


65




26.b. Population development and introgression of new sources of resistance.

26.b.1. Intro-gression, population develop-ment, and/or allelism testing of primary gene pool sources of seedling and adult plant resistance.

Recombinant inbred line populations developed for new sources of seedling and APR resistance identified in Watkins collection wheat landraces. At least two populations advanced two generations per year. (Dec 2010, recurring annually)

Five or more new doubled-haploid and/or recombinant inbred populations for mapping novel sources of resistance in tetraploid wheats. ~200 DH and/or 400 SSD progeny advanced two generations per year. (Dec 2010, recurring annually)

Five Years Resistant accessions provided to both funded and unfunded collaborators for population development, genetic mapping, and germplasm enhancement of new sources of Ug99 resistance. Genetic mapping studies reveal chromosomal location of APR loci.


Fifteen Years Durable rust resistance deployed based on combinations of new major and APR genes. Enhanced diversity of "non-target" traits in the primary gene pool.

H. Bariana, U Sydney PBI

S. Xu, USDA-ARS

26.b.2. Intro-gression, population develop-ment, and/or allelism testing of intractable (secondary/ tertiary gene pool) sources of

New amphiploid and chromosome addition stocks for Haynaldia villosa and Aegilops spp.. Direct introgression lines and synthetic hexaploids with potentially new sources of seedling and APR resistance from Ae. tauschii. Mapping/allelism testing populations for high-priority resistance sources. Five amphiploids, direct introgressions from ten Aegilops accessions, and eight mapping/allelism populations advanced two generations per year. (Dec 2010, recurring annually)

Allelism tests, amphiploids and chromosome addition lines for Sitopsissection species. Six

Five Years Germplasm with new and/or improved alien sources of resistance suitable for development of high breeding value lines. Genetic mapping studies (with populations from both funded and unfunded collaborators) reveal chrom-osomal location of new resistance genes.

Ten Years Elite breeding lines with new sources of Ug99 resistance in variety development programs. Enhanced diversity of stem rust resistance available in wheat

M. Pumphrey, Washington State U

E. Millet, ICCI Tel Aviv U


I. Dundas, U Adelaide

66




seedling and adult plant resistance.

allelism/mapping populations and amphiploids with four Sitopsis accessions produced each year. (Dec 2010, recurring annually)

Backcross introgression/mapping/allelism testing populations with Ug99-resistant Ae. speltoides (4 accessions) and T. dicoccoides (8 accessions) advanced two generations per year. (Dec 2010, recurring annually)

breeding.


26.b.3. Targeted molecular-cytogenetic manipu-lation of intractable sources of seedling and adult plant resistance.

Translocation stocks with minimal alien chromatin for four new Ug99-effective resistance genes from Th. intermedium, Ae. caudata, Th. ponticum, and Th. junceum. (Dec 2014)

Translocation stocks with minimal alien chromatin for new Ae. sharonensis-derived stem rust resistance genes. (Dec 2013)

Translocation stocks with minimal alien chromatin for four Ug99-effective resistance genes from Ae. geniculata, Ae. searsii, Ae. speltoides, H. villosa (7/2011) and additional resistance genes identified in via 26.b.2. (Dec 2014).

Translocation stocks with minimal alien chromatin for Ae. speltoides and Th. ponticum derived resistance genes. (Dec 2014)

Five Years Germplasm with new and/or improved alien sources of resistance in variety development programs.



S. Xu, USDA-ARS



B. Friebe, Kansas State U



26.c. Mapping, validation, and delivery of marker-

26.c.1. Mapping rust resistance loci toward

High-resolution genetic maps of two or more Ug99-effective stem rust resistance loci. Robust DNA markers that are tightly linked or diagnostic for stem rust gene detection. (Dec 2014)

High-resolution genetic maps of two or more

Five Years Efficient pyramiding of diverse stem rust resistance loci in breeding lines.

Ten Years Identification of allelic sources of

M. Sorrells, Cornell

J. Anderson, U Minn

67




selectable resistance genes.

development of diagnostic markers for effective genes.

Ug99-effective stem rust resistance loci. Robust DNA markers that are tightly linked or diagnostic for stem rust gene detection. (Dec 2014)


Chromosomal location two or more new sources of stem rust resistance (Ug99-effective) through molecular mapping and and identification of linked markers. (Dec 2014)


Mapping populations suitable for APR mapping, phenotypic data, and framework genetic maps for three APR populations (Dec 2012)

High-resolution genetic maps of the Ug99-effective stem rust resistance loci in durum wheat. Robust DNA markers that are tightly linked or diagnostic for stem rust gene detection. (Dec 2014)

resistance. Development of diagnostic markers or marker combinations for prediction of Sr genes in germplasm collections. Elite breeding lines with APR in variety development programs. Enhanced diversity of stem rust resistance available in wheat breeding.

Fifteen Years Identification of molecular basis of APR resistance loci. Strategic manipulation of APR loci for routine durable rust resistance deployment (including biotechnology solutions).

J. Dubcovsky, UC Davis

U. Bansal and H. Bariana, U Sydney PBI

E. Lagudah, CSIRO

R. Singh and S. Singh, CIMMYT Mexico

S. Xu, USDA-ARS

26.c.2. Validation of effective APR genes conferring resistance to the Ug99 lineage.

Backcross near-isogenic populations for APR loci in Kingbird, Juchi, and Kiritati. Heterogeneous inbred families suitable for near-isogenic line development. (Dec 2013)

Backcross-derived doubled haploid populations contrasting for APR loci in multiple genetic backgrounds. (Dec 2013)

Near-isogenic lines/populations for two or more

Five Years Reliability information concerning expression of APR QTL in different genetic backgrounds and flanking markers that guides variety development efforts. Stocks for fine mapping and development of diagnostic markers/cloning

Ten Years


D. Bonnett/ CIMMYT Mexico

J. Anderson,

68




APR loci in two or more spring wheat backgrounds (Dec 2013)

Near-isogenic lines/populations for two or more APR loci in two or more spring wheat/durum backgrounds (Dec 2013)

Study of epistatic interactions among APR genes (Dec 2014)

Mutant populations for Kingbird and appropriate parent. Single QTL backcross isolines from Parula (Dec 2013)

Backcross-derived isolines of two APR loci derived from wheat landraces. (Dec 2013)

Near-isogenic lines/populations for two or more APR loci in two or more CWANA winter wheat backgrounds (Dec 2013)

Determine the effectiveness of different APR genes in different genetic backgrounds. Determine the epistatic interactions among different APR genes. More durable resistance based on Sr2 +additional well defined APR loci or genes

Fifteen Years

Durable rust resistance routinely deployed based on APR genes. Integrated APR strategies that incorporate a better understanding of the epistatic interactions among APR genes and their interactions with different wheat genetic backgrounds.

U Minn


E. Lagudah, CSIRO



26.c.3. Parent building and delivery to breeding programs.

High breeding value lines homozygous for two or more effective marker-selectable stem rust resistance genes distributed in International Stem Rust Screening Nursery. Twelve elite genotypes used as recurrent parents (Dec 2011, recurring annually)

Optimized screening conditions for DNA markers linked to Ug99-effective resistance loci and marker-assisted pyramids in high-breeding value lines. (Dec 2010, recurring annually)

Five Years Enhanced diversity of stem rust resistance available in wheat breeding. Pyramided donor lines for CGIAR and National Program breeding efforts. Introgression of resistance genes in germplasm adapted to the targeted regions.

Ten Years Elite breeding lines with new sources of Ug99 resistance in variety development programs worldwide.

Fifteen Years Efficient crossing blocks with multiple resistance genes fixed in the parental


S. Dreisigacker, CIMMYT Mexico

69




lines, which will eliminate the need of additional MAS in these lines.

26.d. Collection, preservation and distribution of genetic resources and information.

26.d.1. Preservation and distribution of germ-plasm.

Genetic stocks, amphiploids, mapping populations, resistance donors, validation, and high-value breeding lines preserved and distributed to international wheat breeding community; Preservation: H.Bockelman/ NSGC Aberdeen, H. Tsujimoto/NBP Japan, B.S. Gill/WGGRC (in-kind collaborators); Additional distribution via International Stem Rust Screening Nursery. (Dec 2010, recurring annually)

Five Years Fluid distribution of information an germplasm among participants and target breeding programs

Ten Years Integrated web resources to facilitate rapid access to information about sources of resistance, available germplasm, and detailed protocols for marker implementation. Generation of feedback mechanisms from the users (e.g. wiki)

T. Payne, CIMMYT Mexico

26.d.2.

Manage-ment of genetic information and resources.

Centralized web-accessible information on effective sources of stem rust resistance, including donor germplasm, mapping information, useful DNA markers, detailed protocols, feedback tools, and available high breeding value lines. Coordination of Obj. 26 germplasm distribution and screening nursery entries. Strong international partnerships. (Feb 2011, recurring annually)

Fifteen Years An active research community engaged in the continuous actualization of protocols and information.


26.e. Evaluation of Genomic Selection Models for Breeding for

26.e.1. Recurrent selection scheme yielding lines with high levels of

Initiation of cycle one of recurrent selection scheme by crossing 10 high performing parents in all possible combinations and intermating the F1s (Jul 2012)

Selection of lines to be intermated in cycle two of recurrent selection scheme using Genetic Estimated

Five Years Advanced breeding materials with high levels of APR combined with good agronomic performance. Evaluation of GS model accuracy and consistency across CIMMYT germplasm.


70




APR

APR while empirically evaluating GS models for APR.

Breeding Values (GEBVs) calculated with GS models (Oct 2012)

Selection of intermated cycle two lines using GEBVs calculated with GS models (Apr 2013).

Phenotypic evaluation in Njoro, Kenya of selected cycle one and cycle two lines for APR, and empirical evaluation of GS models (Apr 2014).

Ten Years Finished varieties with elite agronomic performance combined with high levels of APR and major resistant genes. Use of GS in breeding for APR in other lines.

Fifteen Years Durable rust resistance deployed. Routine use of GS to reduce phenotyping and increase gain from selection per unit time. Gender equity in wheat breeding achieved from the shift from field breeding to molecular breeding using GS.

26.e.2.

Genomic Selection: A Tool to Decrease Work-Life Conflict in Agricultural Research?

Use data from CGIAR and private companies to look at effect of molecular advancements on time spent away from home. (Sep 2011)

Train female graduate student in GS while also testing hypothesis that GS will reduce amount of time spent phenotyping in the field (Jessica Rutkoski). (Sep 2013)

Support publication of paper title “Genomic Selection: A New Tool to Decrease Work-Life Conflict in Agricultural Research.” (Sep 2011)

Five Years Proof of concept that GS shifts the proportion of time spent in lab or data analysis versus field.

Ten Years This technology shifts responsibilities of the scientist from field work to increased management and planning versus field work.

Fifteen Years Gender parity among wheat breeders.


26.f. Molecular Genetics of Rust Resistance

26.f.1. Molecular Genetics of Rust Resist-ance near the Sr9

Identification of markers tightly linked to Sr9 allelles—DArT derived markers and markers linked to Yr5. (Mar 2012)

Linkage testing between Sr9e and SrGabo 56. (Mar 2013)

Five Years

Molecular and functional genetics of the Sr9 locus is molecularly characterized and understood.

Ten Years

M. Rouse, USDA-ARS CDL

71




locus. Publication of genetics and mapping of stem rust resistnace in Gabo 56/alelism with Sr9. (Mar 2014)

VIGS induced gene silencing of putative Yr5 homologs in wheat lines possessing Sr9 alleles. (Mar 2015)

Molecular characterization of SrGabo56 / Yr5 homologs

Efficient pyramiding of diverse stem rust resistance loci in breeding lines. Diverse resistance available in wheat breeding.

Fifteen Years SrGabo56 and homologs are deployed in combination with other resistance genes in CIMMYT germplasm

72


Objective 27: Optimized wheat improvement system in Ethiopia.


Primary responsible scientist/Inst

27.a Optimized wheat improve-ment system in Ethiopia (all)

27.a.1 Coordinate DRRW wheat breeding activities in Ethiopia for an integrated wheat improvement program.

An integrated and evolving national wheat improvement program (breeding, plant protection, extension) that serves Ethiopia, Africa, and the world. (Jan 2011, recurring annually)

Collaboration within the National program and between the National program and International programs, Regional programs, and NGOs is coordinated. • CIMMYT • ICARDA • DRRW (Cornell) • AGRA • ARIs • GCP • USDA • Sasakawa Global 2000 • Other NARS

(Apr 2011, recurring annually)

Agro-ecologies and farming systems identified and confirmed as breeding targets. (Apr 2011)

Wheat-based research centers (RARIs) engaged in evaluation and selection. (Apr 2011)

Staffing positions identified and filled, with responsibilities outlined. (May 2011).

Maintenance and repairs to equipment, purchase of budgeted equipment, with equipment being placed into service. (Mar 2011, recurring annually)

Five Years Nucleus of a cohesive national wheat improvement program is established and functioning as a team.

Ten Years Targeted agro-environments with specific adaptation have improved and durably resistant varieties.

Fifteen Years Ethiopian wheat program is contributing to food security in Ethiopia and in SSA. Scientists are contributing to technology achievements and advancements in wheat pathology, breeding and crop management.

Bedada G., EIAR

73




Breeding and replicated testing programs tailored to match resources and budgeted priorities. (May 2011)

Progress and direction of programs Monitored/Evaluated. (Apr and Sep 2011, recurring annually)

27.a.2. Bread wheat breeding.

Two cycles per year Kulumsa-based spring bread wheat breeding program is operating. Program outlined • Holeta (Septoria hot-spot) • Bekoji/Meraro (Yellow rust) • KARI-Njoro (shuttle SR screening) • KU/DZ/Arsi Robe (stem rust)

(Apr 2011)

Agronomic, pathologic and end-use quality objectives prioritized and listed.

• Seed color • Volume weight • Industrial baking quality • Other

(Apr 2011)

10,000 introductions from international nurseries evaluated and promising lines selected for entry into Observation Nurseries at designated sub-centers. (Jun and Dec 2011, recurring annually)

Parent lines used in hybridization identified and 300 crosses outlined. (Aug and Jan 2011, recurring annually)

Five Years Varieties released from introduced germplasm and/or the National program are resistant to TTKS and other stem rust variants, to stripe rust, and to Septoria; all wheat based research centers evaluating candidate varieties.

Ten Years Durably resistant lines identified that contribute to NARS and CG center breeding programs. Durably resistant varieties from EIAR program compete with CG varieties, and occupy 20% of the bread wheat area.

Fifteen Years EIAR wheat varieties with specific adaptation to Ethiopian environments occupy 75% of the bread wheat area, are durably resistant, and have superior yield potential.

Bedada G., EIAR

74




F2 – F6 germplasm / generations evaluated at hotspot shuttle locations over seasons for traits of interest. (Aug and Jan 2011, recurring annually)

Five sets of 200 promising lines evaluated in observation nurseries at two to three locations. (Jun 2011, recurring annually)

Five sets of 20 high yielding, rust resistant entries evaluated annually in replicated trials (NVT) at 4-6 locations for two years. (Jun 2011, recurring annually).

Four sets of variety release verification trials (VVT) with at least one candidate variety planted on-station and on-farm trials. (Jun 2011, recurring annually)

An array of key breeding lines genotyped at CG centers. (Mar 2011, recurring annually).

Relationships with NARS, CG, and Objective 26 scientists strengthened and cultivated. (Mar 2011)

27.a.3. Durum wheat breeding.

Two cycles per year Debre-Zeit based durum wheat breeding program is operating. Program outlined. (Apr 2011)

Agronomic, pathologic and end-use quality objectives prioritized and listed. (Apr 2011)

International durum wheat nurseries evaluated and promising introductions identified. (Jun and Dec 2011, recurring annually)


Five Years Varieties released from introduced germplasm are resistant to TTKS and other stem rust variants, to leaf rust, and to Septoria; all wheat based research centers evaluating candidate varieties.

Ten Years Durably resistant lines identified that contribute to NARS and CG center breeding programs. Durably resistant varieties from EIAR program

Bedada G., EIAR

75





Two sets of 200 promising lines evaluated in observation nurseries at 2-3 locations. (Jun 2011, recurring annually)

Two sets of 20 high yielding, rust resistant entries evaluated annually in replicated trials (NVT) at 4-6 locations for two years. (Jun 2011, recurring annually).

Two sets of variety release verification trials (VVT) with at least one candidate variety planted on-station and on-farm trials. (Jun 2011, recurring annually).


compete with CG varieties, and occupy 20% of the durum wheat area.

Fifteen Years EIAR wheat varieties with specific adaptation to Ethiopian environments occupy 75% of the durum wheat area, are durably resistant, and have superior yield and quality potential.

27.a.4 Develop the human resource capacity for wheat research in Ethiopia:

Skills of the EIAR technical staff and assistants are enhanced with short-term training opportunities. (Sep 2011, recurring annually)

Training opportunities for EIAR scientists, such as biotechnology, data management and interaction with ARI counterparts result in progressive breeding programs. (Apr 2011) • Exchange visits with ARIs and sister

institutions. • Long-term training at ARIs (Apr 2011)

Five Years EIAR wheat staff has technical skills, which enable efficient evaluation of introduced germplasm in screening nurseries that fit national agro-ecologies. New and renovated equipment contributes to program efficiencies.

Ten Years Breeding program matures and staff manages genetic diversity and breeding technologies, driving genetic gains in host resistance and yield performance.

Bedada G., EIAR

76




Enhanced skills and training in preventative maintenance and repairs to research equipment. • Small engine repair and maintenance. • Preventative maintenance of field and lab

equipment. (Apr 2011)

Fifteen Years EIAR wheat research staffs become leaders in SSA and contribute to wheat research and development, and to global food security.

27.a.5 Acquire necessary equipment to modernize and improve efficiencies of EIAR bread wheat and durum wheat improvement programs.

Necessary equipment has been acquired. (Nov 2011)

Irrigation capacity is maximized to meet program requirements. (Nov 2012)

Lab, greenhouse, cold room, and seed health facilities improved or constructed. (Nov 2012)

Essential field equipment has been acquired and / or received necessary repairs to achieve functional use. (Apr 2011)

Five Years Improved efficiencies for all program activities.

Ten Years Progress realized in breeding for resistance to stem and other rust pathogens. Pathology and breeding programs maturing and contributing to EIAR goals of generating and delivering improved technologies, resulting in contributions to food security in Ethiopia.

Fifteen years Durably resistant and increasingly productive varieties result in a viable domestic wheat industry. Contributions also lead to increased food security in SSA in general and particularly for resource-poor farmers and consumers in Ethiopia.

Bedada G., EIAR

77


Objective 28: Project management, communication, and coordination

Component Activities Activity Outputs (completion date) Activity Outcomes


28.a. Project management.

28.a.1. Financial/ contractual manage-ment.

Subcontracts executed, task orders issued, invoices paid, and ad hoc financial issues addressed. (Feb 2011, recurring annually)

Five Years DRRW Project has been successfully implemented and administered.

Project goals have been successfully communicated to target audiences

Ten Years The livelihoods of millions of wheat farmers and poor consumers worldwide have been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat varieties.

Fifteen Years The livelihoods of millions of wheat farmers and poor consumers worldwide have been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat varieties.

Cornell

28.a.2.

Reporting to BMGF.

Reports from subcontractors submitted; compiled report from Cornell successfully submitted. (Sep and Oct 2011, recurring annually)

Regular communications with BMGF to give program officer good sense of day-to-day progress, challenges, and opportunities. (Dec 2010, recurring annually)


Ten Years The livelihoods of millions of wheat farmers and poor consumers worldwide have been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat

Cornell

78




varieties.


28.a.3.

Program-matic manage-ment.

Milestone monitoring system developed and maintained. (Sep 2009, recurring annually)

Project-wide metrics for impact monitored. (ongoing with annual update delivered to BMGF following September reporting period each year)

Collaborating scientists/institutions visited periodically by DRRW Management. (Feb 2011, recurring annually)

Regular interaction between DRRW Management and Team Leaders and key stakeholders is ongoing. (Feb 2011, recurring annually)

Annual DRRW project meeting held (may be in conjunction with BGRI annual meeting, or may be a separate affair) (Jun 2011, recurring annually)

Ad hoc objective-specific workshops supported. (Jun 2011, recurring annually)





Cornell

79




28.a.4. External Program Advisory Committee (EPAC).

EPAC provides regular input to DRRW and BMGF on project progress and travels as necessary to review DRRW progress. (Jun 2011, recurring annually)




Cornell

28.a.5.

Internal IT. Equipment and IT support provided to assist project administration and internal management and communication. (Jan 2011, recurring annually)

Five years DRRW Project has been successfully implemented and administered.

Ten years The livelihoods of millions of wheat farmers and poor consumers worldwide have been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat varieties.

Cornell

80





28.a.6.

Supplies. Internal administrative and project management supplies acquired and services rendered. (Jan 2011, recurring annually)



Fifteen years The livelihoods of millions of wheat farmers and poor consumers worldwide have been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat varieties.

Cornell

81




28.b. Communi-cations.

28.b.1. Perform communi-cations activities supporting project coordina-tion/man-agement.

Brochures, Power Point presentations, and posters to describe DRRW project developed and distributed to key audiences. (Feb 2011, recurring annually and ongoing)

Information about project progress regularly shared with DRRW collaborating scientists. (quarterly updates, as described in Objective 22) (Mar, Jun, Sep, Dec 2011, recurring annually)


Project goals have been successfully communicated to target audiences.



Cornell

28.b.2.

Maintain comprehen-sive ‘wheat rust’ web presence.

Wheat Rust Knowledge Bank contains scientific information related to the wheat rusts requested by and provided by the rust community, and is a sustainable, well-trafficked online resource for scientists, policymakers, donors, and the public. (Jan 2011, recurring annually)

Virtual Communities for scientific discussion established and maintained. (Jan 2011, recurring annually)

DRRW project website developed and maintained with frequently updated information



Web resources have been developed to serve the wheat rust community and help ensure its sustainability.

Cornell

82




relevant to scientists, policy-makers, donors, the media, and the public. (Jan 2011, recurring annually)

Ten Years The wheat rust community has grown and benefitted from the knowledge produced and models for information sharing developed by the DRRW project.

The livelihoods of millions of wheat farmers and poor consumers worldwide have been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat varieties.

Fifteen Years The wheat rust community has grown and benefitted from the knowledge produced and models for information sharing developed by the DRRW project.


28.c. Global access and impact.

28.c.1. Manage global access.

Annual update developed on DRRW innovations. (Nov 2011, recurring annually)


Global Access Strategy has been fully implemented and all DRRW innovations are delivered to the target users.

Cornell

83








84




28.d. Gender Opportunity Enhancement

28.d.1. Foster activities that enhance gender parity in wheat breeding and training.

Objective-specific gender activities implemented. (Jun 2012)

Gender and diversity issues in DRRW project regularly monitored. (Oct 2011, recurring annually)

Opportunities to enhance gender parity are realized and enhanced through contingency gender funds. (Jun 2011, recurring annually)


Gender equity has been improved as a result of the DRRW project efforts in this arena.





Cornell

85




28.e. Special Initiatives

28.e.1. Stem Rust Isolate Sequencing Initiative

Convening is held to plan special initiative work plan (January 2011)

SSR markers are shared between special initiative partners (Dec 2011)

Puccinia graminis (Pgt) isolates fingerprints are resolved and data are shared (Dec 2012 and ongoing)

Puccinia graminis (Pgt) isolates genomic sequences are resolved and data are shared (Jan 2015 )

Five Years Stem Rust Isolate Sequencing Initiative has been planned and initiated

BGRI community is sharing Pgt genomic resources and data

BGRI community-generated Pgt genetic data are archived and publicly available

Ten Years BGRI community-generated Pgt genetic data are archived and publicly available

The origin and evolutionary pathway of Ug99 is resolved

Fifteen Years The “next Ug99” epidemic is averted due to knowledge of pathogen and its evolutionary patterns.

Cornell

28.e.2. Gene Deployment Initiative


Four post docs are hired (August 2011)

2 x three major gene stacks are developed (non-transgenic)

Major gene stacks are integrated into CIMMYT germplasm

Five Years CIMMYT wheat germplasm contains at least 3 stacked major genes in an APR background

Ten Years National Programs adopt and adapt CIMMYT’s germplasm that contains 3 stacked genes in an APR background.

Farmers adopt this germplasm as made available by the National Programs.

Fifteen Years Globally, no wheat germplasm is released with single major gene-based resistance.

Cornell

86

Appendix B: Budget by Objective / Durable Rust Resistance in Wheat Phase II

Appendix B: Budget Not available in this version.

87

Appendix C: Detailed Description of Proposed Work / Durable Rust Resistance in Wheat Phase II

Appendix C: Detailed Description of Proposed Work

88

Appendix C: Detailed Descriptions of Proposed Work / Durable Rust Resistance in Wheat Phase II Objective 21 Improved testing, multiplication and adoption of replacement varieties

Summary Information (Objective level) Objective Name:

Objective 21: Improved testing, multiplication and adoption of replacement varieties.

Team Leader for this Objective: Gordon Cisar, Cornell Senior Management

E-mail [email protected] Collaborating Institutions with Budgeted activities

Institution Name (Scientist) email Cornell University Gordon Cisar [email protected] Ethiopian Institute of Agricultural Research (Phase I Funding)

Bedada Girma [email protected]

Kenya Agricultural Research Institute

P. Njau [email protected]

Independent Consultant Rob Tripp [email protected]

Amount Requested ($USD):

Project Duration (months):

60

Authorized signature/date (alternatively, provide an appropriately signed cover letter)

89


I. Executive Summary Summary of Short, Medium, and Long Term Outcomes Component a: Transnational Coordination

• Acceptability, diversity, and performance of new stem rust resistant varieties in seed multiplication are not limited by lack of farmer input on variety selection (five years and beyond).

• Capacity and security of Nucleus and Breeder Seed production enables earlier entry of new, farmer endorsed varieties into foundation and commercial seed production (five years and beyond).

• Seed system performance not limited by stability and diversity (in terms of varieties) of Breeder Seed production (five years and beyond).

• Efficiency of seed system performance enhanced by a regulatory framework where existing constraints to variety release and commercialization are eliminated (ten years and beyond).

• Commercial and extension seed production actors access adequate supplies of Foundation Seed early in the commercialization process (five years and beyond).

• Commercial seed availability is optimized (five years and beyond).

• Encouragement of private sector investments in seed systems leads to multiple genetically diverse varieties in the marketplace, resulting in improved stability of production and the opportunity to develop economic investments (fifteen years and beyond).

• Vulnerability of the world’s wheat crop to stem rust is systematically diminished through adoption of improved, diversely resistant varieties that meet farmer requirements including yield stability, acceptable end-use quality, and improved productivity (five years and beyond).

• Engagement with national regulatory agencies in improvements to seed systems has spillover effects applicable to multiple crops and emerging (transgenic, etc.) technologies (fifteen years and beyond).

Component b: Kenya • Kenya wheat seed supply chain is able to identify higher yielding and stem rust resistant

wheat varieties with greater precision (five years and beyond)

• Released varieties that can protect Kenya from stem rust, thus reducing cost of production and increasing food safety through reduced use of fungicides, reach farmers two years earlier than with the system in place in 2008 (five years and beyond).

• One-quarter of Kenya’s wheat area (80% in ten years, 95% in 15 years), both in small and large scale farm sectors, is planted to wheat varieties that yield 10% greater than the weighted average of varieties planted in 2008, and also have resistance to local races of stem rust (five years and beyond).

90


• Rates of genetic gain are not compromised by inefficient Breeder Seed production (five years and beyond).

• 100% of Kenya’s large-scale farmers; and 50% of small scale farmers (90% by ten years) are aware of current stem rust resistant varieties (five years and beyond).

• Rate of variety turnover in farmer’s fields is commensurate with demonstrated superiority of new varieties (five years and beyond).

• Multiple varieties with superior agronomic performance and diverse genetic resistance to stem rust are common in the marketplace (ten years and beyond).

• The private sector becomes increasingly engaged in the wheat seed enterprise (ten years and beyond).

• One of the putative origins of virulent pathotypes of stem rust is no longer contributing to the development of a pathotype that can threaten global wheat production (ten years and beyond).

Component c: Ethiopia • Breeder Seed availability does not limit adoption/production of stem rust resistant

varieties (five years and beyond).

• Main- and off-season multiplication of candidate varieties, enabled by improved irrigation capacity, is a routine practice (five years and beyond).

• The delivery and popularization of an array of durably and diversely resistant varieties emanating from the EIAR breeding programs is a seamless and unbroken continuum, efficiently linked with rapid seed multiplication, variety registration and extension activities (ten years and beyond).

• Seed quality and seed health of varieties in commerce allow increased realization of the genetic potential of varieties, resulting in improved national wheat production (ten years and beyond).

• A robust and comprehensive national wheat breeding program, coupled with an equally robust and comprehensive seed system, begins to contribute to alleviating the persistent food insecurity problems that have plagued Ethiopia (five years and beyond).

Progress to Date

DRRW Phase I included resources to develop seed system intervention plans through a consultative process with National Programs. Dr. Rob Tripp was and continues to be the driving force behind establishment of guiding principles for DRRW Phase II seed interventions, preliminary country-specific seed system analyses, priority targets for interventions, and follow-on planning. Phase I of DRRW examined the status of wheat seed systems in five priority countries of sub-Saharan Africa and South Asia: Kenya, Ethiopia, Nepal, Pakistan, and India. Awareness of the enormous challenges in production and replacement of wheat seed in Ug99 threatened countries appears much higher than just two years ago, both within those countries, and among donors. USAID (six countries) and FAO (Afghanistan in particular) have initiated new investments in the past year.

91


Guiding Principles

Replacing the world’s deployed wheat varieties in the face of Ug99 will require vast sums of money, well beyond the scope of this project. This Objective is aimed at coordinating that investment, from multiple donors, which should support the provision of rust resistant wheat varieties in the short-term, but also ensure the development of sustainable national wheat seed systems that allow more rapid turnover of wheat varieties in the future. Spillover effects from reviewing and modifying regulatory requirements that promote more efficient replacement of wheat cultivars will be of benefit to introducing other crops and technologies, thus mitigating food production and food security issues. An efficient and rational regulatory environment is also desirable for private sector engagement. Thus, it is important to work through current national seed systems. The goal is to mobilize and resource the major national players in each country in terms of varietal testing, seed production and seed delivery to ensure that rust resistant wheat varieties are available to all farmers. This goal dictates the choice of partners in each country.

Priority Targets for Interventions Although the development of germplasm resistant to stem rust and its incorporation into productive and well-adapted wheat varieties occupies the major portion of DRRW resources, the project’s ultimate success depends on the ability of participating countries to deliver seed of rust-resistant wheat varieties to farmers before the advent of any epiphytotic. This implies that the project must evaluate the performance of national wheat seed systems, identify major constraints, and make efforts to address these where necessary.

The path from plant breeding to variety uptake and utilization is an unbroken continuum of activities, but for the purposes of project administration, a seed system has been defined to include the following areas, each of which potentially deserves attention.

• Varietal testing. New wheat varieties not only need to be rust resistant but also must have the agronomic, organoleptic and market characteristics that farmers and consumers require. National varietal testing systems are not always sufficiently organized or resourced to provide efficient and accurate evaluation of new varieties resulting in the identification of the most likely candidates for eventual release.

• Pre-Release seed multiplication. Most public plant breeding programs produce just enough seed of the varieties being considered for release to supply a modest testing program. In normal circumstances this is an understandable conservation of resources, but under the threat of stem rust and in view of ever increasing food security concerns, it is necessary to have more seed of pre-released varieties available for extensive testing and to get a head start on the seed multiplication process. This may imply the need for additional resources at this stage.

• Regulatory compliance. Most countries require that varieties pass independent agronomic performance tests and be examined in a DUS (distinct, uniform, stable) test to ensure that a candidate for release is novel. These regulatory procedures are usually supported by public agencies that may be inadequately funded and hence may require additional support to ensure that useful varieties are identified and released as quickly as possible. To enhance the durability of released varieties, it is important that the

92


distinctness of candidates for release include the evaluation of genetic protection against predominant pathogens.

• Source seed multiplication. Source seed embraces the several generations of seed that are preliminary to Certified or commercial seed. The precise nomenclature is established by national authorities. Responsibilities for source seed multiplication are often divided between the plant breeding institute and seed producing agencies; divisions of responsibilities and incentives for efficient production may not always be perfectly defined. Resources available for pre-release multiplication need to be evaluated. Engagement of the private sector at this juncture needs to be initiated.

• Commercial seed production. The multiplication, conditioning and distribution of seed for farmers may be the responsibility of public or private enterprises. Organizing production of large quantities of seed of a new variety can take several years unless adequate provisions have been made.

• Variety promotion and popularization. The special circumstances of the threat of stem rust demand that particular attention be paid to the way in which information is provided to farmers regarding the advantages of new varieties and the ways to control stem rust.

Phase I Assessments and Planning Kenya: Several trips have been made to Kenya to assess the seed system. The first was a week-long visit in August 2008, when various seed system stakeholders were visited and interviewed (KARI, Kenya Seed Company, wheat growers, extension, KEPHIS). A second visit in June 2009 involved additional meetings with these and other stakeholders. A one-day planning meeting was held in Nakuru on 7 July 2009 to discuss the elements of potential Phase II activities for DRRW. Representatives from KARI, KEPHIS, MoA, KSC, and CGA attended this meeting and agreed to serve as an ad-hoc committee to review the planning process. Preliminary strategies, responsibilities and costs were discussed under the areas of: (i) initial yield trials, (ii) national performance trials, (iii) DUS requirements, (iv) Pre-Release Seed multiplication, (v) Breeder Seed production, and (vi) popularization. A particular feature of the meeting was the agreements reached for inter-agency collaboration and communication.

Ethiopia: An initial visit to assess the seed system was made in August 2008; interviews concentrated on EIAR staff, representatives of ESE, and federal extension and regulatory authorities. A two-day workshop at EIAR in February 2009 provided an opportunity to discuss tentative plans for the second phase of DRRW, including seed-related activities. A visit in May 2009 involved further discussions with EIAR and ESE but also included field visits to three regional agricultural extension bureaus and an examination of regional seed production capacity. Meanwhile, EIAR and DRRW staff continued to identify appropriate investments for the Phase I “Special Initiative” funds targeted for the Ethiopian wheat seed system.

Pakistan: A DRRW consultant visited Pakistan June 15-19, 2009. The visit included discussions with the leadership of NARC, the national coordinator of the Wheat Program, other NARC scientists, the director and members of the Wheat Program of the Ayub Agricultural Research Institute (AARI) (Faisalabad), the ICARDA country representative, and the director of the Federal Seed Certification and Registration Department. Discussions centered on variety testing

93


strategies, source seed production and the status of the commercial seed system. A trip report summarizing the discussions was sent to NARC, AARI and ICARDA.

India: A consultant accompanied Ronnie Coffman on visits (September 28 – October 3, 2008) to the Indian Council for Agricultural Research (ICAR), Indian Agricultural Research Institute (IARI), the Directorate of Wheat Research (Karnal) and Punjab Agricultural University, as well as representatives of CIMMYT, IRRI, NCAP(National Centre for Agricultural Economics and Policy Research) and the Plant Variety Protection Office. This provided an opportunity to discuss aspects of variety development and seed delivery.

Status of Wheat Seed Systems in Target Countries Kenya: Although Kenya grows only about 150,000 hectares of wheat it is the country that has the highest incidence of Ug99. It is a primary source of inoculum that may be borne by wind or travelers well beyond the borders of Kenya. It is therefore imperative that resistant varieties be deployed as quickly as possible. Primarily, wheat breeding is the responsibility of the Kenya Agricultural Research Institute (KARI) although the public Kenya Seed Company (KSC) is also engaged in breeding. Only a few wheat varieties have been released in the past decade and variety turnover has been fairly slow. All commercial wheat seed is produced and sold by KSC. The regulatory system is managed by the Kenya Plant Health Inspectorate Service (KEPHIS). The Ministry of Agriculture performs extension services (e.g. variety promotion for wheat, usually in conjunction with KARI). Also, the Cereal Growers Association (CGA) represents larger farmers (who grow the bulk of Kenya’s wheat), and operates a fairly extensive extension program. An analysis of the Kenya wheat seed system has shown that particular attention is required for source seed production, multi-location testing (for both research and regulatory purposes), efficient management of DUS tests, variety popularization, and education of growers as to economic threshold for fungicidal applications to APR protected varieties.

Ethiopia: Many of Ethiopia’s resource-poor farmers depend on wheat as a source of subsistence and as a cash crop. Wheat breeding is done by the Ethiopian Institute of Agricultural Research (EIAR), as well as by regional research institutes. The Crop Variety Register lists 41 bread wheat varieties “under production,” 28 of which have been released since 1998, but five varieties account for more than 90% (and one variety for more than half) of seed production. Adequate variety testing is a challenge in a country with many wheat-growing environments. Regulatory requirements are fairly straightforward and are rarely a cause of serious delay in variety release. Source seed production is shared between EIAR and the parastatal Ethiopian Seed Enterprise (ESE). All commercial seed production is in the hands of ESE, which sells its seed through government input cooperatives. The regional government extension bureaus are also responsible for organizing local production of wheat seed that accounts for about half of the “formal” seed available. An analysis of the Ethiopian wheat seed system found that attention and resources were required for Pre-Release Seed multiplication, variety testing, source seed production and variety popularization. Limits on Breeder Seed production are widely seen as a key limitation to current supplies of wheat seed, and the ability of the system to rapidly replace current varieties once replacement stem rust resistant varieties are identified. The USAID Famine Seed project component for Ethiopia, with ICARDA as the primary IARC partner, is supporting initial multiplication of approximately ten new lines. EIAR is testing those lines at over fifteen sites in replicated trials.

94


Nepal: Nepal plants close to 700,000 hectares of wheat; it is the country’s third most important cereal crop. Wheat breeding is under the National Wheat Research Program (NWRP) of the National Agricultural Research Council (NARC). Variety testing is done by NARC, but it faces particular challenges in the hill environments, where logistics are difficult. The regulatory system is fairly straightforward and relies in part on data provided by NARC. Regulation and policy are under the National Seed Board. All Breeder Seed is currently produced at one NARC station (Bhairahawa) and Foundation Seed is produced on several NARC stations, most of which lack adequate seed processing equipment. Commercial wheat seed is produced by three entities: (i) the National Seed Corporation (NSC), (ii) a handful of private seed producers, and (iii) Department of Agriculture programs that attempt to multiply seed at the district level. The extension services are underfunded and popularization is often a slow process. Analysis suggested that project priority should be given to: (i) expanding and stabilizing Breeder Seed and Foundation Seed production capacity, (ii) expanding the capacity for variety testing in the Hill Zone, (iii) rationalizing the production of commercial seed, and (iv) expanding popularization efforts, particularly through the production and distribution of “mini-kits” (small introductory packs of seed). Nepal is also one of the USAID Famine Seed project countries, which recognizes the importance of stem rust resistance as well as farmer acceptance. CIMMYT is the primary IARC partner.

Pakistan: Wheat is Pakistan’s major crop, with an annual production of about 22 million metric tons. Approximately 80% of Pakistan’s wheat is sown on irrigated land. Pakistan’s wheat breeding is done by both federal and provincial institutes and it has released about 30 varieties in the past 8 years. Traditionally, provincial seed corporations in Punjab and Sindh and extension programs in the other two provinces have produced most of Pakistan’s wheat seed. That system is undergoing transition with the emergence of many small, private seed companies, and the Sindh Seed Corporation is facing serious financial problems. Although Pakistan’s wheat seed system is quite strong, it has not always achieved the rate of variety turnover that might be expected, with farmers often preferring to grow older varieties. Despite the system’s general strength, a preliminary analysis identified several possibilities for intervention. These include expanding the capacity for Breeder Seed production, supporting current government efforts (particularly in Punjab) to formalize the production of Foundation Seed (through a “Foundation Seed cell”) and establishing better links with commercial seed producers, and strengthening data collection and analysis on variety use and requirements in marginal areas. Pakistan is also one of the USAID Famine Seed project country targets. ICARDA is the primary IARC partner. It appears likely that the US Government will invest in Pakistan’s seed system and any resulting projects will be sensitive to the threat of Ug99.

India: Preliminary discussions were held with various stakeholders in India in late 2008. The assessment at this point is that India’s wheat breeding system is well prepared to meet the challenge of Ug99 and that its exceptionally diverse public and private seed production system can efficiently deliver new varieties.

Narrative of Proposed Work

Description of Proposed Activities. Activities for Phase II will involve transnational coordinating activities supported from Cornell and country components in Kenya and in Ethiopia. The Kenya component is the most advanced

95


in terms of buy-in from key National actors. For Ethiopia, the described activities will be funded with Phase I “Special Initiative” funds, and include planned investments in irrigation capacity, seed processing capability, seed quality lab equipment, operational costs for seed production.

Transnational Coordination (Component a) With representation from the various donor projects anticipated, a committee will be formed to provide guidance and coordination where needed (Activity 21.a.1). Such a committee already exists to coordinate the USAID Famine Seed Project but is not active at the moment. Leadership (chair of the committee) will come from an individual employed by one or more of the seed projects. DRRW will be represented an Associate Director/Plant Breeder and will serve as a secretariat for the committee, organizing meetings and facilitating communications under the auspices of the BGRI.

Kenya (Component b) Activity 21.b.1 will support an increase in the number and precision of multi-location trials by both the breeding program (KARI-Njoro) and the National Performance Trials that are managed by the Kenya Plant Health Inspection Service, KEPHIS, and used as the basis for variety release decisions.

Activities 21.b.2 and 21.b.3 address the timing and efficiencies of Breeder Seed production by KARI. If implemented, the required agreements between KARI and KEPHIS will enable availability of Breeder Seed at the time of release as opposed to 1-2 years later. KARI will also be able to produce subsequent generations of Breeder Seed more efficiently and direct more resources toward varietal development.

Activities 21.b.4 and 21.b.5 address opportunities for system enhancing communication throughout the wheat improvement value chain, from flour millers back to the Kenya Seed Company and KARI plant breeders.

Ethiopia (Component c: indicative) The single activity (21.c.1) aggregates investments all aimed at increasing EIAR’s capacity to generate Breeder and Pre-Basic Seed. Targets include irrigation investments for off-season seed production, and equipment to increase timeliness or efficiencies of field work and post harvest processing/testing. In-service training for staff engaged in all aspects of seed production, processing, and quality testing is to be provided, as is training in maintenance of field and laboratory equipment (27.a.4).

Justification for the Proposed Work The majority of outputs of this project contribute to rapid development of locally adapted and acceptable replacement varieties resistant to prevailing stem rust races in the targeted countries threatened by Ug99. The Project’s goals, however, will only occur when farmers are planting seed of durably resistant and agronomicly improved varieties. Although there is some truth in the belief that “good varieties sell themselves,” variety turnover in most developing countries is very slow. The preponderance of a single variety over a long period of time is common in large wheat growing areas, and is detrimental to durable resistance and stability of production. Both of these features suggest that the systems that link the outputs of breeding programs and farmers are not inherently configured for the kind of performance that is required to replace current varieties in a

96


short period of time. As a result of our planning and analysis during Phase I, we now define a seed system to include the following areas: (i) varietal testing, (ii) Pre-Release Seed multiplication, (iii) regulatory framework, (iv) Breeder and similar source seed multiplication, (v) commercial seed production, and (vi) variety promotion and popularization. During Phase II, DRRW will enlist donor support and assist with coordination of this comprehensive set of activities in the major wheat growing countries in the path of Ug99. Because of the urgency, we will make modest, targeted investments aimed at relieving constraints to rapid adoption of improved varieties in two countries, Kenya and Ethiopia.

The Challenge Wheat has two properties that render rapid impact of new varieties a special challenge: high seeding rates (100 kilograms per hectare or higher), and a very low seed multiplication ratio. One hundred kilograms of seed planted on a hectare of land will usually produce between 3,000 and 6,000 kilograms of grain, with corresponding multiplication ratios of 30 and 60. Multiplication ratios can be increased to 300 with land and labor intensive management, but that is only feasible on very small areas of land.

Assuming seeding rates of 100 kilograms per hectare and a multiplication ratio of 30, then initial seed quantities (from the breeder) of 500 kilograms or 3,000 kilograms could be multiplied in three seasons to 13,500 and 81,000 tons of commercial seed, respectively. This would enable commercial production on a maximum of 135,000 and 810,000 hectares, respectively.

In either of these scenarios, seed production actors involved in multiplying the original source seed rapidly encounter huge logistical, administrative, and financial challenges if all seed is used to produce more seed, which will be the case in an emergency replacement situation. In the examples above (initial source seed quantities of 500 vs. 3,000 kilograms), the cumulative land required to produce the indicated quantities of commercial seed are 4,600 are 27,900 hectares, respectively (all requiring roguing and field inspection). The cumulative quantities of seed (including the resulting commercial seed) to be cleaned, tested, bagged and distributed are roughly 14,000 and 83,000 tons, respectively. The cumulative value of those quantities of grain in the two examples would be $3,000,000 and $16,000,000 US dollars, using a very conservative price of $200 per metric ton.

The magnitude of the challenge of wheat seed systems is further complicated by the small size of farms and correspondingly enormous numbers of customers. Predominance of small-scale farms (1-2 hectares) in Ethiopia, for example, also renders the task of seed production more challenging because of the number of farmers that need to be recruited to produce seed. Arguably, the daunting task of replacing significant areas of at-risk land with replacement varieties is beyond the scope of this project. There are, however, a number of interventions in the final testing of varieties, the very first steps of seed multiplication, and variety popularization that can have dramatic effects on wheat seed systems.

97


Interventions The path from a variety’s inception to adoption by farmers typically involves at least four distinct but necessarily interlinked institutions or groups: (i) the breeding program, (ii) a source seed multiplication enterprise (acting on the first two generations of seed), (iii) commercial seed producers, and (iv) a government regulatory agency to ensure identity and purity of intermediate and final products. A fifth set of actors could be extension systems and NGOs, particularly when final steps of dissemination occur via “informal” as opposed to “formal” approaches. The path from plant breeding to variety adoption is an unbroken continuum of activities involving all of the actors listed above. For example, a breeder’s objectives (variety characteristics) must be informed by farmers, consumers and grain/food processors; the timing of multiplication and quantities needed of the initial source seed is informed by regulatory agencies, strategic plans of post-source seed actors, and the actions and decisions by breeders themselves.

The impact of different quantities of initial source seed from the breeder is illustrated in the examples above. A difference between 0.5 and 3.0 tons of breeder-produced source seed translates into a potential difference of 675,000 hectares of land planted to a superior variety by farmers just three seasons later (and an enormous difference in strategic plans of the seed production system). That difference (0.5 and 3.0 tons of source seed) is also of great significance to the breeder, since both quantities represent a quantum jump in scale for the breeder who ordinarily requires 10-30 kilograms of a line for testing. Only the breeder can produce source seed, but minimizing the target quantity allows more time for her to spend in the breeding nurseries instead of rote seed production. Accordingly, the breeder must be given targets that reflect and originate from the collective strategy of the systems between the breeding program and the farmer.

Likewise, the trajectory of impact of a superior variety is affected by the timing of handover of government sanctioned source seed to the large-scale multiplication enterprises. It is common practice for breeders not to initiate production of government sanctioned source seed until a formal release decision is made. However, with active, pre-release collaboration among regulatory agencies, the breeder, seed production actors, and extension agencies, it is possible to have sanctioned source seed already available at the time of variety release, thus advancing the availability of seed by two or more years.

A factor often overlooked in the effectiveness of a country’s seed system is the performance of its multi-location yield tests upon which release decisions are based. It is of paramount importance that released varieties are in fact the best among their cohort of candidates, and this can only be achieved with high precision data. The most efficient seed multiplication and dissemination system in the world falls short of its potential if the final choices for release are not the best of the available candidates. Modest investments in improving multi-location yield trials can translate easily into a 5% increase in average grain yield once the best varieties are identified and adopted.

II. Logframe Table

See next page.

98

Appendix C: Detailed Description of Proposed Work / Objective 21 Logframe

Objective 21: Improved testing, multiplication and adoption of replacement varieties



21.a. Trans-national coordin-ation

21.a.1. Explore, and establish as necessary, the development of an international committee to evaluate, coordinate, and recommend improvements and investments in seed systems.

Representation from the following would be anticipated:

• Selected NARS • CG centers • FAO • Private sector • Donor agencies • Legal/Regula-

tory policy

Determine the need for developing a seed systems and policy committee, to be established under the umbrella of the Borlaug Global Rust Initiative, which does not duplicate other international efforts. (Jun 2011)

Develop consensus objectives, establish goals and associated budgets. (Dec 2011)

Investments in equipment and training which lead to improvement in the precision of performance trails, providing greater discrimination among a cohort of entries and focusing seed multiplication resources on developing the most promising varieties. (Dec 2012)

Development of efficient regulatory systems which do not impede breeding progress, but do enhance the speed with which improved varieties and new technologies are able to enter the marketplace. (Jun 2011, recurring annually)

Encourage regulations and policies that enable the development of private sector investments. (Jun 2011, recurring annually)

Five Years A seed systems and policy committee is formed and has established objectives, goals and timelines for execution and accomplishment.

Performance, diversity, and acceptability of new stem rust resistant varieties entering seed multiplication are the product of farmer input through participatory variety selection. Capacity and security of Nucleus and Breeder Seed production enables earlier entry of new, farmer endorsed varieties into Foundation Seed production.

Ten Years Seed systems & policy committee has engaged national and international actors and demonstrated progress in interventions leading to efficient seed systems and development of nascent private sector engagement.

Efficiency of seed system performance is enhanced by a regulatory framework where

G. Cisar, Cornell

99




constraints to variety release are eliminated.

Commercial and extension seed production actors are able to access adequate supplies of Foundation Seed early in the commercialization process.

Commercial seed availability to small-holder farmers is optimized.

Fifteen Years Vulnerability of the world’s wheat crop to stem rust is systematically diminished through adoption of improved, diversely resistant varieties that meet farmer requirements including yield stability, acceptable end-use quality, and improved productivity.

Engagement with national regulatory agencies in improvements to seed systems has spillover effects applicable to multiple crops and emerging (transgenic, etc.) technologies.

Encouragement of private sector investments in seed systems leads to multiple genetically diverse varieties in the marketplace, resulting in improved stability of production

100




and the opportunity to develop economic investments in wheat and other crops. This will support an agriculturally diverse and ecologically sustainable environment, leading to improved genetic durability for all crop species in a given agro ecology.

21.b. Kenya.

21.b.1. Improve the capability of KARI and KEPHIS to generate reliable data with improved accuracy from replicated trials (KARI) and National Performance Trials (KEPHIS).

KARI plants International Wheat Information System (IWIS) designed Advanced Yield Trials (AYT) at 8 locations (up from 3 in 2008). Each location has single site, and multi-year analyses conducted in time to inform selection decisions prior to planting of the next season. >75% of data sets enable statistically significant discrimination between the top yielding line and the mean of all lines. (Dec 2010, recurring annually).

KEPHIS plants 5-8 additional locations (or at least 2 sites per location) of the NPT for yield and agronomic evaluation, and in collaboration with KARI, evaluates NPT entries in the KARI Njoro stem rust screening nursery. (Jun 2011 onward).

Five Years Kenya wheat seed supply chain is able to identify higher yielding and stem rust resistant wheat varieties with greater precision.

Ten and Fifteen Years Kenya national wheat yield trends are matching or superior to analogous environments in other countries.

KARI

KEPHIS

CIMMYT (IWIS imple-mentation)

CGA

21.b.2.

Identify and implement collaborative strategies enabling pre-release purification/multipli-cation and availability of KEPHIS endorsed Breeder Seed of KARI candidate lines at the time of approval for Official Release.

KARI and KEPHIS seek agreement on modalities and logistics by which the following anticipatory steps can occur concurrently with descriptor development, DUS assessment, and final stage of National Performance Trials (Apr 2011):

• First round of ear-row purification, • Ear-row derived plot grow-out/purification, and • Follow-on bulking of Breeder Seed

Dedicated and irrigation-enabled land (two hectares) available for ear-row purification of candidate varieties at KARI-Njoro

Five Years Released varieties that can protect Kenya from stem rust, thus reducing cost of production and increased food safety through reduced use of fungicides, reach farmers two years earlier than with system in place in 2008.

One-quarter of Kenya’s wheat

KARI

KEPHIS

101




(Apr 2011)

One or more hectares of seed production concurrent with NPT of each KARI line in 2nd year of NPT; the harvest of which KEPHIS endorses as eligible to be considered Breeder Seed, contingent on KEPHIS inspection; enabling availability of three tons of putative Breeder Seed of each candidate after 2nd year NPT. (Dec 2011, recurring annually; contingent on agreement of first output for this activity)

area, both in small and large scale farm sectors, is planted to wheat varieties that yield 10% greater than the weighted average of varieties planted in 2008, and also have resistance to local races of stem rust.

Ten Years As above, but 80% of area and similar yield trend.

Fifteen Years As above but 95% of area and similar yield trend.

21.b.3.

Identify and implement streamlined approaches to Breeder Seed production subsequent to initial production.

The current three stage ear-row, ear-row derived plot, and follow-on bulk method is employed less often without loss of purity of Breeder Seed lots. (Nov 2012, recurring annually)

Five, Ten and Fifteen Years Rates of genetic gain are not compromised by inefficient Breeder Seed production.

KEPHIS

KARI

21.b.4.

Promote awareness of new Ug99 resistant varieties and/or lines that are candidates for release as varieties.

4-8 Field Days jointly planned and executed by Ministry of Agriculture (MoA), KARI, Cereal Growers Association (CGA), and the Kenya Seed Company (KSC). (Aug 2011, recurring annually)

Five Years 100 % of Kenya’s large scale farmers; and 50% of small scale farmers are aware of current stem rust resistant varieties

Ten and Fifteen Years As above, but 90% of small-scale farmers are aware.

KARI

MoA

CGA

KSC

102




21.b. 5.

Maximize efficiencies and effectiveness of Certified wheat seed supply chain from Pre-Basic Seed to farm and industry/consumer use.

Key representatives of milling/processing, growers (CGA+), MoA Extension, KSC, KEPHIS, and KARI jointly visit key AYT and NPT sites; and actively engage in communication on current and future wheat varieties. (Nov 2011, recurring annually)

Annual production of Breeder Seed by KARI matches KSC needs, (Nov 2011, recurring annually)

Certified Seed production by KSC of stem rust resistant and otherwise improved lines meets producer and consumer demands, (Jun 2011, recurring annually)

Mutual awareness of milling, flour, and processing properties of wheat grain (including characteristics of new varieties) enhanced through a workshop involving flour millers, KARI and other key stakeholders (Mar 2011).

Five Years Rate of variety turn over in farmer’s fields is commensurate with demonstrated superiority of new varieties.

Ten and Fifteen Years Multiple varieties with superior agronomic performance and diverse genetic resistance to stem rust are common in the marketplace.

The private sector becomes increasingly engaged in the wheat seed enterprise.

One of the putative origins of virulent pathotypes of stem rust is no longer contributing to the development of a pathotype that can threaten global wheat production.

MoA

KEHPIS

KARI

KSC

CGA

21.c. Ethiopia (details under dis-cussion, funding through Phase I)

21.c.1 Increase capacity, stability, and quality of Breeder and Pre-Basic Seed production.

Off-season irrigation capacity is created or enhanced for Breeder and Pre-Basic Seed production at Kulumsa, Debre-Zeit, Melkassa, and Werer. (Dec 2011)

Planting and harvest methods and equipment are upgraded to reduce labor costs and ensure timely completion of field work. (Dec 2011)

Seed processing equipment is upgraded at key Centers. (Apr 2012)

Five, Ten and Fifteen Years Breeder Seed availability does not limit adoption/production of stem rust resistant varieties. Breeder Seed availability does not limit adoption/production of stem rust resistant varieties.

Main- and off-season multiplication of candidate

EIAR

103




Seed quality laboratories are upgraded, equipped, and staffed at key Centers. (Apr 2012)

Key staff responsible for seed quality testing, equipment maintenance, field management and post-harvest seed handling are provided in-service training. (Sept 2012)

varieties, enabled by improved irrigation capacity, is a routine practice.

A robust and comprehensive national wheat breeding program, coupled with an equally robust and comprehensive seed system, begins to contribute to alleviating the persistent food insecurity problems that have plagued Ethiopia.

Ten and Fifteen Years The delivery and popularization of an array of durably and diversely resistant varieties emanating from the EIAR breeding programs is a seamless and unbroken continuum, efficiently linked with rapid seed multiplication, variety registration and extension activities (ten years and beyond).

Seed quality and seed health of varieties in commerce allow increased realization of the genetic potential of varieties, resulting in improved national wheat production (ten years and beyond).

104


III. Detailed Work Plan The proposal to develop a coordinating committee (21.a) needs to be vetted with various actors in international and national research centers. Formation of the committee and the follow-on development of goals and priorities will be informed, and the outputs enabled, by the consensus decisions of the committee and the funds available from the donor community. It seems plausible that the committee would serve under the umbrella of the BGRI, and survive beyond the tenure of the DRRW project.

The two countries for which resources are requested under 21.b and 21.c – Kenya for Phase II and Ethiopia for Phase I – need to develop more detailed work plans. This is an ongoing activity. That said, the detail in the Appendix A Logframe for Kenya is substantial and reflects the outcome of a very productive stakeholder meeting in July of this year. The KARI breeder has endorsed the Kenya component of the logframe. DRRW Cornell is in close contact with EIAR DRRW Coordinator Dr. Bedada Girma on details of investment of over $400,000 for irrigation and equipment in support of expanded and stable Breeder Seed production. Over $300,000 will be available in year 3 of Phase I (Feb/Mar 2010) for additional EIAR investment.

IV. Management Plan Dr. Ronnie Coffman will work with potential donors to facilitate the major investments that are needed for effective seed multiplication in the countries in the path of Ug99. Dr. Gordon Cisar, DRRW Associate Director and Plant Breeder, will represent DRRW on the coordinating committee and work with in-country counterparts for the Kenya and Ethiopia activities. Dr. Rob Tripp will continue as a consultant for DRRW on seed issues in Phase II, and invited to serve on the coordinating committee.

V. Potential Risks and Unintended Consequences • Resources. Clearly, the major risk is that sufficient funds cannot be mobilized within the

vulnerable countries or from outside donors. However, it is expected that famine relief and other disaster mitigation funds can be mobilized for this purpose.

• Climate. This is probably the major risk, as events such as droughts or floods can seriously disrupt the process of variety testing as well as seed multiplication. Project strategies address these risks by 1) encouraging wider testing (more locations), which will compensate partially for unexpected weather events that are relatively localized, and 2) providing extra support to the most vulnerable aspects of the seed multiplication process (e.g. supplementary irrigation and use of multiple locations).

• Economics of seed production. In most of these countries seed production is carried out by state entities with relatively insecure budgets. The project will identify those points of greatest risk and attempt to address them.

• Political and policy uncertainties. Success will depend on effective collaboration between research, seed production, regulatory, and extension agencies. Independent of wheat research, national policy or political issues may affect interactions among these entities. The consultation process will serve to impress upon all players the importance of interaction, and

105


the seriousness of the threat of Ug99, which should keep all players focused on the goal, irrespective of political distractions.

VI. Evidenced based rationale for choice of partners (including current and potential funds)

In Kenya, the partners listed in the Logframe Table represent the key actors in the current wheat seed system. In Ethiopia, EIAR is responsible for Breeder Seed.

106

Appendix C: Single Objective Narratives / Durable Rust Resistance in Wheat Phase II Objective 22 Increased levels of global investments and coordination in stem rust research and development

Summary Information (Objective Level) Objective Name:

Objective 22: Increased levels of global investments and coordination in stem rust research and development.

Team Leader for this Objective: Ronnie Coffman, Cornell Senior Management


Institution Primary Contact Email Cornell University Ronnie Coffman [email protected]

Amount Requested ($USD): Project Duration

(months): 60

107


I. Executive Summary In 1953, stem rust wiped out 40 percent of North America’s spring wheat crop, triggering an unprecedented global research collaboration and the development of the stem rust-resistant varieties that helped jump start the Green Revolution led by Dr. Norman Borlaug. Since then, the world has forgotten what stem rust can do to a susceptible field of wheat; research monies have dried up and young scientists have declined to follow in Norman Borlaug’s footsteps. As a result, limited national, regional or global infrastructure exists for addressing the current threat of a pandemic following the evolution of new races of the rust pathogens.

This reality defines the advocacy goals and informs the activities planned by the Cornell and Burness Communications teams. We will inspire action by continuing to raise awareness in the media and among key stakeholders, and by engaging researchers, advocates, and the donor community in the work of advocacy. Our focus in the DRRW project will be on the following as vehicles for our advocacy work.

• The Borlaug Global Rust Initiative, as an established platform for wheat rust research and advocacy, specifically through gender equity initiatives, wheat rust workshops and publications (Component 22.a.).

• Raised awareness in the media and among policymakers of the threat of wheat rust pathogens and the consequences of inaction, including advocacy through the development and dissemination of an annual gap analysis (Components 22.b. and 22.d.).

• Face-to-face meetings between donors and other decision makers and DRRW Managers. These visits to key stakeholders will take place during the course of the managers’ travels to monitor progress in meeting the DRRW scientific objectives (Component 22.c.).

• The development and maintenance of web-based resources to support increased collaboration and coordination in the wheat rust research community (Component 22.e.).

The Cornell team’s activities will foster the growth and influence of the Borlaug Global Rust Initiative (BGRI) and provide opportunities for collaboration and exchange of ideas and information among scientists and other stakeholders involved in wheat rust research. The BGRI will in turn, serve as a global coordinating mechanism for rust research, and the activities defined under this Objective will support that evolving role.

Through the proposed web-based activities, the Cornell team will provide resources to support these collaborations, which are essential to a sustained global effort to track the pathogen’s progress, anticipate its spread, and prepare for and defend against its impact. In Phase I of the DRRW project, we learned that the rust community would like more knowledge resources about wheat rust and about each other, and this lack of information is one of the reasons that collaboration between institutions and countries in wheat rust research currently lags. The sustained ability of the global research complex to address rust threats hinges on a healthy, active rust community, with opportunities for collaboration and learning. Another critical effort of the Cornell team under this Advocacy Objective is the development of an annual gap analysis. This assessment will describe the state of wheat rust research and investment, and how the gaps can be resolved.

The communications activities to be led by Burness will engage the media to communicate the severity of the stem-rust problem and the urgent need for funding. These messages, transmitted through the media, will be important in efforts to engage policymakers, whose influence and

108


action will be critical for addressing gaps in rust research, funding and coordination. For this reason, media outreach will be both vertical and horizontal, reaching stakeholders in the nations that are most at risk, as well as representatives of donor governments and funding agencies able to support research and development activities necessary to contain the threat.

By training scientists to communicate with media and policy makers, Burness and Cornell staff will empower the research community to carry a message that will resonate with policy makers; scientists understand the problem and the consequences of inaction, and will be able to offer solutions. Stakeholders will appreciate these messengers, as noted in a recent report on how best to communicate science to influence policy. The authors found that “policymakers and development practitioners would be able to make greater use of scientific research findings if scientists would engage more openly with the resulting policy implications and present a range of possible policy options.” (See http://www.odi.org.uk/resources/download/338.pdf.) The stem-rust research community can marshal the national, regional and international resources necessary to address the wheat rust threat. They will also address the problem of food security and the role that their work will play in improving crop yields, a goal that will be of significant interest to policy makers. The outcomes of DRRW research, breeding and surveillance activities will provide the content for communications materials and policy statements.

In the short time that the Burness and Cornell teams have worked together, we have established a working relationship that builds on our respective areas of expertise and has led to dramatic results in media coverage. In the process, we have discovered the hunger for information about stem rust in the media, and a great desire on the part of the scientific community to play a role in our work. Burness expressed their willingness to serve as spokespeople in communicating the needs of the research community, the implications of this new research, and the need for action among policy makers in individual nations and on the global stage.

Our efforts surrounding the March 2009 workshop resulted in extensive media coverage that reached more than 29 million people worldwide. We expect to build on these results using the news value of research that is currently in the pipeline to continue to drive this momentum. We are confident that media interest will open doors for advocacy activities and messages, and that, with the help of the highly-motivated network of rust researchers and advocates around the world, we will communicate the key messages about the stem rust threat, bring attention to the important work being done in the DRRW project to address this threat, and inspire action among donors and policymakers to support more fully wheat improvement and rust research. With the help of this global network of supporters, we believe that our communications and advocacy efforts will encourage introduction of new varieties of wheat that are both resistant and productive; will catalyze more coordination among countries and research institutions in pathogen surveillance, research and rust resistance breeding; help build human capacity and infrastructure for combating the rust pathogens; and prevent future pandemics of rust diseases in contribution to global food security.

109


Summary of Short, Medium, and Long Term Outcomes Five Years

• A sustainable platform of advocacy for wheat rust research, plant breeding, and development activities – the Borlaug Global Rust Initiative (BGRI) – will be implemented and maintained. The BGRI, chaired by Dr. Norman Borlaug, replaced the Global Rust Initiative (GRI), which was established as an outcome of the May 2005 Expert Panel report on the Ug99 race of stem rust in Kenya and Ethiopia, and the potential for impact in neighboring regions and beyond. The BGRI has the overarching objective of systematically reducing the world’s vulnerability to stem, yellow, and leaf rusts of wheat. It will do so by advocating for the development of a sustainable international system to understand the biology of these pathogens and manage the threat of wheat rust epiphytotics while continuing the improvements in productivity required to support future requirements of the global wheat crop.

• Members of the BGRI Executive Committee and regular members will be actively engaged and working toward raising funds for wheat rust research and development projects, with evidence of increased funding reaching wheat rust research and development projects.

• More women are participating in BGRI activities

• Regular, comprehensive media exposure to the problem of wheat stem rust will be achieved, keeping the problem and the need for action in front of policymakers.

• Several researchers and research institution leaders will become good communicators and will be engaged in advocacy with key stakeholders and the media, playing a role in raising funds and in communicating with reporters.

Ten Years • Significant scientific advances in stem rust research will be made that would not have

been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project.

• More women occupy senior wheat breeding positions.

• New high-yielding varieties that can withstand newly-emerging pathotypes will be developed and adopted under a rational gene deployment strategy.

• Poverty and hunger will be reduced in vulnerable regions, with the introduction of better varieties of wheat that have offered better yields and yield stability as a result of improved resistance.

• Greater economic resources will be devoted to rust research, breeding and development.

• Developing countries are increasingly involved in research, breeding, and advocacy, and with the tasks necessary in developing and distributing seed stocks.

• Membership in the BGRI will have grown each year and, as a result, scientific collaborations will have increased across countries and institutions in wheat rust research, surveillance, and breeding. More funds will be devoted to wheat rust research efforts at the international, regional, and national levels.

110


Fifteen Years • A worldwide network of rust researchers, wheat breeders, and surveillance focal points

will be working collaboratively and seamlessly.

• Gender parity in wheat breeding is improved.

• Varieties of wheat will be adopted widely that address the need for ongoing resistance to rust pathogens to meet the demand for food from growing populations.

• National Agricultural Research Systems will be strengthened and national seed systems will be improved significantly.

• As insurance against new rust challenges, a strong research and development pipeline will be developed that provides support for research, surveillance, and seed development and distribution capacity on the ground in both industrialized and developing regions.

• Hunger and poverty have been reduced in wheat-growing and consuming households throughout sub-Saharan Africa and beyond, and incomes of wheat growing households have been improved due to adoption of new higher-yielding, rust-resistant wheat varieties.

• The BGRI will serve as the rallying platform for wheat rust researchers and institutions worldwide, its membership will be growing, and it will continue to catalyze increased funding for wheat rust research and development. It will become the model that is emulated in other advocacy and research and development projects.

Progress to Date

Below is an overview of the progress achieved since Norman Borlaug first warned scientists to take notice of wheat stem rust race Ug99 via a report titled “Sounding the Alarm on Global Stem Rust.” Written by an Expert Panel that he convened in 2005, the report reviews the scientific evidence and assesses the potential impact of the pathogen. The concept of the Borlaug Global Rust Initiative, a platform for collaboration and advocacy for wheat-growing countries and wheat research institutes, was endorsed by the Expert Panel’s report, and the BGRI increasingly serves as a beacon for more funding for wheat rust research and development.

From a review of the press coverage since the release of the report, it is clear that in his final years, Dr. Borlaug played a vital role in explaining to key audiences the magnitude of the Ug99 threat to food security and political stability in at-risk countries. An opinion article in the New York Times by Dr. Borlaug in April 2008 (http://www.nytimes.com/2008/04/26/opinion/26borlaug.html) called on governments to aid in the development and distribution of resistant varieties of wheat and asked them to renew a commitment to fund more agricultural research to aid in the fight against the stem rust pathogen. Journalists heard the message of the threat to U.S. and global wheat production, and the warnings were published in influential media outlets throughout 2008. Ultimately, federal funding for stem rust research in the US—$US 1.5 million per year over five years—was included in the Fiscal Year 2009 funding legislation for Agriculture, Rural Development, the Food and Drug Administration, and related agencies.

Internationally, according to advocates and scientists, policymakers took notice of the threat that stem rust poses to wheat production and food security, and this awareness was translated into action. The Food and Agricultural Organization of the United Nations created a 29-country

111


Wheat Disease Global Rust Program in 2008. The FAO-UN also engaged in developing a Global Cereal Rust Monitoring System. And a number of national research agencies, began funding activities that contributed to the response to the stem rust threat.

Though much remains to be done, the governments of Australia, Canada, India, the United Kingdom, Italy, Spain and the United States have responded with investments in research and in support of scientific meetings. The US has committed funds to multiply seedstocks of Ug99-resistant varieties, with the goal of replacing susceptible wheat varieties in the fields of Ethiopia, Egypt, Afghanistan, Turkey, Pakistan, Nepal and Bangladesh.

In March of last year, building on initial coverage of the Ug99 threat in 2008, promotion of the Borlaug Global Rust Initiative Technical Workshop resulted in significant media coverage around the world. It brought public attention to the progress made in stem rust research and the need for more support from governments and international institutions in order to thwart a potential agricultural disaster.

Highlights of the media coverage included wire stories by Agencia EFE (Spain), Agence France-Presse, ANSA (Italy), Reuters, and the Associated Press. AP’s story was picked up by major newspaper websites, including the Houston Chronicle, International Herald Tribune Online, New York Times, USA Today, Philadelphia Inquirer, Forbes, and FOX News, among others. Original stories appeared in Agrarisch Dagblad (Netherlands), Guardian (UK), New Scientist (UK), New York Times, and two stories in El Universal (Mexico). Discovery Channel, New York Times’s Dot Earth Blog, Nature News, SciDev.net (UK), and Scientific American published articles on line. Following the 2010 workshop stories and editorials appeared in major science media such as Nature, The BBC, and especially effective articles in The Economist and The Guardian.

Many of the journalists also quoted Dr. Borlaug’s statement, included in a press release announcing the findings: “Our scientists are making incredibly rapid progress, but we should have no illusions: a global food crisis is still a distinct possibility if governments and international institutions fail to support this rescue mission.”

The research news served as a vehicle for Dr. Borlaug’s stern warning, as well as for other messages communicated to journalists, and through them to key target audiences:

• Averting a crisis will require farmers to replace their susceptible varieties with resistant varieties, even though they may not face an immediate threat.

• Ug99 has demonstrated the ability to spawn new mutations quickly, and will require a continuing investment in research and development of varieties with resistance to these pathotypes.

• Governments and international institutions will need to support increased investment in gene discovery, breeding, development, distribution, and popularization of wheat varieties that carry genetic resistance to this ever-evolving array of virulent rust pathogens.

• A coordinated effort will be needed to replace much of the world's commercial wheat production with new varieties that will be bred and developed to be resistant to developing variants of this stem rust pathogen.

112


• The effort, while costly, will be more affordable and ecologically friendly than chemical control with expensive and potentially harmful fungicides.

• Wheat inventories will continue to plummet to record lows as newly affluent people in the developing world, preferring a wheat-based diet, lift global wheat consumption faster than global production, which currently stands at 650 million tons.

• Food prices will spike as they did last year when grain crops were diverted to biofuel production, sparking food riots around the globe. A major stem rust epiphytotic will send prices skyrocketing, with dire consequences to the urban poor and to resource-poor farmers, and thus to social and political stability.

• Hopes of slowing the spread of Ug99 will require new wheat varieties to be bred with genes designed to protect against this and other evolving rust pathotypes, and these varieties deployed in the fields of wheat farmers.

• CIMMYT, ICARDA, and other wheat researchers from around the world will continue to evaluate thousands of new breeding lines in a Ug99 disease screening nursery in Kenya, where Ug99 has been present since 2001.

• A number of resistant breeding lines developed with genetic protection against Ug99 will offer an improvement in yield performance when compared to susceptible varieties they are expected to replace.

Going forward, efforts will be made to ensure that these and other relevant messages continue to be heard. Whether through traditional and online media or through other advocacy activities, advocacy and communication success will rest on well-developed and focused messages, the translation of research findings into language that is understandable to the lay public, and the training of scientists and others who will communicate that information, whether to journalists or directly to stakeholders.

Scientists from many of the countries attending the BGRI workshops in Ciudad Obregón in March 2009 and St. Petersburg in May 2010 cited the compelling need to engage political and scientific leaders in their work, calling such engagement vital in supporting research efforts and ensuring that scientific accomplishments benefit those most in need in the nations at risk. The activities described below, conducted in partnership and with the support of the stem rust scientific community, will play a significant role in attracting the attention and professional curiosity of influencers around the world, and in engaging their active support.


This narrative lays out a strategy that will continue to promote awareness and cooperation in responding to the threat of emerging wheat rust variants. The overarching goal of Objective 22 will be to increase funding for wheat improvement and rust research globally and to improve coordination among donors, research institutions, and development agencies working in wheat improvement and rust research. It will cover a five-year time period, starting in early 2010, and will focus on strategic plans that support the overall goals of the DRRW project to help the world’s farmers—particularly those in the poorest of nations—meet current and future demand for wheat while addressing the threat posed by Ug99 and its variants.

Our proposed work in advocacy and communications will support the achievement of the DRRW project’s most important goal: A world where the food and livelihood security of the

113


world’s poor will be enhanced through the cultivation of wheat varieties that will have durable resistance to the cereal rust pathogens.

Activities in support of the BGRI (Activity 22.a.1), continuing from Phase I, will include providing quarterly updates on wheat rust research and development activities and news items to BGRI members (defined as any person or institution with a stake in wheat rust research) worldwide, engaging the BGRI Executive Committee and other members actively in advocacy and fundraising, holding the annual BGRI workshop and supporting meetings and ongoing communications of the BGRI Executive Committee, and enabling strategic investments (in non-DRRW workshops to get a rust-related session on the agenda for instance) for leveraged advocacy.

Through the BGRI, we strive to foster the career development of women engaging in wheat breeding research, and retain them as active researchers (Activity 22. a.2). We aim to accomplish this through an early career award (available to women) and a mentor award (available to both men and women). In addition, we will sensitize the BGRI community to gender issues through engaging seminars at well attended BGRI events such as the Annual Technical Workshop.

Media communications will be a new activity in the DRRW Phase II proposal and will be largely implemented by Burness Communications, with leadership from the DRRW Management Unit. Activities under this component will include promoting media coverage of the rust problem and the need for sustained support for rust research through key message development, press releases, media training, and media monitoring.

Face-to-face meetings to advocate for funds, support, or improved coordination and cooperation among institutions and countries will be essential to meeting our overall advocacy objectives. Activities under this component will include visits to donor nation embassies by DRRW Management and/or BGRI Executive Committee members to obtain funds to support research aimed at combating stem rust.

Policymakers are critical allies in the global effort to understand and manage the wheat rust problem, and they need information targeted specifically to them and to their priorities. Activities under this component will include the development of communications materials specifically for policymakers and donors, and the development of an annual gap analysis to identify shortfalls in funding and collaboration in rust research and wheat improvement.

The Internet is fast becoming the global hub for all information, with many knowledge resources being accessible via the web. The DRRW project will continue to harness this “communications revolution” to provide critical information for BGRI members, rust researchers, policymakers, donors, and the public by maintaining and augmenting a catalogue of wheat improvement and rust research projects, institutions and people; and re-designing and maintaining a user-friendly BGRI website.

In DRRW Phase I, the primary vehicle for DRRW advocacy was in large measure driven by the launch and implementation of the project itself. The official announcement of the Project in April 2008 was widely reported, as was the DRRW-managed 2009 BGRI Technical Workshop. Tangible outcomes that we believe were related to the emergence of the DRRW project include the US $5.2M USAID famine seed project, earmark of US $1.5M for rust research to the USDA-ARS budget in the FY09 Ominbus bill, and the multi-national Delhi Declaration on Wheat Stem

114


Rust Ug99 issued November 8, 2009. Senior staff have availed themselves for media interviews and are constantly seeking opportunities to promote wheat rust investments on an ad hoc basis.

For Phase II, we are convinced that more resources can be mobilized for wheat rust and wheat improvement research and development and that proactive advocacy toward that end can be effective. Maximally effective advocacy will be achieved through a comprehensive strategy that unites the research collaboration-enhancing activities of the BGRI and targeted media and policymaker outreach that will keep “sounding the alarm” about wheat rust and food security. Accordingly, this Objective proposes a strategic partnership between the existing DRRW management structure and Burness Communications (http://www.burnesscommunications.com/).

We expect that the activities elaborated in this narrative will build a foundation to help the rust research community inform and inspire national and international political and scientific leaders, cause them to choose an informed course of action, and understand the global implications if they fail to do so.

In Phase II, we will continue to foster the Borlaug Global Rust Initiative and grow its effectiveness to serve as a platform for advocacy and collaboration among wheat rust researchers and institutes. This will be supported by web-based activities of developing and maintaining a comprehensive BGRI website, with resources tailored to and provided by the wheat rust community itself, as well as developing and populating an Advocacy Resource database that contains global inventories of:

• Research institutions working on wheat rust, including advanced research institutes (ARIs), international agricultural research centers (IARCs), and national agricultural research systems (NARS), with information on 1) research personnel, 2) capacities, and 3) projects;

• Donors, traditional and non-traditional, international, regional, and country-specific, including contact information and priorities; and

• Professional societies and other international advocacy groups.

We will continue to produce an annual gap analysis that reports on the global state of wheat stem rust research and the most pressing needs that lie between the current status and our larger goal of reducing the world’s vulnerability to stem rust epidemics. The gap analysis will continue to be a key tool for advocacy efforts, as it will point to specific areas of need that donors will hopefully fund. The gap analysis will also feature prominently in the media strategy described below.

We will also continue to build awareness in the media and among policymakers and donors of the threat posed by Ug99, particularly in developing countries. We will do this by drawing attention to advances in science and technology, as well as the potential benefits of investing in newer technologies, including greater understanding of the pathogen and its wheat host. These messages will in turn encourage political leaders worldwide to support ongoing research to protect wheat from new pathogenic variants, and seed multiplication and popularization efforts of the newly developed resistant varieties. Such a commitment will lead to the replacement of susceptible cultivars now growing in the wheat fields of vulnerable nations.

Because of the project’s direct support for research, sometimes leading to exciting and groundbreaking results, the impact of stem rust related advocacy activities are significant.

115


When appropriate, new research findings—with key results and implications translated for lay audiences—will serve as a vehicle for communicating the promise of new resistant wheat varieties, the trajectory of the pathogen, and the need for funds to support ongoing research and deployment as the new varieties are developed.

Working closely with the stem rust research community—whether funded by the project or by other sources—a team of science writers will help to shape media and advocacy campaigns around compelling findings, targeting both global audiences and important regional stakeholders. Our recent experience shows that a carefully crafted communications strategy will lead to accurate and thoughtful media reports of the stem rust threat and the ongoing research and development that aims to address that threat. Daily reports of media coverage of wheat research, food security, and related issues, will prepare the stem rust research community, when appropriate, to respond to breaking news, negative or positive.

In devising a strategy and related tactics for reaching the target audiences of policy makers and scientists, we will focus on preparing the stem rust research community to serve as spokespeople, whether through interviews with journalists or in direct communication with policymakers. Scientists will be trained and helped to develop messages for communicating their knowledge and asking for the action they know will be needed. We will steadily build a cadre of wheat researchers from the nations most at risk, as well as scientists in global and national agricultural research centers in the CGIAR system and in the public and private sectors of the industrialized world. The message from our colleagues at the 2009 BGRI Technical Workshop was clear: deployment of durably resistant wheat varieties requires the engagement of politicians and ministers of agriculture, environment, and finance who are willing to carry the message. Our goal is to lay the groundwork for successful interactions with policymakers through impactful media efforts, and to give scientists the means to walk out of every meeting with policymakers or donors with a commitment of support.

Justification for Proposed Work Initial experiences disseminating information about Ug99 and its potential impact suggests that news about Ug99 will not be ignored, as long as the science is accurate and results are meaningful. Ultimately most nations will be at risk, but all will benefit from investments in research and adoption of new resistant varieties, regardless of where they will be planted. So the story of stem rust, kept alive through the release of a pipeline of interesting discoveries regarding burden of disease, impact and potential solutions, is ripe for the telling. It is important, however, to tell the story so that it inspires action—the sort of action that will provide solutions today, while building research capacity and infrastructure in key industrialized and developing nations to address future challenges. The work of media relations will draw from the rich pool of findings that will be fed by stem rust and wheat scientists around the world, many of them working with support from the DRRW project. This press coverage will prepare the ground for advocacy work and fundraising, while also inspiring young people to pursue careers in crop science, particularly the field of rust pathology. The job of reaching out to stakeholders—whether donors, policy makers or both, will be carried out by the leadership of the DRRW, and by researchers and advocates trained by Burness and Cornell.

In engaging a global public relations firm with expertise in communicating science for non-profits, the DRRW project will be drawing on the experience of a team that is at the forefront of efforts to place agriculture squarely in the global debate over how best to meet the UN

116


Millennium Development Goals. Their success rests on using the work of researchers to communicate the need for action. The message that underlies their work suggests that whether the challenge is climate change, population growth or emerging plant pathogens, it cannot be met without repairing the world’s agricultural infrastructure. Working with a firm that serves many organizations with a common mission allows the DRRW project and the Borlaug Global Rust Initiative to join a revolutionary worldwide movement that is placing agriculture on the agenda of decision makers, whether the goal is to address poverty, hunger, disease or climate change. Within that space, the problem of stem rust will tell a powerful story, while claiming for itself resources for addressing a significant threat to one of the most important food crops in the world.

II. Logframe Table See next page.

117


Objective 22: Increased levels of global investments and coordination in stem rust research and development



22.a. BGRI.

22.a.1. Act as an effective Secretariat to the BGRI, enabling communication and providing support for the activities of this body.

BGRI members and stakeholder communities receive quarterly updates on rust research and news (information drawn from other relevant activities, media reports, etc). (Mar, Jun, Sep, Dec 2011, recurring annually)

BGRI Executive Committee (ExCo) and other key members proactively engaged in advocacy and fundraising. (Feb 2011, recurring annually)

Annual BGRI technical workshop held; regular ongoing communications arranged among ExCo members. (May and Jun 2011, recurring annually)

Strategic investments outside the purview of the BGRI have been made, and have, as a result, enabled leveraged advocacy. (Sep 2011, recurring annually)

Five years A sustainable platform of advocacy for wheat rust research, plant breeding, and development activities has been implemented and maintained.

Members of the BGRI Executive Committee and regular members are actively engaged and working toward raising funds for wheat rust research and development projects, with evidence of increased funding reaching wheat rust R&D projects.

Ten years Significant scientific advances in stem rust research have been made that would not have been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project



Fifteen years

Cornell

118




Significant scientific advances in stem rust research have been made that would not have been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project.



22.a.2. Foster professional development of women wheat breeders through the BGRI

A Gender Equity luncheon is held at Annual BGRI Technical Workshop, sensitizing the BGRI participants to gender issues in agricultural development (Jun 2010)

BGRI establishes the annual Jeanie Borlaug Women in Triticum (WIT) award (2010, recurring annually)

Three WIT award recipients are chosen annually (2010 & recurring annually)

The Women in Triticum Mentor Award is established by the BGRI (Jun 2010)

One Women in Triticum Mentor Award is granted annually (2011, recurring annually)

Five years BGRI participants are sensitized to gender parity issues.

More female researchers participate in BGRI activities.

More female researchers participate in training at CIMMYT-Obregon

Ten years More women wheat breeders are employed by national programs, universities and International Agricultural Research Centers.

Fifteen years Gender parity improves in the field of

Cornell

119




wheat breeding and genetics. 22.b. Media activities for reaching key audiences.

22.b.1. Promote media coverage of the rust problem and need for sustained support for rust research through key message development, press releases, media training, and media monitoring.

Clear and concise messages developed with input from the stem rust research community (Sep 2011, recurring annually)

Advocacy and communications strategy operates in real-time via ongoing strategic discussion regarding advocacy and media. (Feb 2011, recurring annually)

Two press releases developed in collaboration with Project managers (topics based on review of presentations, peer-reviewed papers, gap analysis, etc. to determine news value and in light of advocacy objectives) translated into relevant languages (Arabic, French, Farsi, etc.), and stories published in key outlets in target countries. (May 2011 and Nov 2011, recurring annually around BGRI workshop and other relevant events)

Desk side meetings with journalists arranged for key spokespeople, organized around four trips a year (these meetings will take place during trips made as part of meeting other objectives). (Sep 2011, recurring annually)

Electronic and hard copy report compiled for each media outreach effort, with a summary of the coverage and original clippings for key donors and policy makers, and DRRW internal files. (Sept 2011, recurring annually)

Five years Regular, comprehensive media exposure to the problem of wheat stem rust is achieved, keeping the problem and the need for action in front of policymakers.





New high-yielding varieties that can

Cornell

120




withstand newly emerging pathotypes are being developed and adopted under a rational gene deployment strategy.


22.c. Targeted fundraising.

22.c.1. Visits to donor nation embassies in nations vulnerable to stem rust.

Funds obtained from donor nation officials to support local research and other activities aimed at combating stem rust. (Jun 2011, recurring annually)





Fifteen years Significant scientific advances in stem rust research have been made that

Cornell

121




would not have been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project.



22.d. Advocacy activities for reaching key audiences.

22.d.1. Promote awareness and action by policy makers and donors to address stem rust in a coordinated way and to support stem rust research and wheat improvement.

Five high-level meetings arranged between critical players and relevant government officials (Sep 2013)

Results of media outreach packaged and disseminated to promote further awareness. (Oct 2011, recurring annually)

Print and electronic materials available in relevant languages to support advocates in their outreach efforts. (Oct 2011, recurring annually)

Five years Greater economic resources have been devoted to rust research, breeding and development



Poverty and hunger have been reduced in vulnerable regions, as better varieties of wheat are introduced that offer better

Cornell

122




yields and yield stability that comes with improved resistance.




22.d.2. Conduct annual gap analysis to identify shortfalls in funding and opportunities for investment in rust research and wheat improvement, and

Gap analysis report finalized and approved (and reviewed for news value, as described under media activities). (Sep 2011, recurring annually



New high-yielding varieties that can withstand newly emerging pathotypes

Cornell

123




disseminate results.

are being developed and adopted under a rational gene deployment strategy.





22.e. Web-based activities in support of advocacy, fundraising and

22.e.1. Maintain and augment a catalogue of wheat improvement and rust

Online resource maintained and in use to support Advocacy activities. (Feb 2010)


Ten years Significant scientific advances in stem rust research made that would not have

Cornell

124




collaboration. research projects and associated information.

been possible without the advocacy efforts of the BGRI and the scientific objectives of the DRRW project.




New high-yielding varieties that can withstand newly emerging pathotypes are being developed and adopted under a rational gene deployment strategy. Poverty and hunger have been reduced in vulnerable regions, as better varieties of wheat are introduced that offer better yields and yield stability that comes with improved resistance

125




22.e.2. Maintain content of BGRI website.

BGRI website content is maintained with input/interaction from rust community; content reviewed regularly for news value. (Feb 2011, recurring annually)

BGRI website will be viewed as a major source of wheat rust knowledge (Dec 2012)







Poverty and hunger have been reduced

Cornell

126




in vulnerable regions, as better varieties of wheat are introduced that offer better yields and yield stability that comes with improved resistance.

127


III. Detailed Work Plan Component 22a. Borlaug Global Rust Initiative (BGRI) Activity 22.a.1. Act as an effective Secretariat to the BGRI, enabling communication and providing support for the activities of this body The Borlaug Global Rust Initiative (BGRI) serves as the umbrella advocacy platform for wheat rust research and development. The BGRI was established as an outcome of the May 2005 Expert Panel report titled “An Assessment of Race Ug99 in Kenya and Ethiopia and the Potential for Impact in Neighboring Regions and Beyond.” The BGRI has the overarching objective of reducing the world’s vulnerability to stem, yellow, and leaf rusts of wheat and advocating for a sustainable international system to contain the threat of wheat rusts and to continue the enhancements in productivity required to withstand future global threats to wheat.

The BGRI is governed by an Executive Committee. Permanent members of the Executive Committee are Jeanie Borlaug Laube (Chair) and representatives from the Indian Council of Agricultural Research (ICAR), CIMMYT, ICARDA, FAO and Cornell University (Ronnie Coffman, Vice Chair). The permanent members select additional members to serve three-year terms, renewable. The current Executive Committee is comprised of the five permanent members plus rotating country representatives of the following countries: Kenya, Ethiopia, Egypt, Turkey, Pakistan, China, Australia, Canada and the United States. The BGRI Secretariat is located at Cornell University and staffed by DRRW project employees.

Maintaining and operating the BGRI secretariat is critical to sustaining global attention and a focused research effort on the wheat rust pathogens. Under this activity, we will implement the membership policies of the BGRI by identifying organizations with a stake in wheat rust research and development and adding them to the BGRI member database. We will keep members of the BGRI informed of relevant activity around the world regarding wheat rust research and funding via a quarterly newsletter with rust research news and updates (including reports on activities in the DRRW project). The BGRI secretariat will continue to be responsible for convening the annual BGRI technical workshop as well as Executive Committee meetings to provide opportunities for research, breeding and pathogen surveillance updates, as well as opportunities for face-to-face networking, knowledge-sharing and partnership-building.

The BGRI secretariat will continue to provide support (in the form of editorial and graphic design support for documents or other print/electronic materials they might need to highlight their specific national or regional causes under the umbrella of the BGRI) and encouragement to BGRI Executive Committee and regular members to proactively engage in fundraising and publicity on behalf of the wheat rust research and wheat improvement community. When opportunities arise outside of the purview of the BGRI to catalyze partnerships or funding for wheat rust research, this activity also includes special initiative funds that will allow us to support ad hoc opportunities to publicize the need for more funding and coordination in wheat rust research.

Outputs • BGRI members and stakeholder communities will receive quarterly updates on rust

research and news (information drawn from other relevant activities, media reports, etc.).

128


• BGRI Executive Committee and other key members will proactively engage in advocacy and fundraising.

• Annual BGRI technical workshop will be held, and regular ongoing communications arranged among BGRI Executive Committee members.

• Strategic investments outside the purview of the BGRI will be made, and will, as a result, enable leveraged advocacy.

Activity 22.a.2. Foster professional development of women wheat breeders through the BGRI. In this objective we strive to work towards a more gender-balanced plant breeding community by fostering the professional development of women interested in wheat breeding and by rewarding outstanding mentors who share this goal. In addition, we will work to sensitize the entire BGRI community to equity issues at the annual meetings.

In order to support early career women working in wheat and its nearest relatives, we have established the Jeanie Borlaug Women in Triticum (WIT) award. Recipients of this award (max of three women per year) will be invited to the annual Technical Workshop and to participate in a training course at CIMMYT-Obregon. We will also award an annual WIT Mentor award to a male or female mentor who contributes most significantly to gender parity at the professional or farmer impact levels.

The desired Outcome of this Activity is that more women will decide to pursue long-term careers in wheat research.

Outputs • A Gender Equity luncheon is held at Annual BGRI Technical Workshop, sensitizing the

BGRI participants to gender issues in agricultural development (June 2010).

• BGRI establishes the annual Jeanie Borlaug Women in Triticum (WIT) award (2010 & reoccurring annually).

• Three WIT award recipients are chosen annually (2010 & reoccurring annually).

• The Women in Triticum Mentor Award is established by the BGRI (June 2010).

• One Women in Triticum Mentor Award is granted annually (2011 and reoccurring annually).

Component 22.b. Media activities for reaching key audiences Activity 22.b.1. Promote media coverage of the rust problem and the need for sustained support for rust research through key message development, media training, press releases and media monitoring. Engaging the media is an important form of advocacy, because many millions of people around the world read newspapers and magazines, listen to the radio, watch television, and, increasingly, comb the Internet. Policymakers and politicians in particular follow the news closely, and the more media coverage a particular theme receives, the more important the problem seems to policymakers, politicians, and the public. Agriculture has only begun to attract the press attention it deserves, and one could argue that this is part of the reason that funding for agriculture for developing countries has not been at the level it should be. This is changing, however, and with

129


the food price hikes in 2008, people’s changing diets, and climate change, agriculture may once again assume its central place among the issues that policymakers and donors are willing to act on with determination—in recognition of their significant strategic value. Wheat stem rust is a very serious problem in its own right, but it also might serve as a test case for how well we can globally organize ourselves to deal with a dangerous agricultural pathogen that is on the move. It serves as an excellent “hook” for communicating the overall need to increase funding for agricultural research, particularly for and in developing countries. Our recent experience shows that the media is indeed interested in the wheat stem rust story; if our story can become a vehicle for advocating for more support for agricultural research and development overall, this is an opportunity not to be missed. The media can be fickle and journalists require news hooks in order to cover even the most compelling stories. Wheat stem rust is news in agriculture at the moment, because of the impending threat of Ug99 in major wheat-producing areas. By using the rust problem to capture media coverage, we are engaging in an activity that offers a unique opportunity to raise awareness of wheat stem rust, as well as creating “the rising tide that lifts all boats” devoted to global agricultural improvement and investment in development.

Burness Communications will work with DRRW Management and key scientists to develop key messages, which Burness can use to craft press releases and DRRW Management and scientists can use when speaking with journalists, policymakers, and other people of influence. For a media effort to work most efficiently, the communications team will need to be in close contact with the project managers, so that Burness will be able to keep abreast of important developments in wheat stem rust research and development and DRRW Management will have dynamic input on advocacy strategy. The scientists working on stem rust will be key advocates for their own work and for expanding funds for research, with an annual media training event to be held in conjunction with other scientific meetings.

Burness maintains relationships with journalists around the world, so they know which journalists can and would cover a story about wheat stem rust, and which journalists should receive specific press releases. Burness will continuously review scientific presentations, peer-reviewed papers, and white papers related to wheat stem rust to determine news value, and from those reviews and in light of DRRW advocacy objectives, will develop three press releases per year and pitch them to key journalists in the US, Europe, and in targeted developing countries. Burness will coordinate the translation of the press releases (as necessary) into three languages and distribute them in relevant countries. Burness will also arrange for two site visits by journalists (foreign press or local, depending on advocacy needs), which is a particularly effective way to orient journalists to the issue and provide them with material for their stories. “Deskside” meetings between key spokespeople (DRRW Managers and rust scientists) and locally-based journalists will also be an effective way to obtain media coverage, and Burness will arrange three desksides per year, organized during other trips made as part of meeting other DRRW objectives. Preparation for the desksides will include discussing possible local news hooks with DRRW project managers and preparing spokespeople to brief media on the progress being made in stem rust research and the need for more support from governments and international institutions in order to thwart a potential agricultural disaster.

Outputs • Clear and concise messages will be developed with input from the stem rust research

community.

130


• The DRRW advocacy and communications strategy will operate in real-time via ongoing strategic discussion regarding advocacy and media between DRRW project managers and Burness Communications.

• Two press releases will be developed in collaboration with Project managers (topics based on review of presentations, peer-reviewed papers, and white papers to determine news value and in light of advocacy objectives) and translated into relevant languages (Arabic, French, Farsi...) and stories published in key outlets in target countries.

• DRRW project leadership will be kept abreast of policy and research issues as covered in the press by “media monitoring” of Burness Communications.

• Deskside meetings with journalists will be arranged for key spokespeople, organized around four trips a year (these meetings will take place during trips made as part of meeting other objectives).

• Electronic and hard copy reports will be compiled for each media outreach effort, with a summary of the coverage and original clippings for key donors and policy makers, and DRRW internal files.

Component 22.c. Targeted fundraising Activity 22.c.1. Visits to donor nation embassies in nations vulnerable to stem rust. In this activity, aggressive efforts will be undertaken by DRRW staff to identify sources of funds and to obtain those funds from donor nations for the purpose of supporting stem rust research and development and seed production and distribution. Visits by the DRRW senior management and BGRI Executive Committee members to these donor organizations, embassies and other funding agencies will be arranged in coordination with other project travel. These visits will strengthen our advocacy efforts and ensure that additional funds to combat stem rust are obtained.

Outputs • Funds will be obtained from donor nation officials to support local research and other

activities aimed at combating stem rust.

Component 22.d. Advocacy activities for reaching key audiences Activity 22.d.1. Promote awareness and action by policy makers and donors to address the stem rust problem in a coordinated way and to support stem rust research and wheat improvement. Political action in countries that are, or may be, affected by Ug99 is critical to preventing stem rust epidemics in those countries and globally. Policymakers will need information that is tailored to their context and targeted to their level of understanding, with clear recommendations for policies and programs they should support. Additionally, global scientific reviews and recommendations, such as clear gene deployment options and strategies, will be very useful to coordinate country responses to the Ug99 threat. Currently, donor efforts to mitigate the rust threat are not well coordinated and this activity seeks to improve coordination. Five meetings per

131


year will be arranged among critical players – DRRW Management, BGRI Executive Committee members, or other key stakeholders – and relevant government officials, as such face-to-face encounters are important for driving home messages and making calls to action. In collaboration with Burness, the DRRW project will develop print and electronic advocacy materials to support the outreach efforts of DRRW Managers and key stakeholders.

Outputs • Five high-level meetings will be arranged between critical players and relevant

government officials.

• Results of media outreach will be packaged and disseminated to promote further awareness.

• Print and electronic materials will be available in relevant languages to support advocates in their outreach efforts.

Activity 22.d.2. Conduct annual gap analysis to identify shortfalls in funding and opportunities in rust research and wheat improvement, and disseminate results. A major objective of the Durable Rust Resistance in Wheat Project will be to continue to foster informed advocacy for more effective coordination among researchers, research institutes, plant breeding, and seed development and distribution, as well as between countries. This will be achieved in part by conducting an analysis that will address three central questions: 1) Where are we in wheat rust research? 2) Where do we want to be? 3) How do we get there? The gaps in wheat rust research will be identified through extensive interviews with key scientists and program directors, literature reviews, and research on global projects and research programs in wheat rust. The DRRW Research Analyst will travel as necessary to interview key stakeholders and to learn about projects (in most cases, such travel will happen in conjunction with already planned travel). The analysis will also be informed by participation of the DRRW Research Analyst in scientific meetings. The Analyst will produce annual reports of the key gaps thwarting the control of wheat stem rust. These reports will be reviewed for news value and press releases will be disseminated by Burness Communications.

Outputs • Gap analysis report will be finalized and approved (reviewed for news value--as

described under media activities)

Component 22.e: Web-based activities in support of advocacy, fundraising and collaboration Activity 22.e.1. Maintain and augment a catalog of wheat improvement and rust research projects and associated information. The preparation of an annual gap analysis will depend on up-to-date awareness of advances in science and technology related to the wheat rust problem. Today, a major challenge in dealing with the wheat rust problem is the lack of a publicly available compilation of investors or research/development agencies and a single source of information on the status of the relevant sciences and technologies. These deficiencies will make it very difficult to describe the status

132


quo or the best-case scenario as regards activities and investments, and will preclude informed advocacy and coordinated global action. Accordingly, the DRRW project will create and maintain a database that will be accessible via the web and targeted to DRRW project scientists, other wheat and rust researchers, donors, and the public with:

• Global inventories of research institutions working on wheat rust including ARI, IARC and NARS with information on

— Research personnel (including contact information),

— Capacities,

— Projects (including goals, and budgets).

• Global Inventories of donors, both traditional and non-traditional, and other interested parties, such as country missions and funding agencies who might be interested in the fight against wheat rust.

• Global Inventories of professional societies and other advocacy groups

This database has been under development during Phase I of the DRRW project, and is currently being beta-tested by DRRW Management. Because of the sensitivity of certain information, it has been important to develop the resource iteratively, populating it with information as we come across it and then conducting searches as a user might to see if the content and interface of the information is what users want. For this reason, the development of the resource has taken longer than originally envisioned, but it will be ready for public unveiling in the first few months of Phase II. Outputs

• Advocacy Resource will be maintained and in use to support Advocacy activities. Activity 22.e.2. Maintain content of BGRI website. The BGRI website continues to be well-trafficked by scientists, journalists, and policymakers who are looking for information ranging from resistance gene catalogs to research summaries of wheat rust projects at BGRI member institutions to photos of Ug99. DRRW staff has received overwhelming feedback from the community that the website is an invaluable resource and already serves as a respected touchstone and convening point for scientists. With a more robust advocacy effort, the BGRI website is likely to serve as the nexus for online information gathering for all things related to wheat rust. The redesign and content management plan for the BGRI site will take into account the website’s increasingly important role.

Outputs: • A plan will be implemented for daily maintenance of globalrust.org, with

input/interaction from the rust community.

• BGRI website will be viewed as a major source of wheat rust knowledge (content reviewed regularly for news value).

133


IV. Management Plan Name (or position if to be hired) Institution Email Relevant Activities and Outputs

Ronnie Coffman, PI

Cornell University

[email protected]

Targeted fundraising, high level meetings, BGRI workshop, interviews with media, strategic communications (in consultation with Burness)

Sarah Davidson, Associate Director

Cornell University [email protected] Assists with fundraising, coordination of BGRI secretariat activities, annual BGRI workshop program, manages gender activities, fosters cross-objective coordination, gap analysis

Gordon Cisar, Associate Director

Cornell University [email protected] BGRI workshop, interviews with media, advocacy with NARS with focus on East Africa

Assistant Director, TBD

Cornell University Strategic communications (in consultation with Burness), all high- level communications, content for knowledgebank.

John Bakum, Website Administrator

Cornell University [email protected] BGRI workshop, Advocacy Resource development and BGRI website, knowledge bank, content development

Cally Arthur, Communications Specialist

Cornell University [email protected] Writing and editing, BGRI newsletter development, web content, BGRI knowledgebank content development. Facilitates annual reporting to Foundation

BGRI Meeting Coordinator, TBD

Cornell University Plans and executes the logistics for all DRRW & BGRI meetings including the annual technical workshop.

Nicole Peppin, Administrative Assistant

Cornell University [email protected] Administrative support, communications support

134


V. Potential Risks and Unintended Consequences • Failure to fully capture the potential of the BGRI because of rivalries or lack of

commitment by key members.

• The global economic crisis, regional/global civil conflicts, or emergence of other global threats (e.g., H1N1 flu) either limits the ability of staff to travel or the availability of funds for new investments.

VI. Evidenced based rationale for choice of partners (including current and potential funds) Burness Communications advances social change for nonprofits worldwide through its public relations work. The firm has served more than 300 organizations since its founding in 1986, including small and large nonprofits, foundations, international agencies and research centers, NGOs, think tanks, and public and private universities. Burness views communications as a critical tool for making a difference and for serving the goals of advocacy. Whether the issue is the life-saving value of agricultural research, vaccines, or malaria prevention in Africa, Burness sees communications as a means for informing those who need to know in order to advance social change.

The Global Health and Science Team at Burness Communications deploys a range of strategic communications approaches to move clients’ issues among key decision makers and other target audiences around the world. Through a Nairobi office and extensive media network in Africa, and Burness’ global network in Europe, Asia and Latin America, Burness provides clients with strategic global reach.

For nearly two decades, Burness has been communicating the evidence-based science side of agricultural development. Burness has worked with the CGIAR Secretariat, most of the 15 centers of the CGIAR, the Rockefeller Foundation, and the Global Crop Diversity Trust. In addition to direct media outreach work, which has generated substantial coverage in every region of the world, Burness’ work in agricultural development has focused on a variety of communications activities—from media and presentation trainings for scientists, to political advocacy for clients’ missions, to writing of scientific reports.

Burness has expertise in a number of interrelated areas of communications: strategy development, messaging, advocacy and media trainings; organizing and facilitating stakeholder meetings to further organizational goals; managing communications among both public and private partners; and last but not least, media relations.

Burness’ expertise in media relations allows for an extensive toolbox to draw on, as appropriate, which includes: press briefings, setting up deskside interviews and media tours; story development; development of press materials (advisories, releases, backgrounders, etc.); placement of feature stories in key outlets; work with radio, broadcast and documentary filmmakers; work with new media and social media; writing and placement of op-eds, and more. Burness staff land regular media placements in key media markets—in Africa, Europe, Asia, the US, and Latin America.

In the area of directly communicating with key target audiences, Burness provides the highest quality writing services, including speech writing and materials that serve to deliver messages

135


directly. All of Burness’ work is anchored by a substantive knowledge of the issues and an understanding of what moves policymakers, donors, and other target audiences.

Burness seeks to use the most appropriate communications tools to move forward policy, funding, or social action to support the issues clients seek to elevate. To this end, Burness’ work in communications has led to significant impact for clients—from increased funding to policy change.

136


References Cited Cohen, D., R. de la Vega, G. Watson. 2001. Advocacy for social justice. Bloomfield, CT:

Kumarian Press Inc.

137

Appendix C: Single Objective Narratives / Durable Rust Resistance in Wheat Phase II Objective 22. Supplemental Document 22.1: Media Impact

Supplemental Document 22.1. Media Impact of Promotion of the BGRI 2009 Technical Workshop

The following chart details the media impact of promotion of the Borlaug Global Rust Initiative Technical Workshop in Ciudad Obregón, Mexico in March 2009. The total media impact figure (i.e. the total number of people who were reached) derived from this analysis is 29,211,863.

This number is based upon an analysis of circulation numbers of daily and weekly newspapers and magazines in which stories appeared in print for this promotion. In addition, this number includes the daily audiences of broadcast outlets on which the story was covered for this promotion.

For newspapers and magazines, all circulation numbers were obtained from Cision MediaSource. For the broadcast outlet, the number was obtained from the outlet’s website.

It should also be mentioned that radio audiences are generally measured on a weekly basis, unlike newspaper circulations, which are measured on a daily basis (or weekly/monthly, depending on the outlet). Thus, for consistency’s sake, the weekly radio audience figure was divided by seven to arrive at an estimated daily audience figure.

PRINT NEWSPAPER OR MAGAZINE

CIRCULATION

(obtained via Cisions Media Source unless otherwise noted) Agrarisch Dagblad (Netherlands) 10,638 Business Daily (Africa) 30,000 Daily Monitor (Africa) 27,000 Guardian (UK) 335,615 Hindu (India) 900,000 El Imparcial (Mexico) 30,477 El Universal (Mexico) 150,855 La Jornada (Mexico City) 108,593 Le Journal de Montreal (Canada) 256,297 New Scientist (UK) 166,663 New York Times 1,039,031 Stock Journal (Australia) 13,837

TOTAL PRINT NEWSPAPER OR MAGAZINE

CIRCULATION = 3,069,006

BROADCAST OUTLET DAILY AUDIENCE

(obtained via outlet website unless otherwise noted) BBC News 26,142,857

TOTAL BROADCAST AUDIENCE = 26,142,857

TOTAL IMPACT = 29,211,863

138


Ciudad Obregón, Mexico — March 17-20, 2009 Promotion of the Borlaug Global Rust Initiative Technical Workshop in Ciudad Obregón, Mexico resulted in significant media coverage around the world, bringing public attention both to the progress being made in stem rust research and the need for more support from governments and international institutions in order to thwart a potential agricultural disaster. Highlights of the media coverage included wire stories by Agencia EFE (Spain), Agence France-Presse, ANSA (Italy), Reuters, and the Associated Press. AP’s story was picked up by major newspaper websites, including the Houston Chronicle, International Herald Tribune Online, New York Times, USA Today, Philadelphia Inquirer, Forbes, and FOX News, among others. Many of the journalists also quoted Dr. Borlaug’s statement, included in a press release, announcing the findings: “Our scientists are making incredibly rapid progress, but we should have no illusions: a global food crisis is still a distinct possibility if governments and international institutions fail to support this rescue mission.”

The research news served as a vehicle for Dr. Borlaug’s stern warning, as well as for other messages communicated to journalists, and through them to key target audiences. Notable print coverage included stories in Agrarisch

Dagblad (Netherlands), Guardian (UK), New Scientist (UK), New York Times, and two stories in El Universal (Mexico). Among the highlights of the original online coverage were stories by Discovery Channel, New York Times’s Dot Earth Blog, Nature News, SciDev.net (UK), and Scientific American. In advance of the event in Ciudad Obregón, desksides in Mexico City with National Public Radio, Reuters, BBC News and El Universal helped to expand coverage of the conference and pique the interest of Mexico City-based foreign correspondents in CIMMYT’s work. Overall, articles featuring the BGRI conference appeared in at least 11 languages, including Arabic, Chinese, Dutch, English, French, Hungarian, Korean, Polish, Portuguese, Russian, and Spanish.

Executive Summary of Media Coverage/Outreach Borlaug Global Rust Initiative Technical Workshop

“A global food crisis is still a distinct possibility if governments and international institutions fail to support this rescue mission," Norman Borlaug, 94, the Nobel Prize-winning American agronomist, said in a statement.”

–Associated Press (March 17, 2009)

139


Selected Coverage Highlights: Agence France-Presse: Wheat experts warn of worldwide disease threat http://www.google.com/hostednews/afp/article/ALeqM5iZvFKe5tBo6eKCzguKXhDgesHC9w New York Times: Dot Earth Blog: New Wheat Strain Could Cut Fungus Threat http://dotearth.blogs.nytimes.com/2009/03/17/new-wheat-strain-could-cut-fungus-threat/

Scientific American: Global Wheat Crop Threatened by Fungus: A Q&A with Han Joachim Braun http://www.sciam.com/article.cfm?id=global-wheat-crop-threatened-by-fungus#comments Associated Press: Scientists gain in struggle against wheat rust http://www.google.com/hostednews/ap/article/ALeqM5g5A7arCYehfHJ2i7eAztrdXpatWQD96VUA8G0 Reuters (UK): New strains of wheat pushed to fight killer fungus http://news.google.com/news?ned=us&hl=en&ncl=1316447875&scoring=n Nature (UK): Wheat fungus threatens global crops http://www.nature.com/news/2009/090317/full/news.2009.168.html Popular Science: Rust in the Food Supply http://www.popsci.com/environment/article/2009-03/rust-food-supply

Prepared by:

140

Appendix C: Single Objective Narratives / Durable Rust Resistance in Wheat Phase II Objective 22. Supplemental Document 22.2: Support for Advocacy

Supplemental Document 22.2. Useful Articles to Support Why Scientists Need to be Better Advocates

Learning to Speak "Science" BY CHRIS MOONEY Seed Magazine, Feb/Mar 2006 Issue I recently spent two and a half months during a book tour across the United States speaking about political attacks on science. At universities from Caltech to Oberlin, I heard a recurring series of questions from my audiences: How can scientists combat the political distortion of science? How can they defend evolution? How can they win back America, and better translate what they know for the public? These aren’t easy questions to answer, since they go beyond hard and fast matters of scientific accuracy and into the more nebulous realm of political communication and strategy. So over the course of my travels, I began to formulate my response, mindful of the conditions that have prompted such a political awakening among scientists in the first place. What the scientific community—not just scientists, mind you, but people who care about the role science plays in building a better society—is realizing is that scientific knowledge itself is politically vulnerable. We’ve seen the Bush administration’s assaults on science on issues ranging from climate change to Plan B emergency contraception (the “morning after” pill); we’re witnessing a newly resurgent anti-evolutionist movement that’s spreading community-to-community and state-to-state. And we’re frustrated with a national media that seeks to hear “both sides,” even on subjects (like evolution) where no scientific debate actually exists. Coming to grips with science’s newly exposed political and cultural vulnerability will require scientists to emphasize a rather different set of skills than they’re used to privileging. Although it’s not true of all scientists, too many have grown accustomed to the security of their labs and university communities, occasionally lamenting the American public’s poor understanding of science but doing little in a concerted way to improve it. And small wonder: American science rewards the publication of peer-reviewed research, but offers little incentive for scientists to communicate and translate what they know to the public. So scientists in the US have little practice when it comes to crafting a message or winning a political debate, and their inexperience sometimes leads to ill-advised actions that have the tendency to backfire. It’s becoming possible to craft a communications strategy that’s based on a rich understanding of how the human mind actually operates. Consider the scientific community’s engagement (or lack thereof) with the anti-evolutionist Kansas State Board of Education. When the Board called hearings on evolution, the scientific community boycotted. When the Board began to rewrite state science standards, compromising biology education, the National Academy of Sciences denied the Kansas Board permission to use their copyrighted educational material. The scientific community’s distrust of the Kansas Board is understandable. But such actions make scientists look like haughty snobs and elitists who simply refuse to engage with ordinary Americans—an already prevalent stereotype that hardly needs reinforcing. What we defenders of science must realize, if we want to combat political attacks effectively, is that we have much to learn about political communication and strategizing. Ideally, and in the best spirit of science, we should view the current political quandary as a problem to be

141


addressed through trial and error—empirical attempts to determine what actually works when it comes to translating science for the general public. Ironically, followers of regular politics are catching on to something that doesn’t seem to have dawned on most scientists yet: It’s actually possible to study empirically which public communication messages work and which don’t. It’s even becoming possible to craft a communications strategy that’s based on a rich understanding of how the human mind actually operates—one that, if properly executed by scientists and their supporters, could help rescue scientific integrity in America while better informing the American public. If we want to defend the knowledge that science has brought into the world, perhaps we should consider drawing upon the talents of researchers—social and cognitive scientists—who have brought empirical methods to bear on the study of effective political communication itself. Take the firm Cultural Logic, an innovative communications consulting company run by psychological anthropologist Axel Aubrun and cognitive linguist Joseph Grady. Aubrun and Grady use empirical techniques to determine how the American public actually thinks and, thus, what types of messages can positively change the way they understand an issue. They stress the importance of accurate but succinct explanations that can help the public get past cognitive blocks that impede their understanding of complex issues. The firm Cultural Logic suggests talking about a “carbon dioxide blanket” encircling the earth. Facts alone, note Aubrun and Grady, aren’t enough to educate people; instead, facts must be carefully packaged (or “framed”) in the context of narratives or explanations if they’re to enhance knowledge. Consider the technically complex issue of climate change, where attacks on science have been rampant and the public has been deeply confused. Grady and Aubrun have found that as an explanation, the “greenhouse effect” simply confuses people. Few Americans have any firsthand experience of greenhouses, and they don’t grasp the proposed analogy between carbon dioxide (a gas) and glass walls. So instead, Grady and Aubrun suggest talking about a “carbon dioxide blanket” encircling the earth—an explanation that instantly helps people understand why a heating effect is taking place. Sure, it’s a metaphor and shouldn’t be taken literally. But then, so was the concept of an ozone “hole”—a phrasing that instantly allowed the public to understand the issue of ozone depletion and that helped to galvanize political action. When it comes to defending evolution, another communications thinker—the celebrated Berkeley cognitive linguist George Lakoff—has other useful suggestions for the scientific community. The United States is, of course, a very religious country; one in which many fundamentalists attack evolution but also one in which many moderate Christians support it. In this context, Lakoff explains that scientists ought to be defending evolution by highlighting scientists who are able to reconcile evolution with religious faith. The ideal messengers to reach the public on this issue, then, would be evolutionary biologists who are also practicing Christians. People, in short, like Brown University evolution defender Kenneth R. Miller, a practicing Catholic and author of the book Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution. Similarly, Lakoff agrees that scientists did a poor job dealing with the Kansas Board of Education. What they should have done instead, he suggests, was to launch a comprehensive national campaign to explain evolution to the public, emphasizing how “converging evidence” from a wide range of areas—the fossil record, radioisotope dating, genetics, and many other disciplines—all independently confirm and strengthen the evolutionary account. In short, the scientific community should be promoting a positive message that teaches the public why evolution is such a powerful scientific theory, and about how scientists weigh evidence.

142


These are just a few suggestions from communications experts who are themselves scientists, and whose work is oriented toward finding scientifically-tested solutions. Their empirical approach to communication ought to be second nature to scientists more generally, and to those of us who care about science. But it isn’t. To be sure, most scientists have figured out how to communicate to their classes or to explain their work at dinner parties. But the American public doesn’t have the same level of background knowledge, or the same attention span. It learns in sound bites; in brief snippets at best. Those of us who care about science had better learn to address and win over this audience, and not just on specific issues like evolution and climate change. We must also explain the nature of the scientific method and the societal importance of scientific knowledge. “One of the biggest explanatory holes that’s waiting to be filled by somebody is: What is the role of science in a democracy?” notes Cultural Logic’s Joseph Grady. It’s a massive challenge, but then, so was every other challenge that scientists have faced. Luckily, the scientific method has led to spectacular successes. Now we must apply that method to the greatest and most crucial challenge of all—teaching the American public.

143


Outreach Training Needed BY ALAN LESHNER Science, January 12, 2007 Scanning the relationship between science and society recalls Charles Dickens' lead for A Tale of Two Cities: "It was the best of times, it was the worst of times …" Scientific advances are coming at an unprecedented pace, and they hold great promise for further improving the human condition. The public is clearly happy about this. At the same time, however, society is exhibiting increased disaffection, fostered by instances of scientific fraud and by scientists charged with financial conflicts of interest. Perhaps worse, public skepticism and concern are increasingly directed at scientific issues that appear to conflict with core human values and religious beliefs or that pose conflicts with political or economic expediency. These include embryonic stem cell research, the teaching of evolution in schools, evidence for global climate change, and controversies over genetically modified foods. The ensuing tension threatens to compromise the ability of the scientific enterprise to serve its broad societal mission and may weaken societal support for science. There is a growing consensus that to lessen this tension, scientists must engage more fully with the public about scientific issues and the concerns that society has about them. Efforts that focus simply on increasing public understanding of science are not enough, because the problem is not merely a lack of scientific comprehension. In some cases, the public generally does understand scientific content in a fundamental way but still doesn't like it. Thus, the notion of public engagement goes beyond public education. We must have a genuine dialogue with our fellow citizens about how we can approach their concerns and what specific scientific findings mean. This kind of outreach is being encouraged by government agencies and private sources in Europe, Canada, and the United States. Effective public engagement requires long-term commitment, because many issues are complex and tension is persistent. The creationism/evolution issue showed us this. It would be convenient to leave this task in the hands of a few representatives selected especially for their communication skills, but that won't work. Given the breadth of issues and the intensity of the effort required, we need as many ambassadors as we can muster. Engaging the public effectively is an acquired skill, and preparation for outreach strategies has seldom been part of scientific training programs. There are a few exceptions, including the Aldo Leopold Leadership Program and Research!America's Paul G. Rogers Society for Global Health Research. Many young colleagues are enthusiastic about discussing their work with the public, but they also are under tremendous pressure to stick to the bench, secure hard-to-get research grants, and publish rapidly and repeatedly in high-quality journals. Many even feel that the culture of science actively discourages them from becoming involved in public outreach, because it would somehow be bad for their careers. What can be done? First, the scientific reward system needs to support our colleagues' efforts to interact with the general public concerning their work and its implications. Funding agencies such as the Wellcome Trust and the U.S. National Science Foundation and National Institutes of Health have begun encouraging the scientists they support to include outreach efforts in their proposals. Academic institutions need to join in this chorus by rewarding faculty members who fulfill commitments to such work. That will entail putting public outreach efforts among the metrics used to decide promotion and tenure. Second, university science departments should design specific programs to train graduate students and postdoctoral fellows in public communication. Unfortunately, this means adding

144


yet another element to already overtaxed research training programs. Many students acquire teaching experience through assistantships, but public engagement activities are different and require other strategies. We need to add media and communications training to the scientific training agenda. This will doubtless be an additional burden on existing systems. Unfortunately, there is no alternative. If science is going to fully serve its societal mission in the future, we need to both encourage and equip the next generation of scientists to effectively engage with the broader society in which we work and live. Alan I. Leshner is chief executive officer of AAAS and executive publisher of Science.

145


Scientists must learn to talk to the media By MICHAEL SKAPINKER The Financial Times, October 29, 2007 I occasionally speak to school students about journalism and they usually ask the same questions. Have you interviewed anyone famous? (Richard Branson and John Cleese seem to pass muster.) What do you do if there is no news? (There is always news.) What should I study if I want to be a journalist? I spend some time on the last one, advising them to study whatever they are most interested in, whether it is history, foreign languages or economics. The craft of journalism is something they can learn later. Far better to acquire some knowledge to bring to the job. And I tell them there is a desperate need for more scientists who can broadcast and write. Science and the media have not always served each other well. Last week, the Royal Society of Arts and the Reuters Institute for the Study of Journalism hosted a stimulating discussion on the theme “Do scientists get the media they deserve?” The speakers were Craig Venter, the genome research pioneer, and Niall Dickson, a former BBC journalist who is now chief executive of the King’s Fund, the independent health charity. On the basis of his performance, Mr. Venter, who was once described in The New Yorker as an “idiot”, does not get the press he deserves. He was amusing and quietly spoken. He was also easier on journalists than Mr. Dickson, who worried about the media’s tendency to sensationalize, to oversimplify and to reduce the world to black and white. On the other hand, Mr. Venter said scientists, driven by their need for research grants, were guilty of exaggerating what they hoped to achieve. They were happy if they fell 50 per cent short of their stated goals. Business executives who fell even slightly short were adjudged failures. Mr. Dickson said he was not entirely pessimistic. Organizations such as the Science Media Centre, whose director, Fiona Fox, chaired the discussion, helped scientists explain themselves. (“Large numbers are very difficult to imagine,” the centre tells scientists. “Rather than 1 in 1,200, talk about one child in a large secondary school.”) The centre also helps journalists with “thumbnail sketches” entitled, for example: “What is peer review? Peer review is where scientists open their research to the scrutiny of other experts in the field.” Based on my experience as a non-scientific journalist, occasionally writing about controversies such as mobile phone emissions, genetically modified food and the measles, mumps and rubella vaccination, here are a few other suggestions for scientists. First, do not assert a certainty that science cannot sustain. Journalists often demand definitive answers. Scientists need to explain this is not always possible. This can work. The Mobile Telecommunications and Health Research Programme last month issued a nuanced report on the health risks from mobile phones. The programme, funded by the UK government and the industry, found no evidence of ill health in mobile phone users but added that “cancer symptoms are rarely detectable until 10 to 15 years after the cancer producing event and, since few people have used their phones that long, it is too early to say for certain whether mobile phones could lead to cancer or indeed to other diseases”.

146


The Daily Express reported it this way: “Scientists have admitted there may be long-term health risks from using mobile phones. A major study published on Monday found no evidence of a link between short-term use and brain cancer. But experts behind the research said it was too early to know what will happen in future.” Not bad. Second, people, however well-meaning, generally make sacrifices for the wider good only if they can see benefits for themselves or their families. People may be prepared to buy hybrid cars because they can see that global warming might affect their loved ones. But European consumers refused to set aside their suspicions about genetically modified food just because US companies claimed it would help farmers in the developing world. Consumers could see nothing in it for themselves and they suspected the alleged benefits would accrue mainly to the companies. Third, while people may be prepared to tolerate some risk for themselves, they are prepared to accept far less for their children. When a lone British doctor claimed the MMR vaccine could cause autism (an assertion that has attracted no scientific support), public health officials violated all these suggestions. They baldly asserted that the vaccine was safe, when people knew no vaccination was completely safe. They told parents who refused to vaccinate their children that they were risking the health of the community. Parents were not prepared to sacrifice their own children for the community. With patient persuasion, and the discrediting of the alarmist research, immunization rates in England are climbing again but, at 85 per cent, are still short of the 95 per cent needed to ensure widespread immunity.

147

Appendix C: Detailed Description of Proposed Work / Durable Rust Resistance in Wheat Phase II Objective 23 Stem rust populations tracked and monitored

Summary Information (Objective 23) Objective Name: Stem rust populations monitored, tracked and characterized

Objective Team Leader:

First name Robert Surname Park

Title Professor Telephone +61 2 9351 8806 Fax +61 2 9351 8875 Mobile +61 414 430 341

Address

The University of Sydney Plant Breeding Institute PMB 11 Camden NSW 2570 AUSTRALIA

E-mail [email protected] Collaborating Institutions with Budgeted activities from other Institutions (add more rows if necessary)

Institution Primary Contact

(name) email Phone University of Sydney Prof Robert Park [email protected] +61 2 9351 8806 FAO UN Dr Dave Hodson [email protected] +39 06 340 699 9730 Aarhus University Dr. Mogens Hovmoller [email protected] +45 8999 1900 ICARDA Dr Kumarse Nazari [email protected] USDA ARS Dr Yue Jin [email protected] +1 612 625 3780 Ag Canada Dr Tom Fetch [email protected] +1 204 983 1462 CIMMYT Dr Petr Kosina [email protected] Sathguru India Mr Vijayaraghavan [email protected] +91 40 2335 0586 CRIFC Turkey Mr Zafer Mert [email protected] +90 312 327 09 02 EIAR Ethiopia Dr Girma Bedada [email protected] +25 1 223 331 509 KARI Kenya Ms Ruth Wanyera [email protected] UC Davis Mr Iago Lowe [email protected]



60

148


I. Executive Summary

Knowledge of the distribution and incidence of the disease stem rust (surveillance) and of races of the stem rust pathogen (race analysis and tracking), and the potential impact of the races on local wheat germplasm, are all fundamental to the formulation and adoption of appropriate national and international policies, investments, and strategies in plant protection, plant breeding and in seed systems. A global decline in the incidence of stem rust over the past 40 years, attributable at least in part to resistance breeding and the widespread deployment of the resistance gene Sr31, led to many countries abandoning stem rust surveillance and an alarming reduction in the global skill base in rust race analysis and general rust pathology. These deficiencies were addressed in Phase I of the Durable Rust Resistance in Wheat (DRRW) project, in which limited and targeted stem rust pathogen characterization was undertaken at three ARIs, the establishment of capacity for in-country stem rust race analysis in Kenya and Ethiopia was initiated, and a Global Cereal Rust Monitoring System (GCRMS) with standardized protocols for surveillance and handing of rust isolates was established.

Objective 23 of Phase II will continue and expand the surveillance activities initiated in Phase I. It is the only Phase II objective targeting the actual causal agent of stem rust, Puccinia graminis f. sp. tritici, and to our knowledge is the only initiative in the world attempting to document and understand global variability in this pathogen. The information generated on the distribution of stem rust races, including Ug99, the incidence and distribution of stem rust, and the potential role of the alternate host barberry in generating genetic variability in eastern Africa will be important in underpinning pre-breeding (Objective 26), breeding (Objective 25), and the release and post-release management of wheat germplasm (Objective 21). It will also provide guidance to the stem rust phenotyping activities planned under Objective 24, and will be instrumental in advocacy efforts under Objective 22. Outcomes

Objective 23 comprises four operational components and a fifth covering Objective management, co-ordination with other Phase II objectives, and co-ordination with surveillance initiatives outside the Phase II project. The four operational components will continue and extend work initiated in Phase I to redress a global decline in stem rust knowledge, by providing information on the occurrence and nature of stem rust populations throughout the world, establishing a stand-alone system of global stem rust surveillance, and developing new tools, all of which are fundamental if successful breeding solutions are to be sought and implemented in controlling stem rust of wheat. The first component (“a”) will extend Phase I work in establishing the Global Cereal Rust Monitoring System (GCRMS) and interfacing it with a Wheat Atlas data platform. In this component we will also leverage funds to establish a Global Rust Reference Center (GRRC) at the University of Aarhus, Denmark—the missing link in a truly functional GCRMS. The DRRW funds for the center will support training for national programs’ scientists in race analysis. The outcomes of this work will be:

• Five years: Accessible, up-to-date information on stem rust incidence and populations in 10 priority countries. This will include an accurate baseline information platform that will inform surveillance and mitigation activities and allow impact assessment and stem rust

149


risk analysis. It is anticipated that at project completion, the GCRMS, including the GRRC and spatial data platform will be predominantly self funded and providing information used routinely by national partners in at least 10 countries to guide decisions regarding control and management of stem rust. The GRRC will be established; training and sample analysis will be ongoing.

• Ten years: The GCRMS will provide information that is used routinely by national partners to guide decisions regarding control and management of stem rust in at least 30 countries. It will also be used by these countries to assess the effectiveness of stem rust mitigation efforts.

• Fifteen years: The GCRMS will be the primary source of information relating to stem rust incidence and populations globally, and will be used routinely by national partners to guide decisions regarding control and management of stem rust globally.

Component “b” will extend the work commenced in Phase I on stem rust surveillance based on direct crop inspections and trap plots. While not funding the operational costs of trap plots, the Objective will support the generation, maintenance and distribution of pure seed of trap plot genotypes to those undertaking surveillance and stem rust research and resistance breeding. Given the unpredictability of stem rust outbreaks and the threat posed by this pathogen to all global wheat growing regions, support will be provided for in-country surveillance in target and non-target countries of strategic importance. Outcomes are:

• Five years: Trap plot nurseries used in global rust surveillance comprise or include standard reference genotypes, and support is provided to stem rust surveillance teams in 10 priority countries to enable effective annual contribution to the GCRMS.

• Ten years: An effective and self-funded network of stem rust surveillance teams is established in 30 priority countries and contributing to the GCRMS annually, and efforts to include other cereal rust diseases in GCRMS are initiated.

• Fifteen years: National agricultural program systems are undertaking routine annual cereal rust monitoring and contributing information to the GCRMS.

Component “c” focuses on improved understanding of the stem rust pathogen throughout the world, primarily targeting areas that are currently under threat from the Ug99 lineage and/or of strategic importance in terms of Ug99 migration pathways. The outcomes from this work will be:

• Five years: Routine standardized annual stem rust race surveys established in at least 5 developing countries, with data incorporated into GCRMS on an annual basis. Major stem rust races present in regions of strategic importance are known and an understanding of the global genetic diversity of the wheat stem rust pathogen is obtained.

• Ten years: At least 10 developing countries are undertaking routine standardized annual stem rust race surveys and contributing data for inclusion into GCRMS.

• Fifteen years: Routine standardized annual stem rust race surveys are conducted in countries representing all major wheat growing regions, with data incorporated into GCRMS. Comprehensive and internationally standardized diagnostic tests based on DNA profiling are used globally to characterize stem rust populations.

150


The potential impact of stem rust races on wheat crops can be predicted if the resistance genes present in commercial cultivars are known. Component “d” will complement the work undertaken in component “c” and focus on host stem rust resistance. The first activity will involve extending the work of Phase I in characterizing the rust resistance genes present in all major wheat cultivars in the world and assaying plant tissue from stem rust infected crops using molecular markers linked to important resistance genes, and the second will involve generating new genetic stocks for future use in surveillance and pathogen characterization.

• Five years: R genes in wheat genotypes from at risk countries are known. Homozygous NILs (BC5) carrying up to 35 stem rust resistance genes developed individually and undergoing final seed increase prior to distribution.

• Ten years: Detailed understanding of stem rust R genes in all main wheat genotypes grown in major wheat production areas. Utility of NILs as greenhouse differential genotypes and field trap plot genotypes assessed in all major wheat growing regions.

• Fifteen years: Geographic distribution and graphical representation of R genes in relation to stem rust race distribution in GCRMS and annual risk monitoring of R gene breakdown. A single set of NILs is used internationally for both greenhouse seedling virulence assays and field trap plots.

The final component (“e”) will ensure coordination of all Objective components, and also of overall inter-objective co-ordination. It is expected that this will lead to successful completion of all Objective components and activities and integration of all outputs with overall project.

Progress Knowledge of the distribution and incidence of the wheat disease stem rust and of races of the stem rust pathogen, and the potential impact of these races on local wheat germplasm, is fundamental to the formulation and adoption of appropriate national and international policies, investments and strategies in plant protection, plant breeding, seed systems, and in rust pathogen research. Following the demonstration of races in the wheat stem rust pathogen in the early 1900s (Stakman and Piemeisel 1917), many countries established race surveys, and some also undertook rust surveillance using networks of trap plots to assess the presence/ absence of rust diseases. A global decline in the incidence of stem rust over the past 40 years, attributable at least in part to resistance breeding and the widespread deployment of the resistance gene Sr31, led to many countries abandoning stem rust monitoring and an alarming reduction in the skill base in rust race analysis and general rust pathology.

The lack of stem rust surveillance and decline in global race analysis were addressed in Phase I of the Durable Rust Resistance in Wheat (DRRW) project by undertaking limited and targeted stem rust pathogen characterization at three ARIs, initiating the establishment of capacity for in-country stem rust race analysis in Kenya and Ethiopia, establishing the GCRMS, and establishing standardized protocols for surveillance and handing rust isolates. The rationales behind these Phase I activities were: the importance of knowing the current distribution and nature of Ug99; the need to assist developing countries in establishing capacity for ongoing national race analysis to underpin in-crop rust management and resistance breeding; the need to

151


establish a system that would allow and ensure sharing of information on rust incidence and occurrence and race composition between countries.

The current distribution and nature of Ug99 Fundamental information on the nature and distribution of the Ug99 lineage was generated, with five presumed mutational derivatives possessing identical SSR fingerprints being identified (Fig. 1). Two of these are restricted to South Africa and include the presumed progenitor of Ug99, identical to Ug99 apart from lacking virulence on Sr31. An important outcome from this work is that meaningful field testing of germplasm lacking Sr31 can be undertaken in South Africa. The remaining 3 races (Ug99, “Ug99+Sr24”, “Ug99+Sr36”) are all present in Kenya, and race Ug99 has also been confirmed in Uganda, Ethiopia, Sudan, Yemen and Iran. FAO played a significant role in announcing the detection of Ug99 in Iran, showing clearly the value of their role in dealing with national governments. Race surveys in Turkey, Syria, Egypt, Pakistan and India over the past 2 years have failed to detect any of these races. Figure 1. The nature and distribution of the Ug99 lineage as deduced from Phase I activities.

Building capacity for in-country race analysis

Ug99 [TTKSK]

+Sr36

Race 4

Race 1

+Sr31

+Sr24

Race 2

+Sr24

Race 3

South Africa only

Uganda Kenya Ethiopia Sudan Yemen Iran

1. TTKSF [Sr24-, Sr31-, Sr36-] 2. TTKSP [Sr24+, Sr31-, Sr36-] 3. TTKST [Sr24+, Sr31+, Sr36-] 4. TTTSK [Sr24-, Sr31+, Sr36+]

Kenya only

152


At its simplest, developing in-country capacity for rust pathogen race analysis involves equipping scientists with the required skills and ensuring the provision of adequate infrastructure. The lack of regional centers or of a global reference center means that all countries in which wheat production is important and where rust diseases are potentially important need to have the capacity to undertake race analysis. This makes developing capacity for in-country race analysis challenging because of: a lack of commitment by some countries both in providing ongoing infrastructure and personnel, particularly problematic at times when rust incidence is low; the time taken to train scientists properly in race analysis (at the very least 3 months); the promotion or movement of trained personnel into other areas. Successful ongoing race analysis is usually typified by long-term commitment of the scientists undertaking race analyses- for example in Australia and North America, some scientists have been doing this work for in excess of 20 years.

Despite these challenges, significant progress was made in Phase I towards establishing the infrastructure needed in Kenya and Ethiopia to undertake in-country race analysis (under Objective 4) and in working with scientists in these countries and in Turkey (with funding from the Australian Crawford Fund) to consolidate existing skills in race analysis.

Establishing a Global Cereal Rust Monitoring System The establishment of a single system to service the world’s needs for rust surveillance, while “theoretically” straightforward, is “in principle” challenging because rust diseases migrate over long distances and there is an absolute requirement for strong international co-operation. The application of race survey outputs to resistance breeding has been most successful in rust epidemiological units (i.e. regions within which rust migrates freely but isolated from other wheat growing regions) within which information on rust incidence and racial composition are shared (e.g. North America and Australasia, see Park 2007). The existence of circumstantial evidence on the progressive occurrence of Yr9-virulence, which suggests that much of Asia comprises a single rust epidemiological unit (Singh et al. 2006), reinforced the need to couple efforts to improve our understanding and capacity in race analysis with a system that would ensure rapid and free sharing of information. Similar challenges were faced in establishing an international system for desert locust monitoring, which was successfully achieved by developing the Desert Locust Information Service (DLIS), located within the FAO’s Emergency Prevention System for Transboundary Animal and Plant Pests and Diseases (EMPRES). The long-term success of DLIS and FAOs ability to enter into dialogue with UN- member countries provided an excellent framework within which to develop an international rust surveillance system. The GCRMS was therefore structured on the organizational model and data flows of the DLIS. It comprises a UN-FAO based International Focal Point (IFP), National Focal Points (NFPs), NARS supported National Surveillance Teams (drawn from both Plant Protection and Research Institutions), a Surveillance Coordinator based at ICARDA, a Coordinating Pathologist based at the University of Sydney, and various international partners (including Agriculture Agri-Foods Canada, CIMMYT, ICARDA, University of Free State (South Africa), and USDA-ARS).

The GCRMS is underpinned by an information platform that includes standardized protocols for methods and systems used in surveys, preliminary virulence testing, data, sample transmission and management at the field, national and global levels. In order to provide access to stem rust

153


information in a timely fashion, two web-based visualization tools were developed that are linked to a centralized database and released in the public domain: Rustmapper (http://www.cimmyt.org/gis/RustMapper/index.htm), a networked Google Earth application and RustMapper Web (http://www.cimmyt.org/gis/rustmapper/RustMapper_Web.html), a browser-based tool. Both tools incorporate updated stem rust survey data, near-real time wind trajectories, country level germplasm susceptibility estimates and distribution of major wheat growing areas. Both the tools and database are being updated on a routine basis, hence delivering the most recent information relating to stem rust in a timely manner.

The GCRMS was brought into operation during Phase I by engaging field surveyors and national information system managers and conducting training in cereal rust survey (including sampling) techniques at 3 workshops (Syria, Central Asia and India) at which 98 GPS units were distributed to ensure geo-referencing of survey data. 30 countries were engaged in the process and efforts to recruit more continue. 18 countries attending the March 08 Baseline Workshop committed to establishing NFPs and to participate in a 2007-08 baseline survey, however, drought in many regions reduced the incidence of rust significantly. Despite this, an increasing number of countries now submit information on a regular basis. In 2005, no partner countries were submitting information on stem rust and no standardized protocols or data management system was in place. By the end of 2008, data from over 1200 survey sites had been incorporated into a centralized database, with three countries regularly submitting standardized field data. At the time of writing (end of 2009), fifteen countries had submitted standardized field data and the centralized database contained approximately 2000 survey sites. These achievements represent significant progress towards the establishment of the foundations for an operational GCRMS.

The progress made was despite considerable delays in the appointment of the IFP at FAO. Sub-contracting agreements were more difficult to put in place than originally anticipated, resulting in the FAO appointment only occurring in April 2009 (nearly one full year after the official start date of the first phase of the DRRW project). Delays also occurred in the generation of updated baseline spatial datasets relating to wheat areas, growth stages and cropping systems. These were the result of internal administrative difficulties at ICARDA. These issues have now been resolved and work is progressing in this area.

Despite this good progress, challenges remain with the two areas of most concern being the lack of capacity and resources to undertake rust surveillance and monitoring, and barriers limiting the exchange and free-flow of information regarding stem rust. Declining support to agriculture in many developing countries has left many, but not all, national systems without the resources or capacity to undertake even cereal rust field surveys on a regular basis, let alone implement race analysis. This situation has been confirmed by informal surveys undertaken at several rust workshops. Political sensitivity, especially in respect to the Ug99 lineage of stem rust, is one factor limiting the free exchange of information. In both of these areas of concern the role of FAO is considered to be vital and some advances are being made. Already the comparative advantage of FAO as an international neutral broker with the ability to assist member countries over potentially sensitive rust issues has been demonstrated. The provision of support by FAO that facilitated the official public announcements of the presence of Ug99 by the governments of Yemen and IR Iran are concrete examples.

FAO’s engagement in the DRRW project has resulted in increased institutional awareness and corresponding institutional prioritization; resulting in the initiation of a global rust disease

154


program at FAO (see http://www.fao.org/agriculture/crops/core-themes/theme/pests/wrdgp/en/). This program is now attracting the attention of other donor agencies and an expanding portfolio of projects is the resulting outcome. To date, 4 additional projects with a combined total budget of over US$4 million are part of the FAOs Global Rust Disease Program (GRDP), the primary focus areas of which include; national preparedness and contingency planning, seed systems, and facility updates. Not all projects within GRDP are focused on surveillance and monitoring. However, this portfolio of new projects is allowing an expansion of the number of priority countries in which the capacity for surveillance and monitoring can be supported and enhanced from 8 to approximately 20. Given the shifting frontiers of countries at risk from the Ug99 lineage, and the current lack of capacity in many countries, this is seen as essential and complementary to the existing on-going activities in Phase I and the planned activities in Phase II. All of the additional projects in the GRDP with surveillance and monitoring components are reliant upon the core GCRMS platform being developed at FAO under the DRRW project. Opportunities are also emerging from other projects for the inclusion and dissemination of information on other cereal rust diseases via linkages and collaboration with other global rust efforts, such as leveraging funds from Aarhus University (home to the global yellow rust global reference center) to establish a global reference center for stem rust.

The stark reality on the ground is that actual governmental support for regular cereal rust surveys is often limited or non-existent. National internal information sharing on rusts is often restricted, not timely and virtually non-existent at the regional or wider scale. This situation mirrors that faced at the initiation of the global DLIS program. Only a concerted long-term effort, comprising direct external support, capacity building, awareness raising and demonstration of information systems with added value managed to raise the profile to the point where locust monitoring was routine and a sustainable network, supported significantly by national funds, was created. The GCRMS has a planned trajectory of development similar to that of the DLIS, with similar time-lines anticipated for national in-country support. A final area of concern relates to the in-country / regional capacity and the will to undertake reliable and routine race analysis. Considerable effort and progress are being made, but there is no simple quick fix and sustained effort over a long period will be required to achieve the overall goal. Narrative of Work

Component 23.a. Global Cereal Rust Monitoring System (GCRMS) Activity 23.a.1. Maintain and enhance the functional information platform and core databases for tracking and monitoring rust populations (D. Hodson/FAO; K. Nazari/ICARDA) The International Focal Point (IFP) at FAO will be responsible for overall coordination and delivery of the proposed outputs of Component “a”. The IFP will supervise technical staff working on database and tool development. Officially nominated National Focal Points will be responsible for data compilation, quality control and information dissemination at the country level. An overall schema on operational aspects, including information and rust sample flows was provided in the DRRW Phase I proposal. Experience in Phase I has allowed refinement of this schema (see Supplemental Document 23.1). The intention is to maintain and enhance the functional information platform and core databases for tracking and monitoring rust populations, by:

155


• Expanding, enhancing and maintaining the core databases that underpin the GCRMS. This includes the routine import and maintenance of field survey data, trap nursery summary information, race analysis summary information and inclusion of trap plot data.

• Facilitating efficient data management by the development of automated or semi-automated procedures for data import into the centralized core database

• Routine updating and maintenance of secondary data, including climatic and environmental data

• Development of customized analytical tools that facilitate easy integration of the core and secondary data sets in a meaningful way.

• Exploratory testing of the use of ‘crowd-sourcing’ methods for early detection of emerging stem rust threats may supplement formal, traditional survey methods. However, any data collected by these means will be validated through the National Focal Points.

To ensure optimal integration of information arising from Trap Plot nurseries into the GCRMS, ICARDA will develop a field-based pathogenicity survey platform, involving:

• The development of standardized protocols and methods for undertaking disease assessments of trap nurseries

• The preparation of a field scoring scale (modified Cobb’s scale) and photo images of individual field responses (adult-plant reaction) for each trap plot genotype

• Guidelines on determining geo-referenced mapping of trap nurseries using GPS units

• Compilation and distribution of an annual report linked into the core databases of the GCRMS.

Activity 23.a.2. Wheat Atlas data platform (P. Kosina/ CIMMYT) To enhance the core rust pathogen information described in Activity 23.a.1 complementary national or sub-national information relating to wheat production, agro-ecologies, varietal composition and performance are important in allowing assessments of rust incidence and threat. Exisiting information platforms developed by CIMMYT, namely; the International Wheat Information System (IWIS) and the Wheat Atlas will be enhanced and integrated into the GCRMS. Using IWIS as an underlying data management platform for wheat variety and performance data, the Wheat Atlas component will extract relevant variety summary information and provide an intuitive user interface to a host of additional wheat sector data at the country level. This data rich electronic atlas of country-level wheat data will be integrated in a seamless manner with the updated rust surveillance and pathogen monitoring information derived from Activity 23.a.1.

Activity 23.a.3. Deliver timely and accurate information on stem rust populations via an expanded Global Cereal Rust Monitoring System (D. Hodson/FAO) Information dissemination on surveillance and monitoring of rust populations will be strengthened by:

• Routine delivery of information products derived from the GCRMS to targeted user groups

156


• Core information products comprising web-based situational updates, bulletins and web mapping tools but additional products are not excluded. Delivery of summarized race analysis and trap nursery data will be important components.

The proposed activities described above are designed to convert the current emerging monitoring system into a fully operational system, delivering accurate and timely information to inform decision making in response to the threat posed by virulent races of stem rust.

Activity 23.a.4. Leverage establishment of a Global Rust Reference Center by supporting race analysis and training (M. Hovmoller, Aarhus U) Funds from Denmark will be leveraged to establish a Global Rust Reference Center (GRRC) including stem rust as a part of a reference center for all three rusts. The DRRW component will support training in stem rust race analysis for pathologists from developing national programs. This advocacy success will lead to a GRRC that will:

• Accept limited and strategically targeted stem rust samples year round, according to capacity, from any National Surveillance effort.

• Be collected in a global reference collection of stem rust isolates.

• Train national program pathologists in standard surveillance and race typing protocols.

The establishment of a GRRC will allow for a fully functional global monitoring system for stem rust.

Component 23.b. Surveillance Activity 23.b.1. Trap plot network support (K. Nazari/ ICARDA) In most of the countries affected or at immediate risk of Ug99, stem rust has appeared in warm areas. Many current stem rust genotypes used in trap nurseries require vernalization or, due to day-length sensitivity, final disease assessment of stem rust infections (on stems) is not possible. Although several laboratories use the North American differential set (NA), most use a combination of NA, Stakman and other tester genotypes and therefore the number and type of differential genotypes and stem rust resistance genes represented varies. Because of differences between differential sets and occasional impurity of trap plot genotypes, interpretation of surveillance data between countries is difficult. To eliminate these problems, ICARDA will undertake central seed multiplication and seed dissemination of wheat genotypes for use as trap plots. This will be achieved by:

• Compiling a set of genotypes currently used in trap plots. A stem rust race analysis set and stem rust monogenic lines were obtained from Dr Jin (USDA, CDL-Minnesota) and Dr Fetch (AAFC) in 2008

• Large-scale seed increase of differential genotypes at ICARDA where both spring and winter type and/or day-length sensitive genotypes can be grown

• Distribution of seed following clearance by ICARDA’s seed health laboratory.

Once adequate quantities of pure seed are available, current and future stem rust trap nurseries will be revised and a new set of Sr-genotypes comprising the most important Sr-genes in spring type and or day-length insensitive backgrounds, selected mega commercial cultivars, and known sources of

157


APR gene/s will be selected by the Objective 23 Advisory Panel to be used as “The International Stem Rust Trap Nursery” (ISRTN), which will be provided to rust laboratories and NARS. Health Certificates will be issued by ICARDA’s seed health laboratory. The nursery will be sown in two 1-meter rows in rust-prone areas in each country and field scoring will be undertaken using a modified Cobb scale. Key Sr-genes and/ or commercial cultivars grown in regions carrying the key Sr-genes (Sr31, Sr24, Sr36 and Sr38) will be planted as large breeding plots (4 X 4-meter rows) in research stations every year. Geo-referenced information of these locations will be mapped and virulence patterns will be monitored every year at each location. Frequencies of virulence will be determined over the years and locations.

Activity 23.b.2. Expand and develop national capacity to undertake rust surveillance (K. Nazari/ ICARDA; D. Hodson/ FAO) The objective is to train young scientists in the field of rust surveillance, field-based pathogenicity surveys (“trap nurseries”), and data management. This will involve:

• Training of field surveyors to use survey protocols, rust sampling, disease data collection, and Global Positioning System (GPS) information

• Expansion of existing networks of national surveillance teams to cover priority countries in Africa, Asia and the Middle East in which there is an emerging threat from virulent races of stem rust. National Focal Points will be identified and established in all new countries incorporated into the network.

• Providing technical support and capacity building to at least 10 countries in the network on an annual basis

Because rust epidemics can develop rapidly, and high rust levels can threaten neighboring regions, there is considerable value in monitoring rust levels in regions where wheat may not be an important crop or which are not been being specifically targeted for surveillance. The Surveillance Coordinator at ICARDA will therefore also provide support for surveillance in such regions if concerns about stem rust arise.

Component 23.c. Pathogen characterization Activity 23.c.1. Stem rust race analysis backstopping ARIs (Y. Jin/ USDA; T. Fetch/ AAFC) Seedling based assays conducted in plant growth facilities remain the only way to determine the pathogenicity spectra of rust isolates. Arguably, some of the most useful information in guiding resistance breeding activities that came from Phase I surveillance and tracking activities was from the race analysis work conducted by AAFC, USDA, University of the Free State (South Africa) and the Seed & Plant Improvement Institute (Iran). In Phase II, Drs Jin and Fetch will continue to provide technical backstopping for countries undertaking race analysis (i.e. verification of putatively new races), and undertake limited and strategically targeted race analysis for countries that do not.

Activity 23.c.2. Stem rust race analysis in-country (K. Nazari/ ICARDA; R. Park/ USy) Ongoing issues associated with quarantine restrictions on the exchange of viable rust isolates between countries have severely hampered efforts to gain insight into the diversity of stem rust races in many countries. While AAFC and USDA will continue to offer limited race analysis that

158


is constrained by seasonality, it will be vital in Phase II to develop in-country race analysis capability, both in terms of skills and infrastructure.

Skills in race analysis and operational infrastructure exist in Syria (ICARDA), India, Iran, Ethiopia and Turkey, and there are funds available in some projects being managed by FAO for additional infrastructure upgrades. Resources for training in race analysis and infrastructure in Kenya and Ethiopia are allocated under Objective 24 in the Phase II proposal. Allocations of limited funding to assist Kenya, Ethiopia, Turkey and India in undertaking stem rust surveillance and race analysis are included and assistance will be provided by the Surveillance Coordinator at ICARDA and the Objective Leader at the University of Sydney.

Notwithstanding the importance of detailed in-country race analyses, the most pressing challenge to resolve is the current distribution of “Ug99.” Because of the difficulties and time required to establish in-country capacity in race analysis in all countries that are under threat from Ug99, efforts to obtain preliminary baseline information on the incidence of stem rust plus the virulence of isolates for the key resistance genes Sr24, Sr31 and Sr36 initiated in Phase I will continue. This will be achieved by: low resolution surveys in each country involving collection of samples, inoculation of duplicate ‘Quicksets’ with the bulk, and marker analysis using host tissue from all plants on which stem rust is found, using “perfect” markers for important rust resistance genes including Sr24 and Sr31 (in Australia).

For at least the next five years, there will likely be differences in the genotypes used for field trap nurseries and for greenhouse seedling race analyses. The increase and distribution of pure seed for trap plots proposed to be undertaken by ICARDA will therefore be extended to include seed of differential genotypes used for race determination. The genotypes to be used and distributed will be based on discussions initiated at Obregon in March 2009 and being coordinated by Dr Fetch. Once pure seed of the agreed set is available, it will be forwarded by Dr Fetch to Dr Nazari, who will then initiate bulk increase and distribution to countries undertaking race analysis.

Activity 23.c.3. Targeted surveillance of barberry for stem rust infection (I. Lowe / UC Davis, Y. Jin / USDA) Preliminary surveys of barberry conducted in Kenya (Jin), Uzbekistan and Turkey (Park) have established the existence of aecial infections by a form of the stem rust pathogen Puccinia graminis. While it is no clear if some or all of these infections are actually due to the form of P. graminis that infects wheat (P. graminis f. sp. tritici), it nonetheless demonstrates clearly that barberry continues to play a role in the life cycle of P. graminis, although likely minor, in at least some regions. This work will involve more extensive surveys of barberry in eastern Africa and possibly neighboring regions, and analyses of any aecial infections found at the USDA Cereal Disease Laboratory to establish what f. spp. are present, and if P. graminis f. sp. tritici is found, what races are present.

Activity 23.c.4. Stem rust fingerprinting (R. Park/ USyd and others) Protocols to extract DNA from dead rust urediniospores and permits to allow importation were developed at USyd several years ago. The distinctive SSR fingerprint of Ug99 and other races within this lineage provide a means of demonstrating stem rust isolates do not belong to the Ug99 lineage. It should be noted, however, that these tests do not allow definitive proof of the

159


actual race of a stem rust isolate, nor do they allow conclusions to be made about the virulence of isolates unless they are coupled with seedling assays. The possibility that a stem rust race unrelated to but more dangerous than Ug99 exists must be acknowledged, and the only way to determine this is by seedling based race analyses.

Published SSR markers and new SSR markers developed by USyd will be used to fingerprint international collections of the stem rust pathogen. This will include situations in which there is concern about the potential presence of a member of the Ug99 lineage, and also more broadly to isolates off both bread wheat and durum wheat from different regions to gain a better understanding of global genetic variability in this pathogen. This work was not possible until the advent of stem rust specific SSR markers about 5 years ago. An output from this work will be the identification of the best SSR markers for use in future assessments of genetic diversity in the stem rust pathogen.

Activity 23.c.5. Stem rust diagnostics (L. Szabo/ USDA, R. Park / USyd) Recent sequencing of P. graminis f. sp. tritici genome provides an important new resource for understanding the evolution and diversity of this pathogen (USDA, Broad Institute). In addition, several isolates of P. graminis f. sp. tritici including Ug99 and 3 members of this lineage have been sequenced using Next-Generation technologies (Illumina) resulting in a PgtSNP database of over 1 million loci. Currently, these results are being used to develop a rapid diagnostic assay (real-time PCR) for the identification Ug99 and members of this lineage (USDA). Next-Generation sequencing of representative isolates from around the world will be used to expand the current Pgt SNP database allowing the development of rapid molecular diagnostic tools for the identification of the major races groups/lineages worldwide, as well as, new emerging race groups.

Component 23.d. Host characterization Knowing the distribution and nature of stem rust races is of fundamental importance in guiding pre-breeding and breeding for resistance. This information is also important in the post-release management of stem rust, but its value is significantly lower in the absence of knowledge of the stem rust resistance genes present in wheat varieties under cultivation. Combined, knowledge of race distribution and of the resistance status of cultivars allows risk assessments and also the threat of new races to current production practices.

Activity 23.d.1. Host R gene determination (R. Park/ USyd; K. Nazari/ ICARDA) To better understand geographical distribution of rust resistance genes in the major wheat-growing areas, this work will involve collecting and multiplying seed of commercial cultivars grown in countries affected or at risk of Ug99 (representative commercial cultivars are available through ICARDA seed collection and, in 2008, the 10 most currently grown cultivars in CWANA countries were obtained and planted for large-scale seed increase at quarantine isolation areas at ICARDA). A Ug99 Regional Rust Screening Nursery (Ug99RRSN) comprising representative commercial cultivars will be established for adult plant field testing in a Ug99 hotspot, and seedling evaluation of all entries using local stem rust races will be undertaken at the University of Sydney and where possible regional rust labs to permit resistance gene postulation. This information will be supplemented by molecular characterization of all entries using markers linked to important rust resistance genes (e.g. Sr2, Lr34/Yr18, Lr46/Yr29).

160


Activity 23.d.2. Genetic stock development (R. Park/ USyd) Race determinations of cereal rust pathogens can only be conducted in seedling tests under controlled growth conditions. Field based trap plots provide useful information on the presence of specific virulences in a region. Both approaches are entirely dependent on host genotypes carrying target resistance genes. Unfortunately, many genotypes used as differentials in wheat rust work carry multiple resistance genes, often leading to great confusion and incorrect virulence determinations. Work over the past 20 years at USyd led to the identification of the Australian wheat cultivar Avocet as a useful background genotype into which single genes conferring resistance to stripe rust have been backcrossed. The Avocet NIL series has been deployed internationally as trap plots and individual NIL stocks have been used by some laboratories as differential genotypes for seedling race analyses. Similar but incomplete sets of NILs exist for stem rust, produced in Canada (LMPG series), Australia (W2691 series), and the USA (ISr series). This Activity will involve compiling, verifying and preserving all current stem rust NIL stocks and the production of a new NIL set for stem rust using a genotype similar in agronomy to Avocet but lacking Sr5 and Sr26 and carrying resistance to leaf rust and stripe rust.

Component 23.e. Coordination Activity 23.e.1. Intra- and inter- Objective communication and coordination (R. Park/ USyd) The Surveillance Advisory Panel (Supplemental Document 23.1) will:

1. Provide quality assurance of surveillance data

2. Facilitate surveillance activities (sample acquisitions, requests for race analysis by a third party, capacity building/ support, data sharing)

3. Support national program activities

4. Raise awareness of significant developments and provide advice (to be channeled through FAO)

5. Manage interactions with rust surveillance activities funded outside the Phase II proposal, to ensure complementarities and to prevent duplication

6. Decide on the composition of trap nurseries – annual review and input from other objective leaders

7. Provide guidance to the Objective Leader (Prof Park) in managing inter-objective coordination (e.g. using surveillance data to inform breeding, pre-breeding and seed systems strategies).

Funds are requested to allow the Objective Leader to convene regular meetings of the Advisory Panel via teleconference, to interact face-to-face with all participants within Objective 23, and also for periodic interaction with Leaders of other Objectives, to ensure the works progresses smoothly and that it is in line with the overall goal of the Phase II proposal.

Justification Directed and optimized mitigation of the threat of stem rust to resource poor farmers cannot be achieved without vigilant monitoring of the incidence and nature of stem rust in regions where this disease has the potential to cause yield loss. Success in achieving the top-level goal of the

161


project, “a world where the food and livelihood security of the world’s poor is enhanced through cultivation of wheat varieties with durable resistance to the cereal rusts”, will not be realized without first “knowing the enemy”. Indeed, most success in controlling stem rust and other cereal rust pathogens using genetic resistance has occurred in regions where active ongoing programs are in place to monitor stem rust incidence and to understand stem rust pathogen populations, and where these activities are closely aligned and integrated with pre-breeding, breeding and post-breeding activities. Understanding the occurrence and incidence of stem rust is fundamental to formulating and adopting appropriate national and international policies, directing investments in disease control, in implementing strategies in plant protection, plant breeding, and in establishing seed production systems that will serve the needs of poor farmers best.

The proposed activities will complement four independently funded cereal rust projects being undertaken by FAO staff in collaboration with other agencies including ICARDA, CIMMYT and the International Atomic Energy Agency. While the primary focus of these projects is broader than just surveillance (encompassing seed systems, policy support and contingency planning), rust surveillance is a component of each including: training; provision of funds to undertake surveillance; limited funding for infrastructure. Across all four projects, a total of 25 countries (Afghanistan, Armenia, Azerbaijan, Egypt, Eritrea, Ethiopia, Georgia, India, Iran, Iraq, Jordan, Kazakhstan, Kenya, Kyrgyzstan, Lebanon, Oman, Pakistan, Sudan, Sudan, Syria, Tajikistan, Turkey, Turkmenistan, Uganda, Uzbekistan and Yemen) have some activities related to cereal rusts. Close integration and complementarities between the entire project portfolio is facilitated through oversight by a single senior FAO staff member. Synergies with proposed Phase II activities include: use of alternative funds to support in-country surveys over a much wider geographical area; alternative funding of training events and workshops; alternative funding of infrastructure upgrades for race analysis. All activities, regardless of funding source, feed data into a single GCRMS and the resulting value-added information helps guide policy support and contingency planning.

This is the only Objective in the overall project that targets the stem rust pathogen, and it is the only initiative attempting to document and understand global variability in the wheat stem rust pathogen. Specifically, the information generated on the distribution of stem rust races, including Ug99, and the incidence and distribution of stem rust will be important in underpinning:

• Pre-breeding (Objective 26). Identifying potentially new and effective sources of resistance, whether it be among alien species or hexaploid wheat, depends on initial rust testing using characterized rust races, either in the greenhouse or in field rust nurseries. The precision with which new sources of resistance can be characterized (mapping, marker development) depends on accurate phenotypic data, which is in turn reliant on characterized rust isolates. Conversely, where new stem rust resistance genes are identified in Objective 26, germplasm carrying these genes will be used in characterizing stem rust races. The genes will also be entered into NIL production under Activity 23.d.2.

• Breeding (Objective 25). In the absence of perfect markers, greenhouse seedling or field based adult plant selection of an effective resistance gene or genes depends on using the correct rust race. The importance of this was clearly established in Phase I with the

162


identification of virulences for Sr24 and Sr36 in the Ug99 lineage in stem rust nurseries at Njoro.

• Activities aimed at increasing the uptake of resistant cultivars (Objective 21). The primary emphasis of developing the GCRMS in Phase I was to create a system that could report the distribution and nature of stem rust, and to integrate it with meteorological and other geo-referenced data, including socio-economic and agro-ecological attributes of resource poor farmers threatened by stem rust. Such integration provides the basis to predict stem rust migration and impact on farmers and the global economic system. The proposed follow-on activities described here will permit the expansion, development and enhancement of the emerging GCRMS into a fully operational monitoring system. The continued spread of Ug99, reaching or in close proximity to highly significant wheat production zones, highlights the critical need for a fully operational monitoring system. Wheat is the primary staple in this region, with per capita consumption rates amongst the highest in the world. The continued food and livelihood security of millions of resource-poor wheat farming families will depend on preparedness and appropriate national and international policies, investments and interventions.

This work will also provide guidance to the stem rust phenotyping activities planned under Objective 24, and will be instrumental in advocacy efforts under Objective 22.

II. Logframe Table

See next page.

163


Objective 23: Stem rust populations tracked and monitored



23.a. Global Cereal Rust Monitoring System (GCRMS)

23.a.1. Maintain and enhance the functional information platform and core databases for tracking and monitoring stem rust populations.

Core data bases populated with quality controlled rust survey data from at least 10 countries per year. (Sep 2011, recurring annually)

Automated / semi-automated data import tools and routines. (Sep 2012)

Customized analytical tools developed. (Sep 2013)

Five Years Accessible, up-to-date information on stem rust incidence and populations in 10 priority countries.

Ten Years Accessible, up-to-date information on stem rust incidence and populations in 30 priority countries.

Fifteen Years The GCRMS is the primary source of information relating to stem rust incidence and populations globally.

D. Hodson, FAO

23.a.2. Spatial data platform.

The Wheat Atlas internet-based data hub populated, with NARs data inputs and validation. (Jun 2012)

Five Years Data exchange through user oriented web portals rapidly affects policies that favor wheat economic productivity for small-holder farmers in developing nations.

Fifteen Years International efforts to mitigate and eliminate the effects to small-holder farmers against wheat stem rust are no longer limited by lack of ready access to germplasm, data, seed and knowledge

P. Kosina, CIMMYT, Mexico

164




23.a.3. Deliver timely and accurate information on stem rust populations via an expanded GCRMS.

A range of targeted information updates for stem rust available on a regular basis (i.e. web situation updates, bulletins, race frequency summaries, trap nursery summaries). (Sep 2011, recurring annually)

Five Years GCRMS information used routinely by national partners to guide decisions regarding control and management of stem rust in at least 10 countries.

Ten Years GCRMS information used routinely by national partners to guide decisions regarding control and management of stem rust in at least 30 countries.

Fifteen Years GCRMS information used routinely by national partners to guide decisions regarding control and management of stem rust globally.

D. Hodson, FAO

23.a.4. Leverage establish-ment of a Global Rust Reference Center (GRRC) by supporting race analysis and training

GRRC is established with significant investments from Denmark. (Sep 2013)

National Program Pathologists from at-risk countries are trained in pathotype (race) analysis. (Sep 2014, recurring annually)

Five Years GRRC is operating. Stem rust samples are received and analyzed in a timely and regular manner. After 5 years, GRRC operating costs are expected to be a regularized activity of the FAO.

Ten Years A new generation of rust pathologists from National Programs are trained in rust surveillance and pathotype (race) analysis.

The GCRMS includes regular high quality international race information generated by GRRC.

M. Hovmoller, Aarhus U

165




23.b. Surveillance.

23.b.1. Trap plot network support.

Pure and adequate seed of genotypes used in trap plots maintained and stored. (Sep 2011, recurring annually)

Seed distributed to all countries participating in trap plots nurseries. (Sep 2012, recurring annually)

Five, Ten and Fifteen Years Trap plot nurseries used in global rust surveillance comprise or include standard reference genotypes.

K. Nazari, ICARDA

23.b.2. Expand and enhance national capacity to undertake rust surveillance.

National survey teams established and contributing annually to national and global cereal rust monitoring systems in at least 10 countries. (Sep 2011, recurring annually)

Technical backstopping provided to national focal points and/or survey teams in at least 10 countries per year (Sep 2011, recurring annually)

Stem rust surveillance in regions of strategic importance but not covered by core activities. (Sep 2011, recurring annually)

Five Years An effective network of surveillance teams for stem rust is supported in 10 priority countries and contributing to the GCRMS annually.

Knowledge of stem rust distribution and incidence and principal races present in non-target regions of strategic importance if stem rust becomes a problem.

Ten Years An effective network of surveillance teams for stem rust operating in 30 priority countries and contributing to the GCRMS annually.

Fifteen Years National agricultural program systems are undertaking routine annual stem rust monitoring.

K. Nazari, ICARDA

23.c. Pathogen characterization.

23.c.1. Stem rust race analysis backstop-ping ARIs.

Selected key stem rust samples or isolates are race typed by ARIs. (Sep 2011, recurring annually)

Five Years Knowledge of stem rust races present in regions of strategic importance.

Y. Jin, USDA

T. Fetch, AAFC

166




23.c.2. Stem rust race analysis in country.

Pure and adequate seed of genotypes used as differentials maintained, stored and distributed. (Sep 2011, recurring annually)

National rust laboratories in at least 5 countries equipped to undertake race analysis (Quick sets and/or full race analysis). (Sep 2012, recurring annually)

Five Years Routine standardized annual stem rust race surveys established in at least 5 developing countries, and data are incorporated into GCRMS.

Ten Years Routine standardized annual stem rust race surveys established in at least 10 developing countries, and data are incorporated into GCRMS.

Fifteen Years Routine standardized annual stem rust race surveys are conducted in countries representing all major wheat growing regions, with data incorporated into GCRMS.

K. Nazari, ICARDA

R. Park, U Syd

23.c.3.

Targeted surveillance of barberry for stem rust.

Preliminary surveys of barberry conducted in Kenya (Jin), Uzbekistan and Turkey (Park) have established the existence of aecial infections by a form of the stem rust pathogen Puccinia graminis. (Nov 2011, recurring 2012 and 2013)

Five Years Role of barberry in the evolution of Ug99 and variants is more understood.

Ten Years Ug99 and other stem rust races are better controlled due to enhanced knowledge of relationships with the alternative host in East Africa and other at-risk countries.

Fifteen Years stem rust is better controlled due to understanding of the alternate host, barberry.

Y. Jin, USDA

23.c.4.

Stem rust fingerprint-

International consensus on a core panel of informative SSR markers for fingerprinting stem rust isolates. (Sep 2012, recurring annually)

Five Years Insight into the global genetic diversity of the wheat stem rust pathogen is obtained.

R. Park, U Syd

167




ing. Selected key stem rust isolates fingerprinted with SSR markers. (Sep 2011, recurring annually).

23c.5. Stem rust molecular diagnostics.

Up to 20 key stem rust isolates sequenced to a depth of about 20X. (Sep 2011, recurring annually)

Five Years The current stem rust SNP database is expanded, allowing the development of rapid molecular diagnostic tools for the identification of the major races groups/lineages worldwide.

L. Szabo, USDA

23.d. Host charac-terization.

23.d.1. Host R gene determin-ation.

R gene determinations in global wheat germplasm, at least 50 cultivars per year. (Sep 2010, recurring annually).

On request, marker genotyping for key R genes of host tissue from stem rusted crops. (Sep 2011, recurring annually)

Information on R genes present in cultivars incorporated into Wheat Atlas. (Sep 2011, recurring annually)

Five Years R genes in wheat genotypes from at risk countries are known.

Ten Years Detailed understanding of stem rust R genes in all major wheat genotypes.

Fifteen Years Geographic distribution and graphical representation of R genes in relation to stem rust race distribution in GCRMS so to moni-tor risk of R gene breakdown (Activity 23.a).

R. Park, USyd

K. Nazari, ICARDA

P. Kosina / CIMMYT Mexico

23.d.2. Genetic stock development.

Up to 35 cataloged stem rust resistance backcrossed into a common genetic background. (Sep 2011, recurring annually)

Five Years Homozygous NILs (BC5) developed, increased and distributed to at least 10 countries.

Ten Years Utility of NILs as greenhouse differential genotypes and field trap plot genotypes assessed in all major wheat growing regions.

R. Park, U Syd

168




Fifteen Years A single core set of NILs is used internationally for both greenhouse seedling virulence assays and field trap plots.

23.e. Coordination.

23.e.1. Objective 23.

Objective 23 outputs harmonized. (Sep 2011, recurring annually)

Intra- and inter-objective (DRRW) harmonization. (Sep 2011, recurring annually)

Five Years Successful completion of all Objective components and activities and integration of all outputs with overall project.

R. Park, U Syd

Objective 23 Advisory Panel

169


III. Detailed Work Plan

Component 23.a. Global Cereal Rust Monitoring System (GCRMS) Activity 23.a.1. Maintain and enhance the functional information platform and core databases for tracking and monitoring rust populations (D. Hodson/FAO) This Activity will build directly upon activities undertaken in Phase I, in which core databases and an information platform for stem rust are being developed. This Activity is managed by the IFP based at FAO with strong links to objective and project partners. Primary data management is undertaken through the use of commercial relational database management systems. Initially, this was achieved using a MS Access database at CIMMYT, but work is in progress to migrate this onto an Oracle platform at FAO headquarters in Rome. Independently funded emerging linkages with the Global Reference Center for Yellow Rust (GRC-YR) and the University of Aarhus in Denmark may result in a synchronized SQLServer database in Denmark in the future.

The GCRMS is planned to encapsulate core databases consisting four major thematic areas, namely; (1) field survey data, (2) country information, (3) race data and (4) trap nursery (plot) information. In addition, secondary spatial data are a vital component of the system. These secondary data include wheat distribution, crop growth stage, variety composition and characteristics, climate and demographic data. Updates and improvements to several of these secondary datasets will be undertaken in Activity 23.a.2 (Wheat Atlas data platform). All data within the system have geo-referencing information at the site, region or country level depending on the nature of the data. Geo-referencing permits direct linkage to a commercial GIS (ArcGIS from ESRI) platform managed by the IFP at FAO headquarters.

Initial attention during Phase I focused on the management of field survey data i.e., incidence and severity of stem rust. An established system of standardized field surveys and geo-referenced data collection was put in place (BGRI protocols manual, 2009). These standardized field surveys will be continued in Phase II, but on an expanded scale. This will be achieved via an expansion in the network of NFP’s and national surveillance teams (Activity 23.b.2). Based on experience obtained in Phase 1, a modified operational schema, (Supplemental Document 23.1), will be implemented to permit more efficient data and information exchange. New primary field data will be managed in the existing relational databases developed in Phase I. Quality control of survey data will be undertaken at two levels, nationally by the NFP and internationally by the Surveillance Advisory Panel and the IFP.

Data import routines will be improved in Phase II. The current system relies on survey data entered into non-standardized MS Excel spreadsheets by NFP’s and sent to the IFP at FAO, or direct transfer of paper survey forms to the IFP. The increasing volumes of field data envisaged in Phase II will require a more efficient and streamlined system to be developed. A customized data entry tool will be created that will allow NFP’s to enter and upload field data in a rapid and standardized way. For practical reasons, this data entry tool will be a stand-alone tool rather than a web-based tool. The tool will permit quality control at data entry, as user selection of standard options will be the preferred option for data entry. Data transfer to international central databases will be made using standard transfer protocols e.g. xml. Existing tools such as Phytophthora.exe developed by Aarhus University might form the basis of development (http://www.agrsci.org/ny_navigation/nyheder/new_publication_phytophthora_exe_ver_2_0_pc_

170


program_for_the_storage_and_upload_of_phytophthora_infestans_isolate_information_to_the_eucablight_database_user_manual).

Options for the use of “crowd-sourcing” tools and methods will be explored with the aim of collecting early information on any emerging threat from stem rust. These techniques will compliment, but not replace formal surveys. A strong emphasis will be placed on ensuring the validation of any data received using crowd-sourcing. The network of National Focal Points will be informed of any emerging situations and national wheat experts used to validate any field reports. Existing technological options that offer quick, cost effective data transmission (e.g., sms) will be prioritized for implementation on a case study basis.

Other core databases will be expanded in Phase II. Of critical importance in this context will be the stem rust race data. It is envisaged that in Phase II reliance on ARI’s to undertake race analysis will diminish and some national laboratories will also produce reliable race analysis data (activities 23.c.1 and 2). Existing relational databases developed in Phase I will be used to manage this new data. A data entry tool similar to that already described for field survey data (or a module within a single tool) will facilitate the entry of standardized data. Quality control of race analysis data will be undertaken by the Surveillance Advisory Panel, with the Surveillance Coordinator and the objective team leader playing key roles. Enhancements will be made to the race analysis database as more information is obtained about host R genes (Activity 23.d.1). The aim will be to incorporate race composition in specific areas with host R gene composition in important cultivars.

During Phase I there was no explicit focus on trap plots, but they were implemented under separate funding. The value of trap plots in surveillance is recognized by the provision of support for trap plot networks included in Phase II (Activity 23.b.1). The data generated from trap plots will form an important component of the overall GCRMS. However, data from trap plots requires careful interpretation and expert validation by pathologists. As a result, raw primary trap plot data will be managed and analyzed by the Surveillance Coordinator and only synthesized and validated interpreted data will be stored in the GCRMS.

Increased analytical capacity will be developed through the development of customized tools and modules as part of the GIS platform managed by the IFP at FAO. As much as possible, these activities will leverage and build upon existing tools and datasets. Examples would include components that already form part of DLIS e.g., climatic data (current and forecasts) and associated automatic capture and management of these data within an ArcGIS / Oracle environment. In addition, options to modify existing disease risk models will be evaluated. The risk assessment approach already used for potato late blight (http://www.planteinfo.dk/BlightMgmt/BlightMgmt.asp?pi_menu=1&item_id=647&appl=647&_sessionid=bjTakJ5GL52&_server=172.23.173.222&_port=5005&pi_menu=1&Fuzz=127), driven by daily meteorological data, is one potential candidate for evaluation and modification. Other similar models for foliar diseases including rusts will be evaluated. There is no intention to develop an entirely new complex risk model for stem rust, but if value added information can be gained from modification of existing modeling approaches this will be incorporated into the GCRMS.

The Activity described here is fundamental for the efficient integration and data management of surveillance data collected or created under Objective 23. This includes field survey, race

171


analysis, trap plots and host R gene determination. It relies on regular and effective field surveys and sampling undertaken by national surveillance teams (Activities 23.b.2 and 3). This Activity forms the foundation for all subsequently derived information products relating to stem rust populations (Activity 23.a.3).

Activity 23.a.2. Wheat Atlas data platform (P. Kosina/ CIMMYT) Whilst pathogen information is a fundamental component of the GCRMS, the integration of broader wheat sector data at the national level is vital in the interpretation of rust incidence and threat. Knowledge of variety composition and characteristics, combined with wheat growing environments are particularly important.

This Activity will capitalize on existing wheat data platforms and applications developed by CIMMYT. As a result of CIMMYT’s global network of national partners contributing information via international trials, the center holds a unique database relating to wheat germplasm performance and traits. All of this information is managed via the International Wheat Information System (IWIS), a comprehensive database management system that is a component of ICIS (International Crop Information System). In addition to IWIS, CIMMYT has also created a web-based application called the Wheat Atlas. This application has been created in response to the need to consolidate and summarize the wealth of wheat sector information held by CIMMYT and partners into a rapid access form. The Wheat Atlas consolidates country-level wheat sector data covering; production, distribution, growing environments, variety information, production constraints, markets, demographics etc into a one-stop fast access data resource. Information is delivered in the form of maps, summary tables and user-generated graphs. All of the user interfaces are linked into underlying regularly updated databases. The Wheat Atlas is currently available as a fully functional beta pre-release.

Within Activity 23.a.2, three major sub-activities will be undertaken:

(i) tight linkages between the existing IWIS database and the graphical interface provided by the Wheat Atlas will be developed and curated. Variety information will be updated by creating a linkage between variety releases in each country with originating lines from IWIS. Analysis of international trials on a site / country level over available years will be undertaken. Resulting summaries on specific traits and trends, especially rusts, will be uploaded to the wheat atlas. This will permit rapid access to country-level summary information regarding wheat germplasm performance and traits in international trials. Rust-related information will be included as a high priority, including country summaries on the reaction of varieties and lines screened at stem rust hot-spots in East Africa.

(ii) further development will be undertaken on the Wheat Atlas application, including; improved functionality, expansion / update of existing information and maintainance of the application platform . Spatial information will continue to be a vital component of the Wheat Atlas with improvements in the wheat distribution, varietal distribution and characteristics, and socio-economic aspects given a high priority. Close existing linkages between CIMMYT’s GIS unit and the Crop Research Informatics Laboratory (CRIL) will facilitate this sub-Activity.

(iii) integration of the Wheat Atlas platform with the information systems being developed in Activity 23.a.3. The overall aim is that updated pathogen information will be linked to

172


more detailed wheat sector information at the country level. Geographical linkages are the mechanism by which this will be achieved. The desired outcome is that any user should be able to rapidly obtain information regarding current stem rust status in a specific country and seamlessly access relevant and detailed wheat-sector information for the country of interest.

Activity 23.a.3. Deliver timely and accurate information on stem rust populations via an expanded Global Cereal Rust Monitoring System (D. Hodson/FAO) The core databases described in Activity 23.a.1 and the Wheat Atlas data platform (Activity 23.a.2) are the foundation for the derived information products to be generated under this Activity. This Activity builds upon and expands activities on-going in Phase 1. A core set of information products have been developed, or are under development, by the IFP based at FAO. The core information products include: web-based situation updates; a web mapping tool; a regular stem rust bulletin; and race summary information. All of these will be continued, expanded and improved during Phase II. An additional information component will be included to provide seasonal updates on the synthesized information coming out of the trap plots.

In Phase I, the initial focus was on the development of a web mapping tool. The resulting product “RustMapper” (http://www.cimmyt.org/gis/rustmapper/RustMapper_Web.html or http://www.cimmyt.org/gis/rustmapper/), based on a Google Earth platform, has proven to be a popular and effective means of presenting timely information. “Rustmapper” includes information on wheat distribution, recent field survey data, updated wind trajectories and country summary information. Continuation of “RustMapper” in Phase II is envisaged with expansion to include close integration with the data-rich content on wheat resulting from Activity 23.a.2 and also trap plot data. Despite success with “RustMapper”, there is a clear need to have a simpler web mapping component. Bandwidth issues and in some instances government blocking of Google mapping tools are the primary concerns. This simpler mapping component might utilize pdf technology (an option already implemented by the USDA CDL http://www.ars.usda.gov/SP2UserFiles/ad_hoc/36400500Cerealrustbulletins/2009wsr.pdf) or be a customized web mapping tool based on existing components at FAO (e.g. the Locust mapper component of DLIS or the KIDS system http://kids.fao.org/glipha/index.html). Different options will be evaluated.

Race analysis information is critical to guide breeding efforts and germplasm deployment strategies. The aim in Phase II will be to develop a set of information products that give a clear picture of the stem rust race composition in different areas, give access to virulence/avirulence profiles, and also ultimately link that to the R gene composition of leading cultivars. For yellow rust, the EuroWheat project spearheaded by the University of Aarhus in Denmark has already developed rapid access graphical display of races and frequencies over time for several European countries (http://www.eurowheat.org/EuroWheat.asp). Through emerging linkages to the University of Aarhus group, similar products will be developed for stem rust using existing ASP/Java script applications. These are planned to include map-based graphic presentation of country race data linked to virulence/avirulence profiles and simple query interfaces. Ultimately, there will be a link to the R gene profiles of major cultivars. All of these tools will be database driven and rely on Activity 23.a.1.

173


The web presence for the pathogen tracking objective (named Rust SPORE) is being established at FAO, this is based on the successful Desert Locust “Locust Watch” site (http://www.fao.org/ag/locusts/en/info/info/index.html). This leverages customized open-source content management systems developed at FAO. Continuation of this system in Phase II may occur, but other options will be explored e.g., the content management system used by the Eurowheat project. There is a clear opportunity to try and establish linkages with the emerging and independently funded GRC-YR with the ultimate goal of having a single global information portal for both stem and yellow rust. This situation would be greatly facilitated by the use of common platforms and content management systems, but is not an absolute requirement.

Activity 23.a.4. Leverage establishment of a Global Rust Reference Center by supporting race analysis and training (M. Hovmoller, Aarhus University) The emergence of stem rust Ug99, as well as a yellow rust genotype that is adapted to higher temperatures, calls for immediate and coordinated multi-national action to delay and alleviate the consequences of rapidly spreading epidemics of the wheat rust. Recently, many wheat experts gathered in Aleppo, Syria, and proposed to establish an international repository laboratory for all three wheat rust fungi as efforts to allow more rapid responses to existing recent rust incursions and to pre-empt new ones http://www.eurekalert.org/pub_releases/2009-09/bc-twe091009.php. The proposed global rust reference laboratory, which was recommended in Aleppo at the Borlaug Global Rust Initiative (BGRI) Coordination Conference, will assist in tracking pathogen migration pathways and evolution and will house a unique collection of a large number of races of stem (black) rust, yellow (stripe) rust, and brown (leaf) rust in a secure containment facility.

Principal objectives of a Global Rust Reference Center • Establishment of a facility that can receive samples of stem rust, leaf rust and yellow rust

throughout the year and facilitate a global early warning system for wheat rusts

o Pathogen fingerprinting to understand and track regional and global dispersal pathways

o Assessment of pathogen virulence and aggressiveness and identifying wheat varieties at immediate risk

o Risk analyses for wheat rust adaptation to changing climates

• Securing unique pathogen resources for future resistance breeding and research

• Facilitating research and training in wheat rust epidemiology, population genetics and evolution

The Global Reference Center should contain scientific expertise across a range of disciplines such as rust pathology, population (and evolutionary) genetics, epidemiology, molecular biology, and bioinformatics as well as statistics and database development. Close interactions with wheat geneticists of Universities in developed countries, national research institutes and CGIAR-centres are expected.

Aarhus University, Flakkebjerg, Denmark is home to the Yellow Rust Global Reference Center, led by stripe rust pathologist, Dr. Mogens Hovmoller and is best equipped to serve as a Global Reference Center for all three rusts. The establishment of a Global Reference Laboratory at Aarhus University, requires new quarantine facilities and staff recruitment. To become

174


sustainable in the long term, a considerable portfolio of activities and associated funding must be ensured to reduce vulnerability due to potential changes in staff, management and political awareness. The scientific input must be sufficient to generate new innovative research, which will need external funding, as well as ensuring sufficient training capacity. GRC will build on the existing Global Reference Centre for yellow rust, which was established in December 2008 via a Memorandum of Understanding between CIMMYT, ICARDA and Aarhus University (recommended by Nobel Peace Laureate, Dr. Norman Borlaug).

Funds from Denmark will be leveraged to establish a stem rust reference center at Aarhus University as a part of a Global Rust Reference Center (GRRC). The DRRW component will support training in race analysis for pathologists from developing national programs. This initiative will result in the following expected outputs:

• Race analyses of limited and strategically targeted stem rust isolates from National Surveillance efforts.

• Junior scientists and graduate students trained in wheat rust pathology and genetics

• Support innovative research securing long-term prevention of wheat rust epidemics

• Annual report including feed-back to national plant health authorities and institutions from where samples were submitted

Component 23.b. Surveillance Activity 23.b.1. Trap plot support (K. Nazari/ ICARDA) In most of the countries affected or at immediate risk of Ug99, stem rust has appeared in warm areas. Many current stem rust genotypes used in trap nurseries require vernalization or, due to day-length sensitivity, final disease assessment of stem rust infections (on stems) is not possible. Although several laboratories use the North American differential set (NA), most use a combination of NA, Stakman and other tester genotypes and therefore the number and type of differential genotypes and Sr-genes varies. Because of differences between differential sets and occasional impurity of differential genotypes, interpretation of surveillance data between countries is difficult. To eliminate these problems, ICARDA will undertake central seed multiplication and distribution of wheat genotypes for use as trap plots. The importance of ensuring purity of these stocks cannot be understated, and the amount of work involved in maintaining pure and adequate quantities of seed of each is substantial. This will be achieved by:

• Collecting current genotypes used as trap plots. A stem rust race analysis set and stem rust monogenic lines were obtained from Dr Jin (USDA, CDL-Minnesota) and Dr Fetch (AAFC) in 2008.

• Large-scale seed increase of differential genotypes at ICARDA where both spring and winter type and/or day-length sensitive Sr-genotypes can be grown.

• Distribution of seed following clearance by ICARDA’s seed health laboratory.

Once adequate quantities of pure seed are available, current and future stem rust trap nurseries will be revised by the Surveillance Advisory Panel and a new set of Sr-genotypes comprising the most important Sr-genes in spring type and or day-length insensitive backgrounds, selected commercial mega cultivars, and known sources of APR gene/s to be used as an international trap

175


nursery will be established. The International Stem Rust Trap Nursery (ISRTN) will be provided to rust laboratories and NARS. Health Certificates will be issued by ICARDA’s seed health laboratory. The nursery will be sown in two 1-meter rows in rust-prone areas in each country and field scoring will be undertaken using a modified Cobb scale. Key Sr-genes (Sr31, Sr24, Sr36 and Sr38) and/ or commercial cultivars grown in regions will be planted as large breeding plots (4 X 4-meter rows) in research stations every year. Geo-referenced information of these locations will be documented and virulence patterns will be monitored every year at each location. Frequencies of virulence will be determined over the years and locations.

Activity 23.b.2. Expand and develop national capacity to undertake rust surveillance (K. Nazari/ ICARDA) This Activity builds directly upon activities on-going in Phase I undertaken by FAO and ICARDA. The aim is to expand the network of functional national surveillance teams contributing annually to the GCRMS. This Activity is a fundamental requirement for the entire GCRMS. Existing protocols established at FAO will be used to obtain officially nominated NFP’s from priority countries. This involves the identification of suitable candidates through in-country discussions, followed by high level approaches to the national governments.

Experience from Phase I indicated the clear need to support the national surveillance teams in a variety of ways. Technical support for field pathology, sampling, trap plot management and scoring, and use of standardized survey protocols implemented by the DRRW is an on-going requirement. This will be achieved by regular field visits to partner countries by both the Surveillance Coordinator (Nazari) and where needed the IFP. Direct participation in field surveys and in-field training will be the mode of operation. Supporting field information materials will also be produced (or modified from existing materials) and distributed. These may include rust identification guides and photo guides for trap plot genotypes.

Because rust epidemics can develop rapidly, and high rust levels can threaten neighboring regions, monitoring rust levels in regions where wheat may not be an important crop or that are not specifically targeted for surveillance can be important. For example, the initial detection of Ug99 in Uganda, a country that produced only 12,000 tonnes of wheat in 2003, was of enormous significance. Furthermore, it is well known that wheat rust pathogens undergo intercontinental long distance dispersal, presumably either by high altitude winds (Watson and de Sousa 1982) or by human mediated means (Wellings 2007). Because supporting stem rust surveillance in all wheat growing countries is not practicable, funding is included to permit travel by the Surveillance Coordinator to “non-target” regions should the need arise.

In many countries, there is still a need for direct support if any field surveys are to be undertaken in a regular and timely manner. Frequent problems include a lack of access to vehicles at critical times, and an absence of resources to cover basic survey costs (e.g. vehicle fuel/ maintenance). The reality on the ground is that to initiate a fully functional surveillance network some of these costs will need seed funding. Raising awareness among national policy makers to prioritize these activities and commit national budgets is seen as essential for long-term sustainability. FAO has a comparative advantage to undertake this political lobbying. Declining direct support for surveys from the Phase II proposal is envisaged.

To ensure information exchange and opportunities for learning, it is anticipated that regular annual meetings of the NFP’s will rotate between different regions (eastern Africa, Middle East,

176


Central Asia, South Asia, North Africa). It is further anticipated that such meetings will piggy back on events funded by other projects and, if possible, include a travelling workshop component.

Component 23.c. Pathogen characterization Activity 23.c.1. Stem rust race analysis backstopping ARIs (Y. Jin/ USDA; T. Fetch/ AAFC) As valuable as trap nurseries are in providing an indication of the presence of a disease in a region, plus initial information on the specific individual virulences present, they provide little or no information on virulence combinations and do not provide any indication of what race or races are present. The only way of doing this at present is to undertake bioassays under controlled conditions, using sets of differential testers (race analysis). Race analyses of cereal rust pathogens have been undertaken in many countries using more-or-less standardized methodologies of inoculation, incubation and then “reading” the sets (data recording).

In Phase II, Drs Jin and Fetch will continue to provide technical backstopping for countries undertaking race analysis (i.e. verification of putatively new races), and undertake limited and strategically targeted race analysis for countries that do not. Rust samples collected from crops, trap plots and other experimental plots will be forwarded to Drs Jin and Fetch between October and March using protocols established in Phase I. Samples will be accompanied by information regarding the location (preferably with GPS co-ordinates), date of collection, the person who collected it, source (crop, experimental plot, etc), and the cultivar did it come from (if known). Up to two single pustule isolates from up to 60 samples per year (30 each) will be established from each sample, increased and applied to the standard North American stem rust differential set for race determination. The information generated for each sample will be returned to the person who submitted it, and all data provided to the IFP at FAO for inclusion in GCRMS.

The Surveillance Advisory Panel, led by the Coordinating Pathologist (based at the U. of Sydney), will coordinate movement of samples to the North American laboratories, and provide data quality control for pathogen/host data sent to the central data platform of the GCRMS.

Activity 23.c.2. Stem rust race analysis in-country (K. Nazari/ ICARDA; R. Park/ USyd) Ongoing issues associated with quarantine restrictions on the exchange of viable rust isolates between countries have severely hampered efforts to gain insight into the diversity of stem rust races in many countries. While AAFC and USDA will continue to offer limited race analysis backstopping that is constrained by seasonality and capacity, it will be vital in Phase II to continue to develop in-country race analysis capability, both in terms of skills and infrastructure. The most efficient and likely sustainable way of doing so will be to identify countries in which the need for race analysis is greatest and to train one or two key personnel. The selection process will be undertaken by Dr Nazari in consultation with NARs, and training of at least 3 months duration will take place at icarda (Dr Nazari), USyd (Prof Park), USDA (Dr Jin), AAFC (Dr Fetch) and/or UFreeState (Prof Pretorius). Skills in race analysis and operational infrastructure exist in Syria (ICARDA), India, Iran, Ethiopia and Turkey and there are funds available in some projects being managed by FAO for additional infrastructure upgrades in these and other countries. Resources for training in race analysis and infrastructure in Kenya and Ethiopia are allocated under Objective 24. Allocation of limited funding to allow Turkey (Mr Zafer Mert) and India (Dr Mohinder Prashar) to undertake race analyses are included. These funds will

177


supplement existing funding and allow more extensive surveillance, sampling and race analysis in each country.

Because of the difficulties associated with developing in-country capacity in race analysis in all countries that are under threat from Ug99, efforts to obtain preliminary baseline information on the incidence of stem rust plus the virulence of isolates for the key resistance genes Sr24, Sr31 and Sr36 initiated in Phase I will continue. The intention is to obtain preliminary baseline information on the incidence of stem rust plus the virulence of isolates for the key resistance genes Sr24, Sr31 and Sr36. This will be achieved using protocols developed in Phase I and training provided at two baseline survey meetings (ICARDA Headquarters Aleppo Syria, March 2008; DWR Shimla India, November 2008). NFPs in each of the 18 countries represented at these meetings will be encouraged to conduct low resolution surveys and to collect samples of stem rust if the disease is found. Samples will be stored individually after a bulk comprising a small sub-sample from all samples is prepared. The bulk will then be used to inoculate duplicate ‘Quicksets’, comprising crucial differential genotypes carrying the resistance genes Sr24, Sr31 and Sr36. Where virulence for any of these genes is detected, individual stored samples will be forwarded to Dr Jin or Fetch to determine the race(s) present.

In addition, should crops with heavy stem rust infection be found during the low resolution surveys, plant tissue will be forwarded to Australia for marker analysis using “perfect” markers for important stem rust resistance genes including Sr24 and Sr31 (in Australia). Host resistance gene detection (by DNA markers) is an indirect means of postulating the virulence(s) carried by stem rust at a given survey point.

Where rust pathogen or host tissue samples are to be forwarded to ARIs, the Surveillance Advisory Panel, led by the Coordinating Pathologist (based at the U. of Sydney), will provide coordination to ensure quarantine restrictions are adhered to, to prevent duplication, and to provide data quality control for pathogen/host data sent to the central data platform of the GCRMS.

For at least the next five years, there will be differences in the genotypes used for field trap nurseries and for greenhouse seedling race analyses (full race analyses and ‘Quickset’ analyses). The increase and distribution of pure seed for trap plots proposed to be undertaken by ICARDA will therefore be extended to include seed of differential genotypes used for race determination. The genotypes to be used and distributed will be based on discussions initiated at Obregon in March 2009 and being coordinated by Dr Fetch. Once pure seed of the agreed set is available, it will be forwarded by Dr Fetch to Dr Nazari, who will then initiate bulk increase and distribution to countries who wish to undertake race analysis.

Activity 23.c.3. Targeted surveillance of barberry for stem rust infection (I. Lowe / UC Davis, Y. Jin / USDA) Preliminary surveys of barberry conducted in Kenya (Jin), Uzbekistan and Turkey (Park) have established the existence of aecial infections by a form of the stem rust pathogen Puccinia graminis. While it is no clear if some or all of these infections are actually due to the form of P. graminis that infects wheat (P. graminis f. sp. tritici), it nonetheless demonstrates clearly that barberry continues to play a role in the life cycle of P. graminis, although likely minor, in at least some regions. This work will involve more extensive surveys of barberry in eastern Africa and possibly neighboring regions, and analyses of any aecial infections found at the USDA Cereal

178


Disease Laboratory to establish what f. spp. are present, and if P. graminis f. sp. tritici is found, what races are present.

The work undertaken under this Activity will utilize standard survey procedures (as outlined under Activity 23.b.2) and greenhouse procedures for rust infections (essentially as outlined under Activity 23.c.1). Surveys of Ethiopia and Kenya, and also possibly Zimbabwe and Malawi, will be undertaken by Dr Jin and Mr Lowe in 2012 and 2013. Where active aecial infections are found, all information will be recorded and incorporated into the GCRMS. Samples will be forwarded to CDL Minnesota, where initial pathology tests will be conducted in which aeciospores are used to infect a range of cereal genotypes. This will allow an initial indication of whether or not the isolate or isolates present can infect cereals, and if so, will permit the establishment of uredinial cultures from which further race analysis using standard differential genotypes can be made.

Activity 23.c.4. Stem rust fingerprinting (R. Park/ USyd and others) While race analyses using greenhouse seedling assays have and will continue to provide the most important information to underpin genetic approaches to rust control, new DNA-based fingerprinting methods provide: an alternative in situations in which race analyses cannot be made; and for the first time, a means of gaining a deeper understanding of stem rust pathogen variability.

If race analyses cannot be made (e.g., samples are collected outside the time window during which North American laboratories can receive viable isolates), stem rust urediniospores will be preserved in ethanol and sent to USyd for SSR fingerprinting. Protocols to extract DNA from dead rust urediniospores were developed at USyd several years ago, and an import permit allow importation of dead rust spores from any country at any time during the year was obtained from the Australian Quarantine and Inspection Service. Protocols to extract DNA from stem rust urediniospores are well established as are protocols for SSR fingerprinting (e.g. Visser et al. 2009). Fingerprinting isolates in this way will provide an indication of the potential presence of members of the Ug99 lineage. The distinctive SSR fingerprint of Ug99 and other races within this lineage provide a means by which stem rust isolates can be shown not to be related to the Ug99 lineage. It should be noted however that these tests do not provide definitive proof of the actual race of a stem rust isolate, and nor do they allow conclusions to be made about the virulence of isolates, which must be determined by seedling assays. On request, up to 200 isolates will be fingerprinted using this approach, and brief reports returned to contributing scientists following vetting by the Surveillance Advisory Panel.

In addition to assessing relatedness to the Ug99 lineage, the results will be used to build an understanding of genetic variability within global populations of the wheat stem rust pathogen. To achieve this, the results will be coupled with those generated from existing historical stem rust collections in Australia, North America (Dr Szabo), South Africa (Prof Pretorius) and India (Dr Prashar). Studies of genetic variability within Australian stem rust populations are being funded independently by the Australian Grains Research and Development Corporation, of Indian populations by the Australian Centre for International Agricultural Research, and in the USA by the USDA. This work will also include a critical appraisal of the nature of stem rust occurring on durum wheat in countries including Ethiopia. Any differences between the stem

179


rust populations occurring in durum wheat compared with bread wheat will have important implications in developing breeding strategies for each crop.

Activity 23.c.5. Stem rust diagnostics [L. Szabo/ USDA, R. Park / USyd] The availability of a genome sequence of P. graminis f. sp. tritici (http://www.broadinstitute.org/annotation/genome/puccinia_group/) provides a new powerful resource for genetic analysis and development of molecular diagnostic tools. Seven isolates of P. graminis f. sp. tritici have also been sequenced using Next-Generation technologies (Illumina) resulting in a PgtSNP database of over 1 million loci (Cuomo, Sakthikumar, Pretorius, and Szabo, unpublished data). This set includes: two North American isolates (75-36-300-3, race SCCLC; 78-21-BB463, race DFBJC); Ug99 (04KEN156, race TTKSK); three members of Ug99 lineage (06KEN19v3, race TTKST; 07KEN24-4, race TTTSK; UVPgt55, race TTKSF); and an unrelated isolate from Yemen (06YEM34-1, race TRTTF).

Current DNA sequence data of P. graminis is focused on the Ug99 lineage and needs to be expanded to include representative races/lineages from around the world. Currently, USDA contains the largest worldwide collection of live isolates of P. graminis f. sp. tritici and continues to actively build this collection. Standard protocols developed at the USDA-ARS-CDL for increasing isolates and extracting DNA will be used. Illumina sequencing will be done through a core sequencing facility, such as Broad or National Center for Genome Resources, using paired-end reads of at least 70 bases. USDA-ARS-CDL has ongoing genome sequencing projects with both of these facilities. Given that the P. graminis f. sp. tritici is dikaryon (n+n), a minimum of 20X sequence coverage will be done for a core set of 30 isolates. Total genomic DNA will be used initially for library construction and sequencing. As methods become available for enrichment of genomic coding regions, these methods will be explored. Next-Generation technologies and methods for data analysis are rapidly evolving and up-to-date technologies/methods will be used as this project moves forward. The overall goal will be to sequence between 50 and 100 P. graminis f. sp. tritici isolates.

A real-time TaqMan PCR assay is currently being developed for Ug99 lineage (Crouch and Szabo, unpublished data). The concept for this assay is to develop a suite of primers/probes to 5 or 6 different loci based on the current SNP data set. At present four primer/probe sets have been developed and this set is able to distinguish between Ug99 lineage and all North American isolates tested (>70). In addition, only three isolates in a worldwide collection test positive with this assay. Based on the current PgtSNP database, we expect to be able to develop primer/probes sets, which will be able to identify individual members of the Ug99 lineage. As the Pgt SNP database expands, additional primers/probes sets will be developed in order to identify the major race groups/lineages in the P. graminis f. sp. tritici population as well as important new race groups/lineages. Development of this assay will allow for the rapid identification of specific race groups/lineages. This assay will greatly enhance the current diagnostic system by being able prescreen collections to reduce the number that will need to be pathotyped and confirm results from pathotyping.

The proposed work is based on sequencing about 20 isolates of Pgt. Should the cost of sequencing go down over time (as most scientists predict), the number of isolates sequenced will be increased and it may be possible to expand work on developing primers/probes for the real-time PCR assay. At this point, it is estimated that a 20X (~3Gb) depth of sequencing will be

180


undertaken for each isolate. This is a conservative estimate, given the complexity of the Pgt genome and the fact that it is a dikaryon. The isolates that have been sequence to date have been sequenced to a depth of >100X.

Component 3.d. Host characterization Knowing the distribution and nature of stem rust races is of fundamental importance in guiding pre-breeding and breeding for resistance. This information is also important in the post-release management of stem rust, but its value is significantly lower in the absence of knowledge of the stem rust resistance genes present in wheat varieties under cultivation. Combined, knowledge of race distribution and of the resistance status of cultivars allows risk assessments and also the threat of new races to current production practices. Establishing resistance status is also an important initial step in identifying new sources of rust resistance in hexaploid wheat germplasm.

Activity 23.d.1. Host R gene determination (R. Park/ USyd; K. Nazari /ICARDA) The presence of known seedling resistance genes in germplasm can be postulated with considerable accuracy using multipathotype tests (Loegering et al. 1971, Browder 1973). In this procedure, characterized rust races are used to test germplasm under greenhouse conditions. Using the principal of the gene-for-gene hypothesis (Flor 1956), the pattern of susceptibility/ resistance to an array of races on a particular genotype is used to postulate what seedling genes are present. The methods involved in inoculating seedlings, recording data, and postulating the resistance genes present are well established (e.g. Pathan and Park 2007).

To better understand geographical distribution of rust resistance genes in the major wheat-growing areas, seed of commercial cultivars grown in countries affected or at risk of Ug99 will be obtained and multiplied, either at ICARDA or at USyd (representative commercial cultivars are available through ICARDA seed collection and, in 2008, the 10 most currently grown cultivars in CWANA countries were obtained and planted for large-scale seed increase at quarantine isolation areas at ICARDA). A Ug99 Regional Rust Screening Nursery (Ug99RRSN) comprising representative commercial cultivars will be established for adult plant field testing in a Ug99 hotspot, and seedling evaluation of all entries using local stem rust races will be undertaken at USyd and where possible regional rust laboratories to permit resistance gene postulation. This information will be supplemented by molecular characterization of all entries using markers linked to importance rust resistance genes (e.g. Sr2, Lr34/Yr18, Lr46/Yr29).

In addition to establishing the resistance genes present in leading wheat cultivars, this work will provide an indication of the potential presence of adult plant resistance (APR) to stem rust in these cultivars. Knowing the identity of any seedling resistance genes present, as well as the pathogenicity of pathotypes used in field nurseries, is essential in evaluating the presence of APR in a cultivar. Where seedling resistance genes are present, the potential presence of APR can only be assessed in field nurseries by using pathotypes with virulence matching the seedling gene (s) that are present. If new sources of resistance to stem rust are identified, initial studies will be made in which segregating populations (F3) are generated and the number of genes involved are determined. Where the presence of new resistance genes is established, further genetic characterization including mapping and marker development will be undertaken using funds from other projects and in conjunction with participants in Objective 26, Pre-breeding.

Activity 23.d.2. Genetic stock development (R. Park/ USyd)

181


Race determinations of cereal rust pathogens can only be conducted in seedling tests under controlled or at least partially controlled growth conditions. Field based trap plots provide useful information on the presence of specific virulences in a region. Both approaches are entirely dependent on host genotypes carrying target resistance genes. Unfortunately, many genotypes used as differentials in wheat rust work carry multiple resistance genes, and/or are poorly adapted to some environments, often leading to great confusion and incorrect virulence determinations. Work over the past 20 years at USyd identified the Australian wheat cultivar Avocet as a useful background genotype into which single genes conferring resistance to stripe rust have been backcrossed. The Avocet NIL series has been deployed internationally as trap plots, and some individual NILs have been used by some laboratories as differential genotypes for seedling race analyses.

Similar but incomplete sets of NILs exist for stem rust, produced in Canada (LMPG series), Australia (W2691 series), and the USA (ISr series). This Activity will involve compiling, verifying and preserving all current stem rust NIL stocks. It will also involve generating a NIL series in a common background, for at least 35 known stem rust resistance genes (Sr2, Sr5, Sr6, Sr8a, Sr8b, Sr9b, Sr9e, Sr9g, Sr10, Sr11, Sr12, Sr13, Sr14, Sr15, Sr16, Sr17, Sr21, Sr22, Sr23, Sr24, Sr25, Sr26, Sr27, Sr29, Sr30, Sr31, Sr32, Sr33, Sr34, Sr35, Sr36, Sr37, Sr38, Sr39, Sr40) using genotype similar in agronomy to cultivar Avocet but with susceptibility to stem rust and resistance to both leaf rust and stripe rust. The recurrent parent will be selected from three existing Doubled Haploid populations developed at USyd from crosses between Avocet and the European wheat cultivars Pegaso (563 lines), Hereward (148 lines), Mec (152 lines) and Capelle Desprez (245 lines). If possible, an awnless selection will be made to provide an easy means of discriminating the new stem rust NILs from existing awned stripe rust NILs. A set of lines selected for agronomic type and rust response in Australia (ca. 20) will be field tested in Kenya (Njoro), Kazakhstan (Astana) and Canada (Winnipeg) along with selected control genotypes (including Avocet) in 2010 to allow the best adapted genotype to be identified.

Existing stem rust races at USyd allow the identification of the 35 genes listed, all of which will be backcrossed into the common background to 6 doses of the recurrent parent (to reconstitute 98.44% of the recurrent parent):

March 2011 F1

December 2011 BC1F1

March 2012 BC2F1

December 2012 BC3F1

March 2013 BC4F1

December 2013 BC5F1

March 2014 Self to generate BC5F2

December 2014 Self to generate BC5F3

Homozygous Resistant (HR) BC5F3 lines identified in greenhouse seedling rust tests in early 2015 will be field sown in June 2015, and individual lines selected and harvested by December 2015. All NILs generated will be freely available upon request. The recurrent parent will also be

182


distributed freely upon request so that NILs carrying any new sources of stem rust resistance (e.g. those identified in Objectives 26 and 28) can also be generated.

Activity 23.e.1. Intra- and inter- Objective communication and coordination (R. Park/ USyd) Travel funds are requested to allow the Objective Leader to interact face-to-face with all participants within Objective 23, and also for periodic interaction with Leaders of other Objectives, to ensure the works progresses smoothly and that it is in line with the overall goal of the Phase II proposal. A Surveillance Advisory Panel (Supplemental Document 23.1) will:

• Provide quality assurance of surveillance data.

• Facilitate surveillance activities (sample acquisitions, requests for race analysis by a third party, capacity building/ support, data sharing).

• Support national program activities.

• Raise awareness of significant developments and provide advice (to be channeled through FAO).

• Manage interactions with rust surveillance activities funded outside the Phase II proposal, to ensure complementarities and to prevent duplication

• Decide on the composition of trap nurseries – annual review and input from other objective leaders.

• Provide guidance to the Objective Leader (Prof Park) in managing inter-objective coordination (e.g. using surveillance data to inform breeding, pre-breeding and seed systems strategies).

Funds are requested to allow the Objective Leader to convene regular meetings of the Advisory Panel via teleconference, to interact face-to-face with all participants within Objective 23, and also for periodic interaction with Leaders of other Objectives, to ensure the works progresses smoothly and that it is in line with the overall goal of the Phase II proposal.

IV. Management Plan Name (or position if to be hired)

Institution Email Relevant Activities and outputs(ID and Name)

Prof R. Park Univ Sydney [email protected] c2 In-country race analysis c3 Pathogen characterization d1 Host characterization d2 Genetic stock development e1 Coordination

Dr D. Hodson FAO UN [email protected] a1 GCRMS a3 GCRMS b2 Rust surveillance capacity

Dr. Mogens Hovmoller Aarhus University

[email protected] 23.a.4. Global Reference Center

Dr K. Nazari ICARDA [email protected] b1 Trap plot support b2 Rust surveillance capacity c2 In-country race analysis

183


d1 Host characterization Dr Y. Jin USDA ARS [email protected] c1 Race analysis

backstopping c3 Barberry surveillance and aecial analyses

Dr L. Szabo USDA ARS [email protected] c5 Molecular diagnostics Dr T. Fetch Ag Canada [email protected] c1 Race analysis

backstopping Dr P. Kosina CIMMYT p.kosina@cgia a2 GCRMS; Wheat Atlas data

platform Dr M. Prashar Directorate of

Wheat Research

[email protected] c2 In-country race analysis

Mr Zafer Mert The Central Research Institute for Field Crops

[email protected] c2 In-country race analysis

Dr Girma Bedada EIAR Ethiopia [email protected] c2 In-country race analysis Ms Ruth Wanyera KARI Kenya [email protected] c2 In-country race analysis Mr I. Lowe UC Davis c3 Barberry surveillance

Other more specific roles of personnel engaged in the Objective and core members of the Advisory Panel are:

Prof. Robert Park (Objective Leader and Coordinating Pathologist)-

• Quality assurance of data

• Facilitating analysis of samples by international labs (liaison)

• Informing breeding, pre-breeding and seed systems strategies

Dr. Mogens Hovmoller-

• Establish and Coordinate a Global Rust Reference Center that includes stem rust

• Accept stem rust isolates from National Programs

• Race typing of stem rust samples from national programs

• Train national program pathologists in race analysis

• Curate a global rust reference collection.

Dr. Kumarse Nazari (Surveillance Coordinator)-

• Support national program activities

• Quicksets, differential sets

• Sample collection, in-country race analysis, data sharing

• Liaison with the ICARDA seed laboratory to ensure disease free status of all seed sent.

Dr. Dave Hodson-

• Through FAO, raising awareness of significant developments and providing advice.

184


Dr. Yue Jin-

• Facilitating analysis of samples by international laboratories (liaison) and advisory

Dr. Tom Fetch-

• Facilitating analysis of samples by international laboratories (liaison) and advisory

Dr. Mohinder Prashar-

• Serve as Regional Coordinator/ Leader for India and South Asia

Final Composition of the Advisory Panel is likely to include other global rust experts.

This Objective involves the integration of several diverse activities across organizations spread across the globe, as well as integration with existing rust surveillance activities that are being funded by other organizations. Travel funds are requested to allow the Objective Leader to interact face-to-face with all participants within Objective 23, and also for periodic interaction with Leaders of other Objectives, to ensure the works progresses smoothly and that it is in line with the overall goal of the Phase II proposal. Travel funds have also been included in individual organization budgets to allow participating scientists to attend annual project meetings (e.g. at the BGRI 2010 Technical Workshop at the 8th International Wheat Conference), to ensure frequent face-to-face interaction.

A critical function of the Surveillance Advisory Panel and the Objective Leader will be to ensure coordination of all activities, including the timely exchange and vetting of data generated from analysis of stem rust between participants, NFPs and the IFP. It is clear from Phase I that logistical problems arose in transferring biological samples to ARIs for follow-on characterization (both race determinations and fingerprinting), including timing and number of samples that could be managed. This will be moderated by the Advisory Panel to ensure optimal functionality. The IFP will circulate any information destined for release (e.g., bulletins, web updates) to the Panel for comment and/or edit prior to publishing in the public domain.

Short progress updates will be circulated within the objective team on a 6 monthly basis, and regular contact will be maintained using a shared community space on the Rustopedia website. Team individuals will meet on a more regular basis.

V. Potential Risks and Unintended Consequences

The overall long-term outcome for this objective is a global stem rust surveillance and tracking system that includes standardized in-country race analysis in all countries in which wheat is an important crop. Because rust diseases migrate over long distances, strong international co-operation will be necessary to achieve this. For this system to be ongoing, all participating countries will also have to commit to provide funding to support rust surveillance and race analysis activities, even during periods when rust incidence is low.

Sufficient progress was made during Phase I to establish that there are no risks associated with developing a fully operational database upon which the GCRMS is built. Using the extensive experience of FAO in developing the DLIS system provided an excellent platform on which this could be achieved in a relatively short period of time. Developing the GCRMS to the point where it is the primary source of information relating to stem rust incidence and populations

185


globally (Activity 23.a.1) will, however, require open and timely sharing of information on rust incidence by all national partners. Should any country be unwilling to share data, the value of this system in providing information to help stem rust control will diminish. If funding from the Foundation does not continue beyond year 5, sufficient funds will have to be secured from other sources to ensure the ongoing viability of the GCRMS. Similar challenges will face ongoing input into the Wheat Atlas data platform beyond the life of the project.

A lack of institutional support in the countries in the region being targeted will also reduce the chances of long-term success. This lack of support could be due to a failure to nominate a National Focal Point and a lack of funding to undertake surveillance (e.g. transport costs). NFPs from participating countries will have to be officially nominated by authorized institutions, and the risk of this not happening will be minimized by close interaction based on historical ties of ICARDA and CIMMYT with NARS.

Lack of national support will also be a potential concern to developing in-country capacity for race analysis. For this to be most successful, a commitment from countries will be needed to ensure staff are able to take leave to undergo training at ARIs, and then post-training support to equip the staff with the infrastructure needed to undertake race analysis and to have long-term active involvement in this work. Difficulties could also arise if the person identified for training does not have the interest or basic knowledge needed. Consultation with staff conducting training at ARIs would be very beneficial in minimizing the chance of this.

The abilities of ARIs to provide race analysis backstopping could be compromised if governmental regulations on the importation of exotic rust isolates change. Such changes could either impede or stop this work. There is always a risk of escape when exotic organisms are imported, and so extreme care will be exercised to ensure this is managed.

Seed exchange between ICARDA and countries participating in the trap plot network and/or undertaking race analyses will require strict control over seed health to ensure the quarantine requirements of the recipient countries are not breached. It is also possible that the certified seed health lab at ICARDA will be unable to provide sufficient certification to satisfy existing current requirements of some recipient countries, and also that the requirements may change over time, making it more difficult and/or more expensive to send.

A risk associated with generating NIL stocks for stem rust resistance genes will be failure to identify a suitable recurrent parent. Although considered very unlikely, this would be a serious impediment to achieving the delivery of at least 35 NIL stocks by project completion. Loss of the USyd rust collection, by equipment failure or fire, would also result in inability to generate the stocks. The collection is however backed up with a duplicate of core isolates being maintained in a separate facility, to further reduce the likelihood of this happening.


The University of Sydney Plant Breeding Institute http://www.agric.usyd.edu.au:8888/pbi/

186


Founded in 1850, USyd has an international reputation for outstanding teaching and research excellence. It has a fundamental moral commitment to intellectual discovery and development, responsible social commentary and the promotion of cultural and economic well being. The University complies with the financial reporting requirements of agencies that contract it to undertake research projects. It has a robust accounting system that is used for all externally funded research programs. Once a research contract is signed, the Research Office establishes a dedicated account specific for that project. USyd has been engaged in teaching, research and development in cereal rust genetics on a continuous basis for over 80 years. This work was initiated by Professor Waterhouse in the early 1900s, continued with Professor Watson at the University’s Plant Breeding Institute (PBI) at Castle Hill (now at Cobbitty), then Professor McIntosh, and currently is being led by Professor Park. The PBI has since the early 1970s hosted the National Cereal Rust Laboratory, under a program currently known as the Australian Cereal Rust Control Program (ACRCP). The ACRCP includes funded cereal rust research and breeding activities at CSIRO Plant industry in Canberra, The University of Adelaide, and CIMMYT Mexico, all funded by the Australian Grains Research and Development Corporation (GRDC), an investment that in 2008 ran at about AUD$3.2 million. The National Cereal Rust Laboratory at PBI provides leadership to the overall ACRCP, undertakes cereal rust research, provides breeding support to all industry stakeholders (including cereal breeders, pathologists, advisors and growers), and is committed to providing high quality training to Australian and foreign scientists in cereal rust genetics. Graduates of USyd in cereal rust pathology and genetics include Dr Sanjaya Rajaram, Dr Ravi Singh, Dr Kumarse Nazari, Dr Davinder Singh, Dr Sridhar Bawani and Dr David Bonnett. The project leader, Prof Park, has 25 years experience in working with cereal rust diseases, 21 years of which have involved project supervision and management. For the past 8 years he has been the Director of Rust Research at PBI, and has managed large externally funded projects that employ 7 senior scientists, 12 technical staff, and 8 postgraduate students. In his role as Director of this program, Prof Park has managerial and financial responsibility, which includes reporting against contracted milestones and management of budgets. He has 24 years experience in rust resistance genetics and has published 70 research papers in international peer-reviewed journals, several book chapters, and a book on rust research.

FAO http://www.fao.org

The FAO has in place fully operational trans-boundary pest monitoring and early warning system for Desert Locusts. FAO has been managing this system continuously since 1978 and the proposed work will leverage the vast experience obtained in establishing this system. The Desert Locust monitoring and early warning system is regarded as one of the most successful operational trans-boundary pest systems. The success of the locust system is based on international cooperation and information sharing. FAO is uniquely positioned to lead such global programs through it’s status as a neutral international organization with linkages to rural communities, national governments, regional bodies, international agriculture research and development institutions and the international donor community. The IFP for the emerging GCRMS is currently based within the Desert Locust unit. The IFP (Dr Dave Hodson) has over 11 years of experience implementing and managing a wide range of GIS projects related to

187


agriculture in developing countries. For the last 6 years he managed the GIS laboratory at the International Maize & Wheat Improvement Center (CIMMYT) in Mexico. Dr Hodson has worked on the application of GIS to the threat posed by the Ug99 lineage of stem rust since 2005, and in this capacity was responsible for much of the currently available information relating to movements and distribution of the Ug99 lineage. FAO has a range of other projects focused on cereal rust diseases that include funding from IFAD (US$1.5 million), USAID (US$1 million), IAEA (US$1 million), Spain (US$551,100) and Italy (US$180,000). The unique position and comparative advantage of FAO to engage at a high level with national ministries concerned with agriculture is being used to ensure that official nominations and agreements are place for effective data and information flows between national and international agencies (and vice versa). The engagement of a neutral UN agency is considered to be the most effective way to ensure that barriers relating to the free flow of information are removed so an effective and sustainable monitoring network can be created. This approach has already been tried and tested with the establishment of the highly successful and long running Desert Locust Information System that is totally dependant on a network of officially nominated National Focal Points. The ability of FAO to engage at a high level with national governments was the key to success of the locust system.

Aarhus University Flakkebjerg http://www.au.dk/en

Aarhus University is home to the Yellow Rust Global Reference Center, led by rust pathologist, Dr. Mogens Hovmoller and is best equipped to serve as a Global Rust Reference Center for all three rusts. The Aarhus based Center has scientific expertise across a range of disciplines such as rust pathology, population (and evolutionary) genetics, epidemiology, molecular biology, bioinformatics as well as statistics and database development. What is more, the staff maintain close ties with wheat geneticists of Universities in developed countries, national research institutes and CGIAR-centres.

ICARDA http://www.icarda.org

ICARDA is a vital partner in the TURKEY/CIMMYT/ICARDA International Winter Wheat Improvement Program and has excellent relationships “on the ground” with national program breeders in CWANA countries.

CIMMYT http://www.cimmyt.org

This reputable international center has developed germplasm and confirmed sources of resistance to Ug99 to be used in crosses by national programs. Dr Petr Kosina, the knowledge sharing and capacity-building coordinator, is responsible for the development of the Wheat Atlas for the Global Wheat Program.

188


USDA-ARS Cereal Disease Laboratory St Paul http://www.ars.usda.gov/main/site_main.htm?modecode=36-40-05-00

The mission of the Cereal Disease Laboratory is to reduce losses in wheat, oat, and barley to major diseases including leaf rust, stem rust, and Fusarium head blight. This mission is accomplished through research on the biology of the pathogens that cause these diseases and on methods to enhance disease resistance in small grains. Program objectives are to: (1) identify genes used by plants in defense against pathogens and determine their cellular and biochemical mechanisms of action; (2) elucidate molecular aspects of the expression of virulence in rust fungi; (3) identify and utilize rust resistance factors to protect small grain crops against existing and future pathogenic races in rust populations; (4) analyze population genetics of cereal rust fungi and devise strategies to enhance durability of resistance against diverse rust populations; (5) identify and characterize resistance in wheat and barley to Fusarium head blight and determine impacts of partial resistance on pathogen populations in crop residue; and (6) identify genetic factors for pathogenicity in Fusarium and explore ways to block their activity and minimize pathogen attack in small grains. CDL has been involved in stem rust research, including nation-wide race analysis of the stem rust pathogen, since the early 1900s. Dr Yue Jin currently leads these national race surveys, has many years experience in working with cereal rust pathogens, and has been involved in race typing samples of stem rust from eastern Africa and beyond for the past 5 years. Along with Dr Fetch (see below), he has produced most of the information available on the virulence spectrum of the Ug99 lineage, including verification of two mutational derivatives carrying virulence for Sr24 and Sr36.

AAFC Winnipeg http://www.agr.gc.ca/index_e.php

Agriculture and Agri-Food Canada (AAFC) provides information, research and technology, and policies and programs to achieve security of the food system, health of the environment and innovation for growth. AAFC, along with its portfolio partners, reports to Parliament and Canadians through the Minister of Agriculture and Agri-Food and Minister for the Canadian Wheat Board. Like USyd and CDL, the Rust Laboratory at Winnipeg (formerly the Dominion Lab) has been engaged in rust research since the early 1900s, and has coordinated national rust pathogenicity surveys, which are currently conducted by Dr Fetch. Along with Dr Jin, Dr Fetch has played a central role in understanding the current distribution and nature of the “Ug99 lineage”.

Central Research Institute for Field Crops, Ankara Turkey Mr Zafer Mert is been employed at the Central Research Institute for Field Crops in Ankara, which is affiliated with the General Directorate of Agricultural Research, Ministry of Agriculture. He has been working as a plant pathologist in the Department of Crop Diseases of this institute since 2000, and part of his duties include race analysis of the wheat stem rust

189


pathogen. He received 2 months intensive training in stem rust race identification and rust resistance gene postulation at the University of Sydney Plant Breeding Institute in 2007-08.

Directorate of Wheat Research, Shimla ICAR India Dr Mohinder Prashar has over 20 years experience in working with cereal rust pathogens, and is currently involved in national wheat rust survey and surveillance and race typing of wheat rust samples at DWR Regional Station at Flowerdale, which is home to the Indian national wheat rust laboratory.

190


References Cited

Browder LE (1973). Probable genotype of some Triticum aestivum ‘Agent’ derivatives for reaction to Puccinia recondita f. sp. tritici. Crop Science 13: 203-206.

Flor HH (1956). The complementary gene systems in flax and flax rust. Advances in Genetics 8: 29-54.

Keiper FJ, Hayden MJ, Park RF, Wellings CR (2003). Molecular genetic variability of Australian isolates of five cereal rust pathogens Mycological Research 107: 545–556.

Loegering WQ, McIntosh RA, Burton CH (1971). Computer analysis of disease data to derive hypothetical genotypes for reaction of host varieties to pathogens. Canadian Journal of Genetics and Cytology 13: 742:748.

Park RF (2007) Stem rust of wheat in Australia. Australian Journal of Agricultural Research 58: 558-566.

Pathan AK, Park RF (2007). Evaluation of seedling and adult plant resistance to stem rust in European wheat cultivars. Euphytica 155: 87-105.

Singh RP, Hodson DP, Jin Y, Huerta-Espino J, Kinyua M, Wanyera R, Njau P, Ward RW (2006) Current status, likely migration and strategies to mitigate the threat to wheat production from race Ug99 (TTKSK) of wheat stem rust pathogen. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 1, No. 054.

Stakman EC, Piemeisel FJ (1917) Biologic forms of Puccinia graminis on cereals and grasses. Journal of Agricultural Research 10: 429-495.

Visser B, Herselman L, Pretorius ZA (2009). Genetic comparison of Ug99 with selected South African races of Puccinia graminis f. sp. tritici. Molecular Plant Pathology 10: 213-222.

Watson IA, de Sousa CNA (1982) Long distance transport of spores of Puccinia graminis tritici in the southern hemisphere. Proceedings of the Linnean Society of New South Wales 106, 311–321.

Wellings CR (2007) Puccinia striiformis in Australia: a review of the incursion, evolution, and adaptation of stripe rust in the period 1979–2006. Australian Journal of Agricultural Research 58, 567–575.

191

Appendix C: Detailed Description of Proposed Work / Durable Rust Resistance in Wheat Phase II Objective Supplemental Document 23.1: Global Rust Monitoring System

Supplemental Document 23.1. Global Cereal Rust Monitoring System, Information and Rust Sample Flows

Surveyors

National Focal Point

Advisory Panel

International Focal Point

Local pathology laboratory

International pathology laboratory

Rust sample(s) Information

192

Appendix C: Detailed Descriptions of Proposed Work / Durable Rust Resistance in Wheat Phase II Objective 24: World-class stem rust response phenotyping facilities in East Africa


Objective 24: World-class stem rust response phenotyping facilities in East Africa.

Team Leader for this Objective: Sridhar Bhavani, CIMMYT Nairobi, Kenya


Institution Primary Contact Email

International Center for Maize and Wheat Improvement (CIMMYT), Mexico

Hans Braun [email protected]

International Center for Agricultural Research in the Dry Areas (ICARDA) Syria

Richard Brettell [email protected]

Ethiopian Institute of Agricultural Research (EIAR)

Bedada Girma [email protected]

Kenyan Agricultural Research Institute (KARI)

Peter Njau [email protected]

University of Free State, South Africa Zak Pretorius [email protected]

University of Sydney, Australia Robert Park [email protected]

United States Department of Agriculture-Agricultural Research Service (USDA-ARS)

Kay Simmons [email protected]

Washington State University Michael Pumphrey [email protected]



60


193


I. Executive Summary This Objective will contribute to the protection of global wheat production and food security through the phenotypic screening of wheat germplasm and the development of replacement varieties that are durably resistant to Ug99 stem rust. In collaboration with Objective 25 (Breeding), germplasm will be evaluated with the goal of developing varieties having adult plant resistance (APR) or pyramided combinations of major genes. The discovery of new sources of resistance in both domestic and wild relatives of wheat, in conjunction with Objective 26 (Pre-breeding) activities, will increase the diversity of genes available to breeding programs. The precise phenotypic evaluation of plants for APR, in the field and in tunnel houses, is central to the DRRW project and is a necessary complement to the activities of Objectives 25 and 26. The development of world-class screening facilities in the center of origin of Ug99 and other threatening pathotypes of stem rust is critical to our ability to evaluate germplasm for new sources of resistance, to incorporate them in breeding programs, and deploy them as durably resistant varieties. The activities in this objective serve not only the global wheat community, but also have a direct benefit to East African wheat growers, producers and consumers. Summary of Short, Medium, and Long Term Outcomes

Within five years • The frequency of APR in advanced breeding lines has increased and the average

resistance response improved from moderately resistant/moderately susceptible (MR/MS) to resistant/moderately resistance (R/MR) (Joint with Objective 25).

• The frequency of major single gene-based resistance in released varieties is reduced.

• APR candidate bread wheat and durum wheat varieties for East Africa are in advanced stages of release (joint with Objectives 21 and 25).

• Quantitative trait loci (QTL) for APR in bread and durum wheat are identified and exploited in breeding programs (joint with Objective 26).

• New sources of stem rust resistance are identified, genetically characterized and mapped (joint with Objective 26).

• New sources of resistance are available to breeders and deployed in breeding programs (joint with Objective 25 and 26).

• The genetic basis of resistance of released and candidate varieties is used to inform national and international resistance management strategies that enhance the overall sustainability of wheat production.

• Changes in virulence or races during a given screening season are detected and used to enhance the value of field data by informing decisions on inoculations and interpretation of data.

• Regular monitoring of the frequency and evolution of the Ug99 lineage assists in the development of breeding and gene deployment strategies (joint with Objective 23).

• EIAR and KARI strengthened seed health and biosecurity protocols preclude import or export of seed borne disease and stem rust spores.

194


• Screening facilities in Kenya and Ethiopia are fully operational and contribute significantly to the global wheat improvement effort to minimize stem rust epidemics.

• Scientists and staff at critical facilities in Ethiopia and Kenya conduct high caliber international cereal rust research and are active collaborators in international projects.

Within ten years • 90% of Kenyan and 70% of Ethiopian bread wheat areas are predominantly planted with

durably resistant varieties (joint with Objectives 21 and 25).

• Durably resistant bread wheat varieties are planted in >10% of Central and South Asian bread wheat areas (joint with Objectives 21 and 25).

• APR candidate bread wheat varieties for China’s at-risk areas are in advanced stage of release (joint with Objectives 21 and 25).

• 30% of Ethiopia’s durum (tetraploid) area is planted with resistant varieties (joint with Objectives 21 and 25).

• Durably resistant durum wheat varieties are planted in >10% global wheat areas (joint with Objectives 21 and 25).

• Diagnostic markers for bread wheat APR genes are employed by IARC and NARS breeders (joint with Objective 26).

• All deployed cultivars are durably resistant to Ug99 and other evolving stem rust variants (joint with Objective 25).

• Stability of production gains are not threatened by losses to stem rust.

• Long-term database informs understanding of the biology and evolution of the stem rust population in East Africa.

• Enhanced knowledge of pathogen migration and distribution will facilitate decision and adoption of appropriate national, regional and international policies, investments, and strategies in plant protection, wheat breeding and seed systems.

• Development of technical expertise and human resources, and investments in equipment and lab facilities allow EIAR and KARI staff to develop research programs that contribute to understanding and management of the stem rust pathogen in East Africa.

Within fifteen years • More than 50% of the areas of CWANA, South Asia and China that are at risk of a Ug99

incursion are planted to improved durably resistant bread wheat varieties.

• Cultivated resistant varieties ensure both global food security, and increased production.

• Cereal cropping systems for resource poor growers in at-risk countries are stabilized and small-holder economies have improved by 10%.

• More than 50% of at-risk areas of global durum wheat production are planted with improved, durably resistant varieties.

195


Progress to Date

Since the inception of Phase I, KARI, EIAR and CIMMYT collaboratively addressed all four key project activities outlined in Objective 4 (Supporting Critical Rust Screening Facilities in East Africa) of Phase I. Dr. Davinder Singh, CIMMYT’s International Coordinator, assumed his post in Kenya in August 2008. Dr. Singh, along with the Principal Investigator at KARI, Peter Njau, established and trained a scientific team capable of managing the activities of the screening nursery. Dr. Singh has recently taken a new position in Australia but has been replaced by CIMMYT employee, Sridhar Bhavani. EIAR appointed Dr. Bedada Girma to a newly created post of DRRW coordinator. Under Bedada Girma’s direction, scientific teams initiated germplasm screening and gene discovery activities in Ethiopia. Specific work plans for improving irrigation capacity, greenhouses, and laboratory facilities were developed collaboratively between KARI, EIAR, and CIMMYT with input from the Cornell staff and consultants. Guidelines for submission and screening of germplasm were crafted by CIMMYT in cooperation with KARI and EIAR and are posted at www.globalrust.org. Vehicles and field equipment were acquired, nursery areas quarantined, and irrigation projects underway or completed. Facility upgrades in Kenya and Ethiopia were initiated, but are far from complete. Progress has been slow for many capital improvements due to the challenge of identifying expertise in-country to submit bids and implement activities, due to a failure to understand import requirements, bureaucratic and personnel “difficulties,” and simply due to the amount of time required to accomplish these activities in developing countries. Such delays have hindered progress in rearing inoculum, (although locally collected inoculum was successfully used in the Debre-Zeit nursery), initiating race typing analyses, and developing in-country pathological expertise. Many issues have been resolved with the identification of qualified contractors, as well as progress on our own personal learning curve in managing capital projects in developing countries. It should also be recognized that the team leaders of this Objective, some relatively new to their responsibilities, have also learned much since the inception of the project and are now poised to move the activities ahead more expeditiously. Communications upgrades in Ethiopia required an understanding of Ethiopian Telecom (ETC) operations, and resulted in significant improvements in band-width and internet connectivity there, as well as all critical facility locations. Improved communications will expedite all other proposed activities, and clearly enable improved execution. Consistent electrical power to EIAR facilities and the entire country of Ethiopia remains a problem, and intermittently stymies communications.

KARI and EIAR, in coordination with CIMMYT, began Ug99 screening activities on bread wheat and durum wheat, respectively. The screening was conducted for three seasons since the project’s inception. This included screening in the 2007-2008 off-season, 2008 main-season, and 2008-2009 off-season at both sites. The 2008 main-season nursery at KARI-Njoro had more than 20,000 plots (from CIMMYT, ICARDA and 20 countries) and experienced the heaviest stem rust severity seen to date at that site. During the June-October season at EIAR more than 7000 entries were screened under conditions of heavy infection pressure. The 2008-2009 off-season screening nursery accommodated more than 18,000 lines at Njoro (the largest off-season nursery ever), and 5000 lines at Debre-Zeit. Work plans for 2009 main-season at KARI and EIAR were developed and implemented in June/July 2009. EIAR, KARI, CIMMYT and ICARDA have all advanced their combined breeding efforts as an outcome of this objective. As a cross-objective project deliverable with Objective 5, scientists at ICARDA and CIMMYT advanced materials in their durum breeding programs with a Ug99 screening shuttle at Debre-Zeit, and with a bread

196


wheat screening shuttle at Njoro. Local capacity in managing screening nurseries’ operations has improved with assistance from CIMMYT staff, and seminal steps toward physical and procedural capacity enhancements were achieved. Continuing improvements are necessary to meet the increasing demand for screening nursery services, which have increased three-fold at Njoro since 2005. Irrigation capacity in both Ethiopia and Kenya need additional investments to avoid a repeat of the 2008-2009 off-season in Njoro, where stand establishment and disease development in the nursery suffered due to an extended drought.

For Activity 4.4 (providing in-service learning opportunities for KARI and EIAR staff), KARI scientists and technical staff received training in key areas such as scoring germplasm and data entry by the CIMMYT scientist posted in Kenya as well as by scientists visiting from CIMMYT-Mexico, ICARDA and the United States. The CIMMYT-Kenya scientist is currently organizing visits for KARI and EIAR staff training in South African (Professor Z. Pretorius) and Australian (Professor R. Park) rust laboratories in August of 2009.

KARI-Njoro’s Center Director, M. Gethi, and scientist P. Njau participated in the International Wheat Genetics Symposium in Brisbane, Australia. KARI pathologist, Ruth Wanyera, visited Dr. Yue Jin at the USDA rust lab in Minnesota. One scientist from KARI and three scientists from EIAR participated in the November 2008 rust surveillance meeting at Shimla, India. Four scientists from EIAR (B. Girma, B. Ayele, S. Gelalcha, and W. Getaneh) and two scientists from KARI (P. Njau and R. Wanyera) participated in 2009 and 2010 BGRI workshop at Obregon, Mexico and St. Petersburg Russia, respectively.


The proposed work is an expansion of the phenotyping work of Objective 4 undertaken at the Kenya Agricultural Research Institute (KARI) Njoro Research Center and the Ethiopian Institute of Agriculture Research (EIAR) during Phase I of the DRRW project. The Activities in this Objective will increase the capacity to accurately phenotype germplasm for reaction to stem rust races TTKSK, TTKST, and other Ug99 variants. Specifically, and in concert with Phase I, bread wheat germplasm will be screened in Kenya and durum wheat in Ethiopia (Activities 24.a.1 and 24.b.1, respectively) in accordance to the procedures and guidelines developed and posted on BGRI DRRW website. The data generated will be collated and shared with collaborators, major stakeholders, and the international community, as relevant. The major outcome will be the development of durable adult plant resistant breeding germplasm and, in conjunction with Objectives 21 and 25, varieties that will be released by IARCs and NARS and grown in Ug99 at-risk countries.

Activities 24.a.2 and 24.b.2 are new to Phase II and complement Objective 26 (Pre-breeding) by providing high quality phenotypic data and mapping information on germplasm containing new sources of resistance (about 3000 genotypes/year). The phenotypic data will be generated both for seedlings in controlled greenhouses and on adult plants in semi-controlled tunnel houses. Highly reliable data will result from conducting the screening under controlled conditions. The coordinated screening of seedling and adult plants will distinguish between two types of resistance—major gene resistance (seedling or hypersensitive response genes) and minor gene (adult-plant) resistance. The outcomes of these activities will include the identification and mapping of novel sources of durable stem rust resistance (with Objective 25) which will be made available to breeders to deploy in breeding programs (with Objective 26 and the CIMMYT

197


Generation Challenge Program). This activity will have the larger impact of increasing the diversity and number of resistance genes in well-characterized germplasm and released varieties. Using the same approach, resistance will be characterized and confirmed in both bread wheat (Activity 24.a.3) and durum wheat (Activity 24.b.3) varieties being considered for release in at-risk countries. The genetic basis of resistance of candidate and released varieties will inform national and international resistance management strategies that foster sustainable wheat production. The selected elite resistant material and populations developed will be conserved in CIMMYT Gene bank (Germplasm Research Unit) for future use by global plant breeders and relevant scientists.

Underlying all of these activities (24.a.1, 24.a.2, 24a.3, 24.b.1, 24.b.2, and 24.b.3) is the need to maintain and multiply pure isolates and regularly monitor stem rust races in the field. Activities 24.a.4 and 24.b.4 will ensure proper management of the pathogen and field epiphytotics. These activities will also support national pathogen surveillance and race analysis in conjunction with Objective 23, but with a specific commitment to East Africa. Regular monitoring of the frequency with which Ug99 occurs and the evolution of this lineage will inform appropriate use of inocula in screening nurseries and the development of subsequent breeding and gene deployment strategies. Gaps exist in our current understanding of the nature and distribution of the stem rust population in Ethiopia’s durum wheat crop. Activity 24.b.6 addresses these gaps through of the establishment of trap nurseries. As an outcome of this activity, we will be more effective in identifying durable stem rust resistance combinations in durum wheat.

The intended outcomes of this objective rely heavily on the ability to move seed material in and out of East Africa. Movement of seed increases the risk of introducing exotic diseases and pests into Kenya and Ethiopia, putting these national ecologies at risk, and thus jeopardizing the international screening nurseries’ operations. However, the national regulatory authorities in these countries have protocols for safe germplasm exchange, and we propose to complement those protocols to further minimize such risks. Activities 24.a.6 and 24.b.7 are introduced in Phase II to facilitate seed health units within KARI and EIAR. These units will work in complementation with national quarantine authorities to preclude the import or export of seed borne disease and stem rust spores into and out of Kenya and Ethiopia through regular and thorough inspection of seed materials.

In Activities 24.a.7 and 24.b.8, a set of training events, exchange visits and participation at international fora by KARI and EIAR scientists are proposed. Exchange visits by national scientists from KARI and EIAR staff to advanced cereal rust laboratories will foster information exchange, technology sharing and research skill development in rust pathology. CIMMYT will provide training in field skills in the areas of data recording and database management, recognition and screening of rust pathogens, selection, resistance breeding and seed health management. KARI and EIAR scientists will participate in international conferences and workshops focused on wheat rust pathology, breeding and genetics. Post-graduates from national universities will be recruited as interns and trained in cereal rust pathology, genetics, and breeding by the screening facilities teams and by international visitors.

During Phase I, modest screening facilities were established at Kenya and Ethiopia for phenotypic evaluation of germplasm. At this juncture, it is necessary to further strengthen these facilities for adequate phenotyping and the long-term sustainability of the screening nursery operations. These fully operational world-class screening facilities in East Africa will be a hall-

198


mark of an ongoing international effort to support wheat breeding programs, and an important contribution in minimizing the threat of global rust epidemics.

Justification for Proposed Work Continuing Phase I activities and the improvements on the screening facilities both in Kenya and Ethiopia will be important aspects of the second phase of the DRRW project. Progress to date, and expected progress through the rest of Phase I, will result in significant outcomes in the short, medium and long term. Key first steps in physical and procedural capacity enhancements were achieved in Phase I. The facilities in Kenya and Ethiopia are developing into world-class facilities where scientists from CIMMYT, ICARDA, and more than 25 NARS interact in a collaborative manner. Further strengthening of Ethiopian and Kenyan national capacities, while keeping an international focus, will consolidate, strengthen, and sustain Phase I achievements.

The activities proposed in Objective 24 complement the activities in Objectives 21, 23, 25 and 26. Perhaps most importantly, the activities of Objective 24 and their inclusion in Phase II, enable wheat rust screening efforts by establishing a robust platform to evaluate and identify durably rust resistant, high yielding germplasm. This germplasm will be developed in close collaboration with IARCs, ARIs and NARS, and will benefit millions of poor farmers by contributing to food security through protection of the world’s wheat crop.


199


Objective 24: World-class stem rust response phenotyping facilities in East Africa



24.a. Kenya Phenotyping.

24.a.1. Common wheat stem rust phenotyping of breeding germplasm and research materials in the field screening nursery at Njoro, Kenya (KARI).

Main season nurseries planned, seed imported and planted, and resulting material phenotyped (Oct. 2011, recurring annually).

Main season data recorded, data and/or seed returned to collaborators and shared where appropriate and as governed by the Germplasm Acquisition Agreement (GAA). (Nov 2011, recurring annually).

Off-season nurseries planned, seed imported and planted, and resulting material phenotyped (April 2012, recurring annually).

Off-season data recorded, data and/or seed returned to collaborators and shared where appropriate and as governed by the GAA. (Jun 2012, recurring annually).


APR candidate bread wheat varieties for east Africa in advanced stage of release (joint with Objectives 21 and 25).

QTL for APR in bread wheat identified (joint with Objective 26)

Ten Years 90% Kenyan and 70% of Ethiopian bread wheat areas are planted to predominantly APR varieties (joint with Objectives 21 and 25).

APR bread wheat varieties are planted to >10% of central and south Asia bread wheat areas (joint with Objectives 21 and 25).

APR candidate bread wheat varieties for China’s at-risk areas are in advanced stage of release (joint with Objectives 21 and 25).

Diagnostic markers for bread wheat APR genes are employed by IARC and NARS breeders (joint with Objective 26).

Fifteen Years

P. Njau, KARI


200




>50% of at-risk areas of CWANA, S. Asia and China planted to improved APR bread wheat varieties.

Cultivated resistant varieties ensure both global food security, and increased production.

24.a.2.

Seedling and adult plant phenotyping of bread wheat in greenhouse and tunnel house in support of gene mapping and novelty studies (joint with Objective 26) at Njoro Kenya (KARI).

Greenhouse and tunnel house screening planned and seed imported (Feb2011, recurring annually); material screened (Oct 2011, recurring annually).

Accurate seedling (greenhouse) and adult reaction (tunnel house) phenotype data generated and returned to collaborators and shared where appropriate (Nov 2011, recurring annually).


Novel sources of resistance available to breeders are deployed in breeding programs (joint with Objective 25 and 26).



P. Njau, KARI


201




24.a.3. Confirm-ation and initial char-acterization of resistance in bread wheat germ-plasm at Njoro, Ken-ya (KARI) for varieties under re-lease consid-eration in at-risk countries.

Field resistance of candidate or released varieties is re-evaluated in greenhouse for seedling reaction (Dec 2011, recurring annually) and tunnel house for adult response (Jun 2011, recurring annually) to confirm resistance and initiate resistance gene postulation work (Nov 2011, recurring annually).



Frequency of single major gene based resistance in released varieties is reduced.




P. Njau, KARI

24.a.4. Collection, character-ization, and maintenance of stem rust cultures, and moni-toring of field races of stem rust in the screen-ing nursery (KARI-Njoro).


Effective epiphytotics of stem rust on screening materials maintained in field and tunnel house (Apr and Nov 2011, recurring annually)

Predominant virulent pathotypes in the screening nurseries are serially collected throughout the season and race typed to aid interpretation and validation of phenotypic data recorded during each screening cycle. Frequency and predominance of pathotypes recorded and reported to collaborators. (May 2011 and Nov 2011, recurring annually)




P. Njau, KARI


202




24.a.5. National pathogen surveillance and race analysis in Kenya.

Rust surveys during wheat growing seasons conducted and samples collected (methods conforming to Objective 23, 2011 onwards).

Race analysis conducted at KARI-Njoro/AAFC on collected samples and virulence patterns of races in Kenya determined (Dec 2011, recurring annually).



P. Njau, KARI


24.a.6. Establish-ment of a Seed Health unit, including standard protocols to be implement-ed for seed exchange in comple-mentation with national regulatory authorities.

Seed health unit operational (Apr 2011).

Seed health management protocols established and communicated (Jun 2011).

Staff trained in seed health (Aug 2011)


Five Years KARI strengthened seed health protocols preclude import or export of seed borne disease and stem rust spores

Ten Years As above.


P. Njau, KARI


203




24.a.7. In-service learning/ training opportun-ities for KARI and national skill develop-ment.

Scientists trained in the area of cereal rust genetics, race surveillance, and race analysis, screening and rust pathology techniques by visiting scientists and by CIMMYT IFP. (Sep 2011, 2012, 2013).

Three staff trained (one per year) at CIMMYT in the area of field management, screening, data collection, data management, and methodologies related to rust resistance evaluation, selection and breeding (Aug 2011, 2012, 2013). KARI scientists attend and participate in international conferences (relevant time/conferences in, 2011, 2012, 2013).

One national Post-graduate student trained per year in area of plant pathology, breeding and genetics (summer semester 2011, recurring yearly).

Five Years Scientists and staff at critical facilities in Kenya conduct high caliber international cereal rust research.

KARI scientists are active collaborators in international rust research/breeding projects.

Ten Years As above.

P. Njau, KARI


24.a.8. Strategic investments to enhance the precision and capacity to generate reliable and accurate stem rust phenotypic data.

Fifteen hectares of land and excellent research facilities are available for national and international rust screening activities (Oct 2011).


Tunnel house capable of generating reliable and repeatable phenotypic data is available (Apr 2011). Seed health unit operational (Apr 2011)

Five Years Fully operational screening facilities in Kenya are a robust and vibrant component of an ongoing global wheat improvement effort to minimize stem rust epidemics

Ten Years As above


P. Njau, KARI


204




24.b. Ethiopia Phenotyping.

24.b.1. Durum wheat stem rust phenotyping of breeding germplasm and research materials in the field screening nursery at Debre-Zeit, Ethiopia (EIAR).

Main season nurseries planned, seed imported and planted, and resulting material phenotyped (Jun 2011, recurring annually).

Main season data recorded, data and/or seed returned to collaborators and shared where appropriate and as governed by the Germplasm Acquisition Agreement (GAA) (Nov 2011, recurring annually).

Off season nurseries planned, seed imported and planted, and resulting material phenotyped (Nov 2011, recurring annually).

Off-season data recorded, data and/or seed returned to collaborators and shared where appropriate and as governed by the GAA (Apr 2011, recurring annually).


APR candidate durum wheat varieties for east Africa in advanced stage of release (joint with Objectives 21 and 25).

QTL for APR genes in durum wheat identified (joint with Objective 26)

Ten Years 30% of Ethiopia’s durum (tetraploid) area is planted to resistant varieties (joint with Objectives 21 and 25).

APR durum wheat varieties are planted to >10% global wheat areas (joint with Objectives 21 and 25).

Diagnostic markers for durum wheat APR genes are employed by IARC and NARS breeders (joint with Objective 26).

Fifteen Years >50% of at-risk areas of global durum planted to improved APR durum wheat varieties.

Cultivated resistant varieties ensure both global food security, and increased production leading to economic security.

Bedada G., EIAR


205




24.b.2. Seedling and adult plant phenotyping of durum wheat in greenhouse and tunnel house in support of gene map-ping and novelty studies (joint with Objective 26) at Debre-Zeit, Ethiopia (EIAR).

Greenhouse and tunnel house screening planned and seed imported. (Feb 2011, recurring annually)

Material screened. (Oct 2011, recurring annually)

Accurate seedling (greenhouse) and adult reaction (tunnel house) phenotype data generated and returned to collaborators and shared where appropriate. (Nov 2011, recurring annually)


Novel sources of resistance available to breeders and deployed in breeding programs (joint with Objective 25 and 26).



Bedada G., EIAR


206




24.b.3. Confirm-ation and initial char-acterization of resistance in durum wheat germ-plasm at Debre-Zeit, Ethiopia (EIAR) for varieties under re-lease consid-eration in at-risk countries.

Field resistance of candidate or released varieties is re-evaluated in greenhouse for seedling reaction (Dec 2011, recurring annually);

and tunnel house for adult response (Jun 2011, recurring annually); to confirm resistance and initiate resistance gene postulation work (Nov 2011, recurring annually).



Frequency of single major gene based resistance in released varieties released is reduced.



Bedada G., EIAR


24.b.4. Collection, characteri-zation and maintenance of stem rust cultures and monitoring of field races in the screening nursery (EIAR Debre-Zeit and Ambo).


Effective epiphytotics of stem rust on screening materials maintained in field and tunnel house (Mar 2011, recurring annually).

Predominant virulent pathotypes in the screening nurseries field are serially collected throughout the season and race typed to aid interpretation and validation of phenotypic data recorded during each screening cycle. Frequency and predominance of pathotypes recorded and reported to collaborators. (May and Dec 2011, recurring annually)




Bedada G., EIAR


207




24.b.5. National pathogen surveillance and race analysis in Ethiopia. (EIAR-Ambo)

Rust surveys during wheat growing seasons are conducted and samples collected (methods conforming to Objective 23). (Sep 2011, recurring annually).

Race analysis conducted by EIAR-Ambo on collected samples and virulence patterns of races in Ethiopia determined. (Dec 2011, recurring annually)



Bedada G., EIAR


24.b.6. Charac-terize the nature and distribution of the stem rust popu-lation in Ethiopia’s durum/ tetraploid wheat crop through surveys and established trap nurseries. (EIAR-Ambo)

Rust samples systematically collected from farmer fields and trap nurseries of durum wheat (Sep 2011, recurring annually)

Distribution of stem rust virulences and races determined (Jun 2011, recurring annually).

Five Years Durum stem rust evaluation is more effective in identifying diverse and durable resistances using enhanced knowledge of stem rust virulences/races in Ethiopia.

Ten Years As above.


Bedada G., EIAR


208




24.b.7. Establish-ment of a Seed health unit, including standard protocols to be imple-mented for seed ex-change in comple-mentation with national regulatory authorities.

Seed health unit operational and complementing role of national quarantine authorities (Apr 2011).

Seed health management protocols established and communicated in consultation with national quarantine authorities. (Jun 2011).

Staff trained in seed health issues and protocols (Aug 2011)


Five Years EIAR strengthened seed health protocols preclude import or export of seed borne disease and stem rust spores

Ten Years As above.


Bedada Girma / EIAR


24.b.8. In-service learning/ training opportun-ities for EIAR and national skill devel-opment.

Three scientists trained (one per year) at international cereal rust labs in the area of cereal rust genetics, race surveillance, race analysis, screening and rust pathology techniques (Jul 2011, Jul 2012, Jul 2013).

Three staff trained (one per year) at CIMMYT in the area of field management, screening, data collection and methodologies related to rust resistance evaluation, selection and breeding (Aug 2011, Aug 2012, Aug 2013)

Five Years Scientists and staff at critical facilities in Ethiopia conduct high caliber international cereal rust research.

EIAR scientists are active collaborators in international rust research/breeding projects.

Ten Years As above.

Bedada Girma / EIAR


209




EIAR scientists attend and participate in international conferences (relevant time/conferences in Sep 2011, Sep 2012, Sep 2013).

National technical staff trained by two local training events relevant to field and greenhouse rust screening (Apr 2011, Apr 2012).

24.b.9. Strategic investments to enhance the precision and capacity to generate reliable and accurate stem rust phenotypic data.

Seven hectares of land and excellent research facilities are available for national and international rust screening activities (Oct 2010).


Tunnel house capable of generating reliable and repeatable phenotypic data is available (Apr 2011)

Seed health unit is operational (Apr 2011)

Five Years Fully operational screening facilities in Ethiopia are a robust and vibrant component of an ongoing global wheat improvement effort to minimize stem rust epidemics.

Ten Years As above.


Bedada Girma / EIAR


210


III. Detailed Work Plan Components 24.a (Kenya) and 24.b. (Ethiopia). Activities 24.a.1 and 24.b.1: Common wheat stem rust phenotyping of breeding germplasm and research materials in the field screening nursery at KARI-Njoro, Kenya (24.a.1); Durum wheat stem rust phenotyping of breeding germplasm and research materials in the field screening nursery at EIAR-Debra-Zeit, Ethiopia (24.b.1). These activities are a continuation of Phase 1 activities. Approximately 20,000 bread wheat breeding/research lines (24.a.1) and 10,000 durum wheat lines (24.b.1) will be screened per season. The materials will be received from collaborating national and international research centers and other contributing organizations. Two screening cycles, a main season cycle (Jun to Oct, recurring yearly) and an off-season cycle (Nov to Apr, recurring yearly) will be managed at stations in both Ethiopia and Kenya as per guidelines established in Phase I (www.bgri.com). As in Phase I, periodic work plans for both screening facilities will be developed in collaboration with the CIMMYT Kenya-based scientist. The CIMMYT Kenya-based scientist will be responsible for coordinating each season’s nursery entries through communication with the facilities’ coordinators and international collaborators. Work plans (including all logistics) required for screening in Kenya (24.a.1) and Ethiopia (24.b.2) will be executed by the screening facility teams during two consecutive seasons using modern field research methods for evaluating the host-pathogen interaction. Responses of adult plants to stem rust (and yellow and brown rust as opportunities arise under natural field epidemics) will be evaluated. These data will be collated and distributed to the collaborating partner countries and project partners in Objectives 25 and 26. Where relevant, the data will also be shared internationally via the BGRI web site (managed under Objective 28). Internet-based and e-mail communications will facilitate planning and reporting of phenotyping protocols to IARCs, NARS, ARIs, and the private sector, as appropriate. Selected germplasm will be conserved with CIMMYT and/or KARI/EIAR and exchanged under standard Material Transfer Agreement of international treaty on plant genetic resources, and as outlined in the Germplasm Acquisition Agreement (GAA), where relevant (see Figure 1). The schematic flow of steps and outputs for an entire screening cycle is highlighted in Figure 2.

211


Figure 1. DRRW Germplasm Acquisition Agreement (GAA) for materials under development, not included in the International Treaty for Plant Genetic Resources for Food and Agriculture’s Multilateral System of Access and Benefit Sharing 1. [Supplier] grants germplasm and related information to the Kenya Agricultural

Research Institute (KARI) or Ethiopian Agricultural Research Institute (EIAR) and International Maize and Wheat Improvement Centre (CIMMYT) under the terms and conditions of this agreement. The germplasm being provided is identified in the attached list, which forms part of this agreement, and is outside the International Treaty’s multilateral system of access and benefit sharing (MLS).

2. [Supplier] warrants that it is legally free to provide the germplasm to KARI or EIAR and CIMMYT, and that all necessary permissions have been obtained.

3. KARI and EIAR will hold the germplasm in accordance with the terms of the Standard Material Transfer Agreement of the International Treaty for Plant Genetic Resources for Food and Agriculture.

4. KARI and EIAR will be free to use the germplasm and related information available for the purpose of conservation for research, breeding and training for food and agriculture in accordance with the standard material transfer agreement (SMTA) currently in use and in accordance to Delhi Declaration 2008.

5. DRRW will be free to post screening data and relevant information related to pedigree and selection history on BGRI website and CIMMYT website.

6. CIMMYT will be free to conserve, use and upon agreement with the originator make available to third parties, the material and related information available and generated for the purpose of research.

___________________ ____________________ Signed Signed [Supplier] [KARI or EIAR] ___________________ ____________________ Date Date ___________________ ____________________ Signed Signed [CIMMYT] [DRRW] ___________________ ____________________ Date Date

212


Figure 2. Flow chart of logistics and procedures for screening, data distribution, curation, and exchange of germplasm evaluated in the nurseries of KARI and EIAR.

213


Activities 24.a.2 and 24.b.2: Seedling and adult plant phenotyping in greenhouses and tunnel houses in support of gene mapping and novelty studies for bread wheat at KARI-Njoro, Kenya (24.a.2), and for durum wheat at EIAR-Debre-Zeit, Ethiopia (24.b.2). New sources of resistance and mapping populations will be identified in cooperation with scientists in Objective 26, CIMMYT, ICARDA, USDA, CSIRO-Australia, University of Sydney, or other relevant organizations with an interest in identifying new sources of resistance genes for gene mapping projects. Selected lines and genetic populations will be screened against Ug99 at the seedling stage under controlled greenhouse conditions and at adult plant growth stages under semi-controlled tunnel house conditions. Two cycles (adult plant cycle from June to October and a seedling cycle from December to April) will be initiated for screening 3,000 lines at each site for bread wheat (24.b.1) and durum wheat (24.b.2). The first twelve weeks of the seedling cycle (Dec 2010 and recurring yearly) will be devoted to seedling screening followed by screening in the tunnel house during the adult plant cycle (Jun 2011 and recurring yearly). Epidemics in the tunnel house will be created using the same races as those used in seedling tests. The phenotypic data generated for seedlings and adult plants will be collated and distributed to the collaborators for interpretation (Nov 2011 and recurring yearly).

Activities 24.a.3 and 24.b.3: Confirmation and initial characterization of resistance in bread wheat germplasm at KARI-Njoro, Kenya for varieties considered for release in at-risk countries (24.a.3); Confirmation and initial characterization of resistance in durum wheat germplasm at EIAR Debre-Zeit Ethiopia for varieties considered for release in at-risk countries (24.b.3). Field resistance of candidate or released varieties will be re-evaluated in the greenhouse for seedling response (Dec 2010, recurring annually) and in the tunnel house for adult response (June 2011, recurring annually) using the methods described in 24.a.2 and 24.b.2. The objective will be to confirm the resistance response, and to initiate resistance gene postulation work (Nov 2011, recurring yearly). This will be done in consultation with Objective 25 scientists and international nursery collaborators. DNA of confirmed resistances will be shared with Objective 26 scientists and the genotyping platform of CIMMYT Generation Challenge Program to enable marker-based determination of the genetic basis of resistance (Dec 2011, recurring yearly).

Activities 24.a.4 and 24.b.4: Collection, characterization, and maintenance of stem rust cultures and monitoring of field races of stem rust in the bread wheat screening nursery at KARI-Njoro (24.a.4); Collection, characterization, and maintenance of stem rust cultures and monitoring of field races of stem rust in the durum wheat screening nursery at EIAR-Debre-Zeit (24.b.4). The source of inoculum for the pathogen being used at both screening sites will be maintained, catalogued, and multiplied in the greenhouse throughout the year, for the life of the project. Phenotypically uniform isolates will be generated from single pustules (uredinospores), multiplied as pure isolates (genetically uniform) or bulk isolates (which may be genetically heterogeneous) and stored in liquid nitrogen or the -80 freezer. The genetically pure isolates will be used for controlled inoculations in the greenhouse and tunnel house, whereas bulk isolates will be used for field inoculations. For short-term storage, purified cultures will be stored in a refrigerator while long-term storage will be in the -80 degree freezer. Monitoring and validation of field stem rust races will be done by collecting 30 random rust samples from both screening

214


sites over the duration of the screening season. These collections will then be analyzed using the standard Canadian rust differential set. Seed of these differentials, originally introduced as an output of Objective 23, will be regularly multiplied and maintained for purification at both stations. An understanding of the pathotypes in the screening nursery will inform data interpretation and the subsequent use and deployment of resistance genes (jointly with Objective 25). Data will be shared with Objective 23, which will coordinate our understanding of global virulence frequencies and patterns, and verify our understanding of existing threats and inform the probability of potential threats. Collecting and characterizing these cultures in Ethiopia and Kenya will provide learning opportunities for staff and students, and contribute to the technical capacity at these institutions. Activities 24.a.5 and 24.b.5: National pathogen surveillance and race analysis in Kenya (24.a.5); and Ethiopia (24.b.5) Regular monitoring of the frequency with which the Ug99 race occurs will provide an understanding of its evolution, which will inform the development of future breeding and gene deployment strategies. Knowledge of the spatial and temporal distribution of the pathogen will also inform the use of appropriate races in screening nurseries. Rust surveys will be conducted during the wheat growing seasons, and samples collected according to the methods specified in Objective 23. Race analyses will be performed on collected samples and virulence patterns will be determined for Kenyan races (as directed in Objective 23). Data will be shared with Objective 23, 25 and 26 and relevant stakeholders (Dec 2010, recurring yearly).

Activity 24.b.6: Characterize the nature and distribution of the stem rust population in Ethiopia’s durum wheat crop through surveys and the establishment of trap nurseries. A clear prerequisite for an optimized disease screening nursery and genetic analyses in tetraploid wheat species is an understanding of the nature and distribution of stem rust races in Ethiopia’s durum and tetraploid crops. Rust samples will be systematically collected from farmers’ fields and durum wheat trap nurseries (Sep 2010), and the nature and distribution of stem rust races will be determined (Jun 2011). Information developed on virulence frequencies and distribution patterns will be shared with other Objectives’ Activities (Aug 2011). Knowledge of virulence frequencies will be useful in developing inocula for disease screening nurseries and genetic studies. This work may lead to an understanding of the current paucity of resistance genes in the tetraploid species, and will inform a rational gene deployment strategy for tetraploid and hexaploid wheat cultivars. Activities 24.a.6 and 24.b.7: Development of a seed health protocol to be implemented in coordination with national regulatory agencies in Kenya (24.a.6) and Ethiopia (24.b.7) for receiving (importing), planting, and shipping (exporting) seed. This activity will complement the role of national quarantine regulatory authorities in Ethiopia and Kenya in providing additional protection against unintended seed borne pathogens that may arrive with incoming seed shipments. Protocols for the export of seed will also be developed in consultation with national quarantine authorities to provide additional protection to countries that receive seed from the screening nurseries. Necessary resources such as laboratory facilities and personnel will be developed at KARI-Njoro, Kenya and EIAR-Ambo, Ethiopia (Apr 2011). Seed quarantine management protocols will also be established in consultation with national quarantine authorities and CIMMYT’s seed health unit (Jun 2010). Relevant staff will be trained

215


by CIMMYT’s seed health unit professionals and national quarantine representatives (Aug 2010). Seed health management protocols will be implemented (Sep 2010, recurring for each seed shipment imported or exported), resulting in greater security against unintended incursions of seed borne pathogens.

Activities 24.a.7 and 24.b.8: In-service training opportunities and national skill development for staff members at KARI (24.a.7) and EIAR (24.b.8). A total of six opportunities will be provided for ‘Hands-on-training in Wheat Breeding’ (three month course) offered by CIMMYT for three scientists from KARI and three from EIAR to develop field skills in data recording, screening, selection and resistance breeding methods (Feb 2011, 2012 and 2013). Three exchange visits by three scientists from EIAR Ambo will be made to cereal rust labs in the USA (Y. Jin), South Africa (Z. Pretorius) and Australia (R. Park). These exchange visits will allow close and focused interaction of scientists in greenhouse cereal rust methods and host-pathogen genetics (Jul 2011, 2012 and 2013) at these advanced research institutes. . Three scientists from KARI and three from EIAR will participate in three international conferences or workshops (relevant conferences in 2010, 2011, 2012, 2013). These meetings will be identified in collaboration with the project management unit taking advantage of previously scheduled meetings. During the main season of each of five years of the project, one post-graduate student intern from Kenya will be recruited and trained in area of cereal rust genetics, breeding, and pathology by the screening facilities team and international visiting experts. In Ethiopia, at least two local training sessions will be held for technicians working on wheat pathology in greenhouse and field experiments at each center (Apr 2010 and Apr 2011). Five annual seminars (one during each main season) will be organized by KARI staff during the peak time for international visitors and experts coming to the screening nursery. Similar seminars organized by EIAR for scientists visiting Ethiopia are contemplated, though formal details have yet to be arranged.

Activities 24.a.8 and 24.b.9: Strategic investments to enhance the precision and capacity for generating reliable and accurate stem rust phenotypic data at KARI-Njoro screening facilities (24.a.8); and EIAR-Ambo plant health lab and EIAR-Debre-Zeit screening sites (24.b.9) Immediate investments will be made in key areas identified during Phase I, such as improving the reliability and accuracy of data collection. The development of screening nursery field research areas including a complete irrigation system and land leveling, and the renovation of greenhouses, laboratory, seed preparation, and threshing facilities are among the areas targeted for immediate improvement identified during Phase I by those who frequently use these facilities: CIMMYT scientists, principal scientists at KARI and EIAR, Objective 25 CIMMYT staff (Drs. Ravi Singh, Karim Ammar, Yann Manes), ICARDA staff (Dr. Osman Abdalla), DRRW contributors Drs. Mike Pumphrey (Objective 26), Robert Park, Yue Jin and Zak Pretorius (Objective 23), as well as key NARS and USDA personnel.

The demand for screening of breeding germplasm and mapping populations has almost doubled at KARI-Njoro since the project’s inception, thus requiring more irrigated land for reliable screening of germplasm (Activity 24.a.1). This will result in an increase from 12 to 15 hectares of irrigated nursery, with five hectares available per season to accommodate a three year rotation. Three and one-half hectares per season will be used at Debre-Zeit for screening durum germplasm. All capital investments in equipment and facilities will be initiated or encumbered

216


within one year from the commencement of Phase II activities. New staff members requested under the Phase II proposal will be interviewed within three months of the project start date. Within three months from the inception of Phase II, revised Memoranda of Understanding (MOUs) that define the relationship between CIMMYT and EIAR, and between CIMMYT and KARI with regard to disbursement of funds and management of screening facilities’ operations will be developed. IV. Management Plan Management of Objective 24 will be carried out jointly by staff members of KARI, EIAR and CIMMYT with support from the Cornell Project Management Unit. The CIMMYT Objective leader will be the International focal point and is responsible for overall management of the objective in consultation with two national coordinators/focal points from each institute (KARI and EIAR). The CIMMYT Objective leader will ensure timely communication, data sharing and germplasm exchange with international collaborators as per guidelines outlined in Fig 1 and in the Germplasm Acquisition Agreement. He will also maintain communications between Objective 24 collaborators and those from Objectives that intersect with its activities (Objectives 21, 23, 25, and 26). At the end-of-each season, he will also compile report on the frequency of R / MR / MS / S phenotypic response to the predominant pathotype. This becomes a long-term measure of progress toward resistance to Ug99 lineage. KARI and EIAR coordinators will be responsible for managing their respective teams and reaching the milestones of all in-country activities (e.g. seed import/export, timely planting, inoculation, irrigation, communications regarding nursery visits, preparation of data and/or seed for return to cooperators) and generating financial and management reports. For Ethiopia, single-site managers will be designated under the EIAR coordinator for the Debre-Zeit and Ambo research investments.

Memoranda of Understanding (developed during the first phase) between CIMMYT/EIAR and CIMMYT/KARI that clearly delineated respective roles and responsibilities will be modified and implemented. Within the first phase, both KARI and EIAR identified teams to carry out project activities with specified responsibilities. New recruitments or adjustments in team responsibilities will be made to address additional activities. The CIMMYT Objective leader and national coordinators are already in place and will be employed in Phase II. Work plans for individual seasons at each facility will be developed jointly (one season in advance) between the CIMMYT team leader and national coordinators. Separate sub-grants will be issued by Cornell to KARI, EIAR, and CIMMYT. Developed countries that fall outside of the CGIAR mandate can access nursery services through a fee-for-service model (Figure 3) developed in Phase I and extended to Phase II. Fee-for-service will be either in-kind services or in US dollars and negotiable, where appropriate. Management of the fee-for-service income will be by the CIMMYT Objective leader in consultation with KARI and EIAR coordinators. Income generated from this activity will be invested in facilities or projects that foster outcomes which contribute to this Objective. The budget proposed for this Objective is designed to cover all operating costs with the assumption that the full resources (capital and human investments, or other details described in the work plan) are approved. Annual budgets are accordingly not tied to fee-for-service, and MOUs will confirm that the land developed and designated for phenotypic screening is not used for any other purpose (except non-research rotation crops).

217


The BGRI website www.globalrust.org will serve as a central information hub. Protocols and forms for submitting materials for testing, agreements (material transfer and fee-for service), site visits and data are already posted or developed for Phase I, and will be regularly updated in Phase II. The Cornell Project Management Unit, CIMMYT Objective leader, and national coordinators will communicate via password-protected areas on the BGRI website, as well as by email, VOIP, monthly conference calls and strategic visits.

Figure 3. DRRW Fee for Service Agreement (FSA) for materials not included under General Acquisition Agreement (GAA) of Standard Material Transfer Agreement of the International Treaty for Plant Genetic Resources for Food and Agriculture. [Supplier] agrees to pay a fee for service under the [Category] category selected from the list of categories established under DRRW for screening of germplasm at KARI or EIAR. This is for germplasm that is not covered under the Standard material transfer agreement (sMTA) of the International Treaty for Plant Genetic Resources for Food and Agriculture

Category Applicable to Specification Charges (USD$)

LDC 1 LDC sharing both data and germplasm 0

LDC 2 LDC sharing only information but not germplasm 10

LDC 3 LDC sharing germplasm but not information 10

LDC 4 LDC sharing neither information nor germlasm 15

IDC 1 IDC sharing data and germplasm 10

IDC 2 IDC sharing only information and not germplasm 15

IDC 3 IDC sharing germplasm but not information 15

IDC 4 IDC Sharing neither information nor germlasm 20

LDC = Developing Country Partners IDC = Industrial Country /Private Industry Partners ___________________ ____________________ Signed [Supplier] Signed [KARI or EIAR] ___________________ ____________________ Date Date

___________________ ____________________ Signed [CIMMYT] Signed [DRRW] ___________________ ____________________

Date Date

Name Institution Email Relevant Activities and Outputs Sridhar Bhavani CIMMYT [email protected] 24.a.1, 24.a.2, 24.a.3, 24.a.4,

24.a.5, 24.a.6, 24 a.7, 24.a.8, 24.b.1, 24.b.2, and 24.b.3, 24.b.4, 24.b.5, 24.b.6, 24 b.7, 24.b.8 and 24.b.9

Peter Njau (wheat breeder, Njoro Team

KARI [email protected] 24.a.1, 24.a.2, 24.a.3, 24.a.4, 24.a.5, 24.a.6, 24 a.7, 24.a.8,

218


Leader) 24.b.1, 24.b.2 Additional members of the KARI -Njoro team

KARI 24.a.1, 24.a.2, 24.a.3, 24.a.4, 24.a.5, 24.a.6, 24 a.7, 24.a.8, 24.b.1, 24.b.2

B. Girma EIAR [email protected] 24.b.3, 24.b.4, 24.b.5, 24.b.6, 24 b.7, 24.b.8 and 24.b.9

Additional members of EIAR Ambo and Debre-Zeit teams

EIAR 24.b.3, 24.b.4, 24.b.5, 24.b.6, 24 b.7, 24.b.8 and 24.b.9

R. Park U Sydney [email protected] 24.a.5, 24.a.6, 24.a.7, 24.b.5, 24.b.6, and 24.b.8

Z. Pretorius U Free State [email protected] 24.a.7 and 24.b.8 Y. Jin USDA [email protected] 24.a.7 and 24.b.8 R. Singh CIMMYT [email protected] 24.a.1, 24.a.2, 24.a.8 and 24.b.8 M. Pumphrey Washington

State U [email protected] 24.a.2 and 24.b.2

K. Nazari ICARDA [email protected] 24.a.5, 24.b.5 and 24.b.6

V. Potential Risks and Unintended Consequences The success of this Objective relies heavily on the routine exchange of germplasm to and from screening nurseries in East Africa. Risks can be associated with the germplasm exchange in relation to phytosanitary problems, quarantine requirements, and germplasm ownership. In Phase I we experienced a commitment to the successful import (both Ethiopia and Kenya) and export (Kenya) of seed. Substantial caution will be exercised in Phase II to further preclude import or export of seed borne disease and stem rust spores by working with national quarantine regulatory authorities and establishing seed health units for both screening sites (activities 24.a.6 and 24.b.6). All germplasm will be exchanged under the international treaty of standard material transfer agreement (SMTA).

It has been argued that of the large amount of inoculum in screening nurseries may increase the likelihood of new virulent races emerging. However, it is our opinion that the evolution of a new virulence arising from nursery operations is very low, and is a risk which must be accepted if the reward of developing cultivars with resistance to Ug99 is to be realized.

Establishment of stem rust inoculum and development of an epiphytotic in screening nurseries requires careful agronomic management, pure and viable pathotypes, and consideration of plant growth stages and climatic conditions which may be controlled with irrigation. Failure to meet these conditions can result in seasonal variability in the nursery data. For example, during the main season of 2008, a severe epidemic developed because of fortuitous climatic conditions, but the 2008-2009 off-season nurseries faced drought conditions and, due to limited irrigation capacity, the epidemic did not fully develop. However, these variables can be addressed through nursery management, and resources have been included in this Phase II proposal to mitigate these risks.

219


Key to the effectiveness of this objective is the efficient coordination between the screening facilities teams (KARI, EIAR, and CIMMYT) and other relevant stakeholders in the international stem rust community. Such effective coordination was experienced in Phase I, and the guidelines developed at that time will provide the framework to ensure continuing smooth operations and international exchange of information.

National policies could change, and a change in national support for operations of the screening facilities could adversely affect project outputs. This is a negligible risk since both screening sites have been designed to be financially independent of KARI and EIAR budgets. Furthermore, the national advantages associated with these facilities and projects serves to further reduce these risks.

East Africa is vulnerable to civil or international conflicts, and risks related with these issues are unavoidable. Though Ethiopian and Kenyan screening sites are designed to target specific virulence and/or wheat ploidy levels, a short-term solution would be for either to undertake the responsibilities of the other in the event that one is rendered inoperable by such circumstances. The likelihood of this risk is deemed to be very low.

Inadvertent trans-boundary spread of Ug99 is a continuing concern. Prevention of this possibility is of utmost concern to this project. Protocols have been developed and are enforced to mitigate this concern.

VI. Evidenced based rationale for choice of partners (including current and potential funds) For each institute/scientist listed as a funded participant or close collaborator, the relevant activities and outputs for each are listed in Table 24.1. The choice of organizations and the key staff to implement activities and outputs of the project have been made based on the following advantageous merits and profiles of these organizations and staff:

KARI is the Kenya Agricultural Research Institute, established as a semi-autonomous government institution and has a national mandate of implementing national, regional and global agricultural projects. Over the last 25 years, KARI has developed a strong physical resource base with support from the Kenyan government and a number of multilateral and bilateral donors. KARI has 21 research centers and 14 sub-centers across Kenya. KARI-Njoro’s research focus is on crop improvement with a strong wheat breeding component. KARI-Njoro displayed good leadership and cooperation during the first phase of the project. The KARI staff has national expertise to support desired areas of the proposed objectives. Peter Njau is the principal plant breeder for KARI, and also holds the title of Deputy Director. He will be the acting coordinator for the Kenya component of this Objective. Peter has more than 15 years experience in plant breeding and has updated his skills under Phase I of DRRW. Peter is currently obtaining his in-service Ph.D. in Plant Breeding in Switzerland, and has contributed significantly to this project in Phase I. His team includes principal pathologist Ruth Wanyera who has more than 20 years of experience in plant pathology and rust epidemiology.

EIAR is one of the principle NARS of Ethiopia with regional centers including Debre-Zeit Agricultural Research Center (with a strong focus on durum improvement), Kulumsa Agricultural Research Center (focusing on bread wheat improvement) and Ambo Plant

220


Protection Research Center (focusing on plant pathology and plant protection). EIAR has successfully implemented the activities of Phase I, and has the capacity to undertake the activities of Phase II. Facility upgrades have been planned or initiated at these stations, and will have reasonable capacity for screening international germplasm for rust resistance upon completion. Dr. Bedada Girma, the national cereals research program coordinator (also coordinator for DRRW in Ethiopia), will be acting coordinator for the Ethiopia component. His team is comprised of doctorate-qualified scientists (Dr. B. Ayele at Debre-Zeit and Dr. W. Getaneh at Ambo) at both research centers with good knowledge of breeding and pathology. Dr. Bedada Girma is also coordinating another project funded by AGRA to develop and disseminate adapted wheat varieties with tolerance to wheat stem rust for the moisture stress and marginal areas of Ethiopia to reduce hunger and poverty among smallholder Ethiopian farmers. Dr. Bedada Girma is instrumental in linking the project with other regional projects and agencies.

CIMMYT is an internationally funded, nonprofit scientific research and training organization, (headquartered in Mexico) with a strong global wheat program emphasizing the improvement of wheat in developing countries including sub-Saharan Africa. CIMMYT acts as a catalyst and leader in a global wheat innovation network that serves the poor in the developing world. Drawing on strong science and effective partnerships, CIMMYT researchers create, share, and use knowledge and technology to increase food security, improve the productivity and profitability of farming systems and sustain natural resources. It has a regional office both in Kenya (Nairobi) and Ethiopia (Addis). The CIMMYT scientist will be based in Kenya and will benefit from the strategic location of CIMMYT East-Africa offices and the networks developed by these offices in coordinating the regional and global activities. The CIMMYT scientist (Dr. Sridhar Bhavani) is trained by Robert Park and Ravi Singh and has spent several years in the Cereal Rust Laboratory at the University of Sydney and at CIMMYT-Mexico as a DRRW collaborator in Phase I. He has strong expertise in area of cereal rust genetics, breeding for resistance and molecular techniques. Dr. Ravi Singh, based at CIMMYT headquarters, has a strong shuttle-breeding program with East Africa under Objective 25. Dr. Ravi Singh has expertise in rust resistance breeding, genetics and pathology, and is instrumental to training KARI and EIAR staff. Dr. Hans Braun is the Director of the Global Wheat Program of CIMMYT. He will handle the management issues on behalf of CIMMYT. The other CIMMYT scientists involved will be Dr. Yann Manes (leading CIMMYT rain-fed wheat breeding program), Dr. Karim Ammar (leading CIMMYT durum wheat program) and Dr. Monica Mezzalama (leading CIMMYT seed inspection and distribution unit).

Two world-established and renowned cereal rust laboratories of University of Sydney and University of Minnesota (historically associated with Drs Waterhouse and Stakman, respectively) and one regional African lab (University of Free State, South Africa) have been chosen for capacity and skill development of KARI and EIAR staff. These three labs will be involved in training national staff members in cereal rust pathology and genetics. Dr. Robert Park (University of Sydney) is currently the Director of the Australian Cereal Rust Control Program and is also the team leader of Objective 23. He is widely recognized as a leader in cereal rust pathology. Dr. Yue Jin is a Research Plant Pathologist with USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota. He is very proficient in stem rust pathology and holds good knowledge of regional rust epidemiology. Dr. Zak Pretorius (who identified Ug99) is a Professor at the University of Free State and is a globally renowned rust pathologist. He has a well-equipped rust lab with good race analysis and screening facilities. His regional location is

221


important for upgrading the capacity of labs and staff in Kenya and Ethiopia. Dr. Kumarse Nazari (Cereal Pathologist of ICARDA) will also be involved in race analysis activities by providing trap nurseries and pure seed of differential sets. Dr. Nazari has commendable expertise in rust pathology and trap nurseries. Dr. Michael Pumphrey, formerly a Senior Geneticist with USDA-ARS and now a Professor at Washington State University, will be the Objective 26 contact for screening of mapping populations and novel sources of resistance. He has strong expertise in molecular genetics and mapping of resistance genes and will be the primary contact for rationalizing the resources for Activities listed in the management Plan section of this proposal.

222

Appendix C: Detailed Description of Proposed Work / Durable Rust Resistance in Wheat Phase II Objective 25 Durably resistant, high yielding wheat varieties

Summary Information (Objective Level) Objective Name: Objective 25: Durably resistant, high yielding wheat varieties. Team Leader for this Objective: Hans-Joachim Braun

E-mail [email protected] Collaborating Institutions with Budgeted Activities

Institution Primary Contact) email CIMMYT Dr. Hans-Joachim Braun [email protected] ICARDA Dr. Michael Baum [email protected] EIAR (Ethiopia) Dr. Solomon Assefa [email protected] ICAR (India) DG or DWR KARI (Kenya) Peter Njau [email protected]



60


223


Executive Summary

Summary of Short, Medium, and Long Term Outcomes Five years

• Spring bread wheat varieties with resistance to TTKSK and other derivatives of Ug99 with >5% higher yields are planted in Afghanistan, Bangladesh, Egypt, Ethiopia, India, Iran, Kenya, Mexico, Morocco, Nepal, Pakistan, South Africa, Syria, Tanzania, and Turkey.

• Durum wheat varieties with TTKSK and broad stem rust resistance, with >5% higher yields are planted in Ethiopia and India.

• Enough seed is available in target countries to replace >20% wheat area as necessary from Ug99 migration.

• Higher proportions of CIMMYT and National Programs’ breeding materials contain parents with diverse resistance to TTKSK and its derivatives, ensuring long-term sustainability of wheat improvement research related to stem rust resistance.

• Scientists and staff at critical facilities in Ethiopia, India and Kenya possess skills to collect and manage quality-assured data.

• A new generation of wheat scientists engaged is in short-term and long-term wheat improvement research to meet future demands on wheat as a global food staple.

• Data quality is assured, and data management tools are in use beyond the tenure of this project.

Ten Years • Enough spring bread wheat seed is available in target countries to replace >40% wheat area

as necessary from Ug99 migration.

• Durum wheat varieties with stem rust resistance to Ug99 and its derivatives and with 5% higher yields are planted in Ethiopia, India, Morocco, Syria, Tunisia and Turkey.

• Several diverse second generation spring bread wheat varieties that have a high level of adult plant resistance (APR) or at least two effective major genes, and with 10% greater yield potential than current varieties, are released in various countries and comprise 5-20% of the spring wheat area.

• The Ug99 threat is mitigated through the wide cultivation of diversely resistant varieties. The critical facilities in East Africa are fully sustainable operations, actively contributing to improving food security in their respective countries and regions, while continuing to contribute to global wheat improvement efforts.

• All NARS partners have efficient variety development and replacement systems in place to benefit all wheat growers. Losses due to stem rust are minimized.

• The project partners have fully sustainable operations and are actively contributing to improving food security in their respective countries and regions while continuing to contribute to global wheat improvement efforts.

224


• Data exchange through user-oriented web portals rapidly affects policies that favor wheat economic productivity for small-holder farmers in developing nations.

Fifteen Years • Spring and winter bread wheat and durum wheat productivity is enhanced by 10% in the

majority of countries sown with varieties resistant to the Ug99 family of pathogypes, and with broad resistance to all stem rust variants.

• Several diverse third generation spring and winter bread wheat and durum wheat varieties that have a high level of APR, or are protected by at least two effective major genes, and with 15% greater yield potential than current varieties are released in various countries and occupy 10-40% spring wheat area.

• Global wheat production, and the stability of this production, is increased and able to meet the demands of growing populations.

• International efforts to mitigate the effects of stem rust on small-holder farmer are no longer limited by lack of access to germplasm, data, seed and knowledge.

• The methods developed as a result of this Objective render plant breeding a more family friendly career for both men and women.

Progress to Date Recognizing that wheat stem rust race Ug99 (TTKSK) posed a threat to global food security, screening efforts to identify effective sources of resistance began in 2005 in Kenya and Ethiopia. Crossing, though limited, was initiated in 2006 to transfer sources of resistance in high-yielding wheat varieties and new breeding materials. Phase I of the DRRW project enabled us to build on our initial work and implement an aggressive approach to provide wheat programs in at-risk countries with more resistant germplasm and information regarding the genetic basis of resistance. During Phase I, more than 20,000 CIMMYT, ICARDA, and National Program lines were evaluated annually in Kenya and/or Ethiopia. Resistant seedlings were challenged with Ug99 (TTKSK) in the greenhouse of USDA-ARS at St. Paul, MN. Where applicable, molecular markers linked to known major genes were used to identify the gene providing resistance. The information generated from this massive screening effort provided the following:

• Identification of a few existing varieties, or candidate varieties in various stages of advanced testing in National Program’s wheat materials that are resistant to TTKSK. As a result, the variety “Lasani 2008” was released in Pakistan in 2008.

• Identification of elite CIMMYT lines resistant to stem rust for potential release. CIMMYT and ICARDA are providing three tons of seed of several resistant lines through a USAID-funded project to six at-risk countries (Afghanistan, Bangladesh, Egypt, Ethiopia, Nepal and Pakistan). India, Iran, and Turkey are also engaged in seed multiplication of resistant varieties. Two varieties were released in Egypt and three in Afghanistan.

• Distribution of international observation nurseries and yield trials of spring bread wheat having resistance to TTKSK: Elite Bread Wheat Yield Trial (EBWYT, initiated in 2005), and the Stem Rust Resistance Screening Nursery (SRRSN).

225


• The percentage of resistant or moderately resistant accessions in CIMMYT’s most recent standard International Spring Bread Wheat Nurseries (30thESWYT and 42ndIBWSN, which are nurseries not specifically distributed in response to Ug99), is now at 80 and 50%, respectively1. Since a majority of entries in the ESWYT are becoming resistant to the Ug99 and its derivatives, it is expected that the 5th EBWYT, to be distributed for the 2010-2011 crop season, will be the last trial for this nursery.

• Diverse sources of resistance were identified and information for the majority of lines regarding the genetic basis of resistance (major gene, APR), are provided with the nurseries.

• Eighty percent of the crosses made in the CIMMYT and ICARDA spring bread wheat programs have at least one Ug99 resistant parent. At the end of Phase II most accessions distributed in international nurseries will be resistant to stem rust, including Ug99 and its derivatives.

• Global exchange of Ug99 resistant germplasm has been established.

• Pre-release seed multiplication of TTKSK resistant lines selected from 2nd EBWYT, 3rd EBWYT and 4thEBWYT is ongoing in Ethiopia, Egypt, Pakistan, Afghanistan, Bangladesh, and Nepal (all supported by USAID funding). India, Turkey and Iran are also increasing seed of resistant varieties, with more than 150 tons of seed available for 2008-2009 season multiplication. Available harvest data from Nepal and India showed excellent performance of resistant lines selected for distribution. Based on available data, the CIMMYT-derived variety “Frankolin” had more than 10% performance advantage over local cultivars (Figure 25.1) in Nepal and the Eastern Gangetic Plains.

• Two Ug99 resistant cultivars from ICARDA are being promoted. One in Ethiopia, and the other, a red-seeded PBW343 derivative, in India.

• New wheat lines were developed as a result of Mexico-Kenya shuttle breeding of segregating populations utilizing two crop seasons per year in Mexico (Cd. Obregon and Toluca) and two (main season and off-season) in Kenya.

1 While these rates may appear to be low, the majority of germplasm distributed prior to the initiation of Phase I was Ug99 susceptible. In these standard CIMMYT nurseries, the levels of resistance to leaf, stem and yellow rust need not reach 100% since the germplasm can be targeted to regions where one or more of the rusts do not occur.

226


Figure 25. 1. Mean performance of ten new early maturing CIMMYT-derived bread wheat genotypes, including Francolin#1 (Waxwing*2/Vivitsi) in comparison to the best check cultivar ‘HUW 234’ at research station of B.H.U. Varanasi, India and eight farmers fields in different villages in northeastern Gangetic Plains of India, during 2006-2007 crop season

(Source: Dr. A.K. Joshi, B.H.U., Varanasi). Yield Performance Results of Ug99 Resistant Entries in the 4th Elite Bread Wheat Yield Trial (4thEBWYT). The 4thEBWYT was multiplied in El Batan during 2008 summer season and 51 sets were prepared and distributed for planting during 2008-2009 crop season. Twenty-four entries have adult plant resistance whereas resistance of 4 entries was based on Sr25 and one on SrHUW234. Shipment details of 4thEBWYT are the following: Nepal: 2 sets, Bangladesh: 2 sets, India: 10 sets, Pakistan: 5 sets, Afghanistan: 3 sets, Iran: 5 sets, Turkey: 3 sets, Syria: 1 set, Egypt: 4 sets, Morocco: 3 sets, Ethiopia: 3 sets, Kenya: 1 set, Mexico: 5 sets, Sudan: 2 sets, Azerbaijan: 1 set and Tunisia: 1 set. Data were obtained from seven countries (India, Pakistan, Afghanistan, Iran, Nepal, Bangladesh and Mexico). Results for five countries are summarized in Table 25.1.

Twenty-eight entries on the average had 100-114% yield of the local checks used at 10 sites in India. Five entries, including Munal#1 (CIMMYT check) yielded on the average 10-14% higher than the checks. Ten sites represent very diverse environments in NWPZ, NEPZ, and Central and peninsular zones. Considering NWPZ (6 sites), all entries yielded more than the local check and 11 entries had 110-119% higher yields than the checks (mostly PBW343). Whear/Sokoll (entry 529) with Sr25 gene was the best yielder with 19% higher yield than the check in NWPZ. This was followed by Waxwing*2//PBW343*2/Kukuna (entry 527), which had 17% higher yields and APR to stem rust. NWPZ is the main wheat basket of India. CIMMYT check Munal#1 has

227


continued to demonstrate significant superiority over the checks in India now for three years of testing in EBWYTs and is under broad testing and seed multiplication by a private seed enterprise.

Trials were grown in Pakistan at five diverse sites from Peshawar in the North and Sindh province in the South. Four entries, numbered 508, 515, 519 and 530, on the average yielded 7-11% higher the mean of the local checks (different check at each site). Similarly in Iran, trials were grown at five diverse sites including sites where facultative wheats are grown. On average eight entries had 100-108% yields compared to the check. The best line based on the overall average was entry 527 (Waxwing*2//PBW343*2/Kukuna), the 2nd best entry in India.

Fourteen lines yielded 10-26% higher in Afghanistan based on the means for three sites. We could not conduct a combined analysis for Afghanistan as the cooperator had submitted analyzed means. Data from one site were returned from Nepal, with 10 lines yielding 10-28% higher than the check. Munal#1 was the 2nd best yielder (24% higher yield than the check) and entry 527 (Waxwing*2//PBW343*2/Kukuna) yielded 28% higher than the check.

Data for Bangladesh are not presented as no entry was superior to the local check. Clearance of trials was delayed in Egypt, Turkey and Morocco and hence planting was done during the 2009-2010 crop season. For other countries we await results from our cooperators. Trials were grown in Ethiopia, however data are not available to us though it has been requested and is committed.

Entries included in 4thEBWYT were also multiplied in Mexicali during 2008-2009 crop season. Extra seed of selected entries was provided to various countries (Nepal, Bangladesh, Afghanistan, India, Pakistan and Iran) for simultaneous seed multiplication and further testing.

228

Table 25.1. Yield performance of entries in the 4th EBWYT in five countries. India (10 sites) Pakistan (5 sites) Iran (5 sites)

Afghanistan (3 sites) Nepal (1 site)

Entry Cross kg/ha % Ck Kg/ha % Ck kg/ha % Ck Kg/ha % Ck kg/ha % Ck 501 LOCAL CHECK 3460 100 3193 100 6916 100 4369 100 3644 100 502 MUNAL #1 3828 111 3077 96 6750 98 4692 107 4519 124 503 KIRITATI/4/2*SERI.1B*2/3/KAUZ*2/BOW//KAUZ 3466 100 3272 102 6838 99 5129 117 3148 86 504 TRCH*2//PFAU/WEAVER 3567 103 2670 84 7092 103 4815 110 3963 109 505 SAAR/2*WAXWING 3577 103 2912 91 6643 96 4457 102 4000 110

506 SERI.1B*2/3/KAUZ*2/BOW//KAUZ*2/5/CNO79//PF70354/MUS/3/PASTOR/4/BAV92 3504 101 3164 99 6662 96 4672 107 3852 106

507 PBW343*2/KUKUNA/3/PASTOR//CHIL/PRL/4/PBW343*2/KUKUNA 3700 107 3334 104 6331 92 5058 116 4082 112 508 WHEAR//INQALAB 91*2/TUKURU 3385 98 3615 113 7105 103 5516 126 4074 112 509 PBW343*2/KUKUNA//PBW343*2/KUKUNA 3705 107 3180 100 6173 89 4649 106 2933 80 510 PBW343*2/KUKUNA//PBW343*2/KUKUNA 3823 110 3285 103 6736 97 4652 106 3585 98 511 PBW343*2/KUKUNA//PBW343*2/KUKUNA 3625 105 3276 103 6286 91 5078 116 3111 85

512 CNDO/R143//ENTE/MEXI_2/3/AE.SQ.(TAUS)/4/WEAVER/5/2*PASTOR/6/SKAUZ/PARUS//PARUS 3533 102 3236 101 6977 101 5049 116 3496 96

513 MINO/898.97 3590 104 3045 95 6179 89 4337 99 3459 95 514 PICAFLOR 3609 104 2801 88 7129 103 5111 117 3889 107 515 WBLL1*2/BRAMBLING 3647 105 3447 108 6777 98 5032 115 4037 111 516 BECARD 3857 111 3157 99 6941 100 4643 106 4185 115 517 BECARD 3616 105 3251 102 6959 101 5067 116 4148 114 518 BECARD 3581 104 3319 104 6838 99 4500 103 3259 89 519 PRL/2*PASTOR//PBW343*2/KUKUNA 3655 106 3431 107 6454 93 4919 113 4000 110 520 PBW343/HUITES/4/YAR/AE.SQUARROSA (783)//MILAN/3/BAV92 3372 97 2965 93 5736 83 4638 106 3341 92

521 KAUZ//ALTAR 84/AOS/3/PASTOR/4/MILAN/CUPE//SW89.3064/5/KIRITATI 3444 100 3142 98 5968 86 4688 107 3704 102

522 SW89.5277/BORL95//SKAUZ/3/PRL/2*PASTOR/4/HEILO 3631 105 3228 101 6807 98 4618 106 3526 97

523 SERI.1B*2/3/KAUZ*2/BOW//KAUZ/4/PBW343*2/TUKURU/5/C80.1/3*BATAVIA//2*WBLL1 3652 106 3286 103 6039 87 4221 97 3852 106

524 PFAU/SERI.1B//AMAD*2/3/PBW343*2/KUKUNA 3641 105 2928 92 6502 94 4445 102 3563 98 525 PFAU/SERI.1B//AMAD*2/3/PBW343*2/KUKUNA 3758 109 2992 94 6117 88 4618 106 3778 104

526 PRL/2*PASTOR//PBW343*2/KUKUNA/3/TACUPETO F2001*2/KUKUNA 3808 110 3060 96 6604 95 4725 108 3556 98

527 WAXWING*2//PBW343*2/KUKUNA 3937 114 3160 99 7469 108 4977 114 4667 128 528 HUW234+LR34/PRINIA//PBW343*2/KUKUNA/3/ROELFS F2007 3623 105 3057 96 6570 95 4902 112 3556 98 529 WHEAR/SOKOLL 3959 114 3370 106 6881 99 5285 121 4333 119 530 WHEAR//2*PRL/2*PASTOR 3541 102 3535 111 7015 101 5361 123 3348 92 LSD 199 299 519 606 CV 8.8 4.77 8.85 8.00

Herita-bility 0.4 0.69 0.59 0.74

229


Narrative of Proposed Work The work described here continues the Durable Rust Resistant Wheat (DRRW) Phase I wheat breeding activities. The overarching and near-term goal is to provide National Programs in at-risk countries with a continually improved and diverse array of situation-appropriate candidate varieties that combine stem rust resistance with attributes required for rapid uptake by small-scale farmers. An equally important mid- and long-term goal is to provide a focus and capability for research organizations to maintain resistance to a variable pathogen population. For spring bread wheat (Activity 25.a.1 and 25.a.2) and durum wheat (Activity 25.b.1), CIMMYT’s long standing two generations per year Mexico-based ‘shuttle’ breeding system continues to be augmented with selection at the East Africa phenotyping sites (see Objective 24) to enable selection of candidate replacement varieties with resistance to the Ug99 family of pathotypes, and broad stem rust resistance in general. Durum breeding, now more directly focused in Ethiopia, provides continued benefits to India and other at-risk durum producing countries. The durum work described here will involve close collaboration with in-country breeding supported by EIAR at the Debre Zeit Agricultural Research Institute. Candidate replacement varieties derived from all International Center breeding activities are distributed to national programs through CIMMYT’s international testing network. The past years have demonstrated a pressing need to expose National Program scientists to techniques not only in stem rust pathology and resistance breeding, but also in the design, execution, and analysis of multi-location performance trials. In Activity 25.d.1, we describe a suite of training events to address this need. We also propose to invest in the wheat component of ICIS (International Crop Information System, http://www.icis.cgiar.org/icis/index.php/ICIS) in order to reach the long-sought goal of a user-friendly common platform that will facilitate information management and sharing aspects of field nursery, yield trial, pedigree, and molecular marker data. Collectively, these Activities and associated investments address nearly 50 million hectares of wheat in developing countries that are threatened by Ug99 and its derivatives and lay the foundation for a new era of cooperative, global wheat improvement.

Justification for Proposed Work The best control strategy for rust diseases of wheat for resource poor farmers in the developing world—and the most environmentally friendly and profitable strategy for commercial farmers everywhere—is to grow genetically resistant varieties. The cost of protecting one hectare of wheat from rust epidemics through modern chemicals can range from USD 50-80 (Singh et al. 2004). Cultivation of resistant wheat varieties has no additional cost to farmers and has succeeded in reducing chemical use across about two-thirds of the 215 million hectares sown to wheat worldwide. The use of resistant varieties thus increases profit margins, helps keep the price of staple crops affordable, and has a beneficial effect on human and environmental health, given that fewer agrochemicals are applied to the crop (Marasas et al. 2004). Improved varieties are also vehicles to enhance farmers’ profitability by delivering new scientific innovations as a package of various genetically controlled desirable traits such as higher yield potential, water and nutrient use efficiency, tolerance to heat and other stresses, and end-use quality characteristics. A small group of improved breeding lines of wheat with diverse sources of both race-specific and complex adult-plant resistance to the Ug99 race of stem rust, identified recently through rigorous

230


field and greenhouse testing, can now be employed in developing and delivering wheat cultivars with more durable resistance and other desired characteristics (Singh et al. 2006).

II. Log Frame Table

See next page.

231


Objective 25: Durably resistant, high yielding wheat varieties



25.a. Bread wheat.

25.a.1. Spring bread wheat varieties with Ug99 resistance for irrigated and higher production environ-ments of Africa, Middle East, West, Central and South Asia

Between 30–50 high yielding, rust resistant potential replacement varieties tested annually in replicated yield trials in various countries at more than 50 field sites (Oct 2011, recurring annually)

Between 100–150 additional high yielding, multiple rust resistant lines distributed annually for evaluation and selection as small plots at more than 100 sites worldwide (Oct 2011, recurring annually)

About 10 new multiple rust resistant varieties with >5% higher yield potential than current cultivars released officially in various countries (Dec 2014)

Application of appropriate breeding methodology and use of germplasm with durable resistance promoted for NARS breeding programs (Dec 2010, recurring annually)

Strong partnerships built for the fast release and promotion of new stem rust resistant cultivars (Feb 2013)

Five years Bread wheat varieties with Ug99 resistance and >5% higher yields are planted as follows (joint with Objective 21): • Kenya (50% of wheat area), • Ethiopia (20% of wheat area), • India (5% of wheat area), • Pakistan (10% of spring wheat area), • Egypt (20% of wheat area), • Afghanistan (20% of spring wheat

area) • Iran (40% of spring wheat area) • Nepal (10% of wheat area) • Bangladesh (10% of wheat area) • Mexico (10% of wheat area) • Other spring wheat growing countries

(1-5% of the wheat area) Enough seed availability in target countries to replace >80% wheat area as necessary from Ug99 migration.


Ten Years Between 40-80% spring wheat area in above and other countries replaced by Ug99 resistant varieties that enhance wheat production through increased yield

R. Singh, CIMMYT, Mexico

232




potential.


Ug99 threat mitigated through the wide cultivation of resistant varieties and production enhanced due to their higher yielding capacity.

Fifteen Years 80% spring wheat area in majority of countries sown to Ug99 resistant varieties that enhance wheat productivity by about 10%.

Several diverse 3rd generation of wheat varieties that have a high level of APR or protected by at least two effective major genes and with >15% high yield potential than current varieties released in various countries and occupy 5-40% spring wheat area.

More wheat available to meet the increasing demand.

25.a.2.

Spring bread wheat varieties with Ug99

15–20 lines sent every year to NARS coming from rainfed international trials and screening nurseries with good yield potential, tolerance to drought and resistance to yellow rust, leaf rust and

Five Years Bread wheat varieties with Ug99 resistance and >5% higher yields are planted as follows (joint with Objective 21). • Afghanistan (5% of spring wheat area)

Y. Manes, CIMMYT, Mexico

233




resistance for drought-stressed and low production environ-ments of Africa, Middle East, West, Central and South Asia..

Ug99 stem rust (Oct 2011, recurring annually)

At least 50 lines sent to NARS with good yield potential, tolerance to drought, resistance to yellow rust, leaf rust and Ug99 stem rust (Mar 2011), recurring annually)

3–4 stem rust resistant varieties selected for release by NARS (Dec 2014)

• Ethiopia (10% of wheat area) • India, (1% of wheat area) • Iran (5% of spring wheat area) • Kenya (5% of wheat area) • Mexico (5% of wheat area) • Morocco (1% of spring wheat area) • Nepal (1% of wheat area) • Pakistan (1% of wheat area) • South Africa (1% of spring wheat area) • Syria (5% of wheat area) • Tunisia (5% of wheat area) • Turkey (1% of spring wheat area)


Ten Years Enough seed availability in target countries to replace >40% wheat area as necessary from Ug99 migration.

Several diverse new wheat varieties that have a high level of APR or protected by at least two effective major genes and with >10% high yield potential than current varieties released in rainfed areas of various countries and occupy 5-40% spring wheat area.

Fifteen Years Between 40-60% rainfed spring wheat area

234




in above and other countries replaced by Ug99 resistant varieties that enhance wheat production through increased yield potential and drought tolerance.


25.b. Africa and South Asia

25.b.1. Durum wheat varieties for Ethiopia, South Asia, and North Africa with resistance to Ug99 and its derivatives.

Approximately 50 high yielding, stem rust resistant durum lines distributed worldwide in CIMMYT screening nurseries. (Mar 2012)

20–30 stem rust resistant durum varieties with >5% higher yield than current varieties distributed worldwide for yield/adaptation testing by NARS. (Mar 2014)

2–3 stem rust resistant candidates varieties for release in Ethiopia. (Dec 2014)

Five Years Durum wheat varieties with Ug99 resistance and >5% higher yields are planted as follows (joint with Objective 21) • Ethiopia (1% durum wheat area) • India (1% durum wheat area).

Ten Years Durum wheat varieties with Ug99 resistance and >5% higher yields are planted as follows (joint with Objective 21). • Ethiopia (20% durum wheat area) • India (20% durum wheat area) • Morocco (20% durum wheat area) • Algeria (5% durum wheat area) • Tunisia (20% durum wheat area) • Syria (20% durum wheat area) • Turkey (20% durum wheat area)

K. Ammar, CIMMYT, Mexico

235




• Azerbaijan (20% durum wheat area)

Enough seed availability in target countries to replace >50% durum wheat area as necessary from Ug99 migration.


Fifteen Years >60% durum wheat area in above and other countries replaced by Ug99 resistant varieties that enhance wheat production through increased yield potential.

Several diverse 2nd generation of durum wheat varieties that have a high level of APR or protected by at least two effective major genes and with >10% high yield potential than current varieties released in various countries and occupy 5-40% durum wheat area.

25.b.2.

Kenyan wheat improve-ment for East Africa and South-Asia.

Strengthen research capacity in wheat improvement through close collaboration with wheat scientists in Kenya. (Oct 2011, recurring annually)

Assist the Kenyan Njoro ARI in building research infrastructure. (Oct 2011, recurring annually)

Liaise with multiple partners for germplasm and data exchange. (Oct 2011, recurring annually)

Five Years Scientists and staff at critical facilities in Kenya possess skill sets enabling quality assured data collection and management.

Ten Years The critical facilities are fully sustainable, actively contributing to improving food security in their respective countries and

P. Njau, KARI


236




regions while continuing to contribute to global wheat improvement efforts.

Kenya has an efficient variety development and replacement system benefiting all wheat growers. Losses due to stem rust are minimal. Education of small and large farmers for optimum management of APR protected varieties is accomplished.

The process and outcomes of this project have positive effects on gender issues in development


25.b.3. South Asia hub for Ug99 wheat improve-ment

Strengthen research capacity in wheat improvement through close collaboration with wheat scientists in South Asia. (Jan 2011, recurring annually)

Assist South Asia (Afghanistan, Bangladesh, India and Nepal) national programs in identifying and promoting new improved wheat cultivars with genetic protection to rust and other pathogens, including cultivars for the newly opened irrigated areas. (Jan 2011, recurring annually)

Liaise with multiple partners for germplasm and data exchange. (Jan 2011, recurring annually)

Five Years Scientists and staff at critical facilities in South Asia possess skill sets enabling quality assured data collection and management with engagement in ICIS implementation.

Ten Years The critical facilities are fully sustainable, actively contributing to improving food security in their respective countries and regions while continuing to contribute to global wheat improvement efforts.

South Asian NARS have an efficient

Sathguru

Cornell

237




variety development and replacement system benefiting all wheat growers. Losses due to stem rust are minimal.

The process and outcomes of this project have positive effects on gender issues in development.

Fifteen Years International efforts to mitigate and eliminate the effects to small holder famers against wheat stem rust are no longer limited by lack of ready access to germplasm, data, seed and knowledge.

25.c. Whole Family Variety Selection

25.c.1. Foster the engagement of the entire household in participa-tory variety selection through “Family variety selection” in India and Ethiopia.

All organizing partners from NGOs, national programs, and DRRW project are convened to plan Whole Family Variety Selection approach and implementation. Realistic targets are agreed upon including: • What data to be collected at Family Field

Days is determined; • A strong mission statement is drafted for this

project component; • MoUs are agreed upon. (Sep 2011)

Whole Family Variety Selection is implemented in two countries (by Sep 2012)

Results of Whole Family Variety Selection are shared with DRRW breeders. (Sep 2013, recurring annually)

Five Years Whole Family Participatory Variety Selection is implemented in 2 countries. Desired end-use quality traits identified.

Ten Years Whole Family Participatory Variety Selection becomes standard practice (replacing gender segregated variety selection)

Genetic variation and heritability of desired traits investigated and informs breeding programs.

Fifteen Years Breeders breeding for qualities important for entire wheat producing family unit.

Increased food of desired quality in the household.

S. Davidson, Cornell

238




Women’s household labor input lessened.

25.d. Strength-ened national program capacity

25.d.1. Foster a new generation of wheat pathologists and breeders in contemp-orary wheat improve-ment with emphasis on durable adult plant resistance to stem rust.

A cadre of young research technicians and scientists (40) trained, enabling uniform reporting of global wheat rust surveillance data and knowledge. (Aug 2013)

Senior scientists (24-30) trained at CIMMYT and ICARDA on wheat pathology/breeding, particularly on the use of minor gene resistance in pathology research and variety development. (Oct 2014)

IWIS3 (an ICIS application) implemented across all Objective 25 DRRW partners, enabling better sharing of germplasm phenotypic data and information, and deployment of molecular breeding platform tools to enable more robust application of marker assisted selection. (Dec 2012)

Five Years New generation of wheat scientists engaged in short-term and long-term wheat improvement research needed for meeting future wheat demands.

Data quality is assured, and data management tools are in place and used beyond the aims of the project.

Ten Years The project’s partners have fully sustainable operations, actively contributing to improving food security in their respective countries and regions while continuing to contribute to global wheat improvement efforts.


P. Wenzel and P. Kosina, CIMMYT, Mexico

239



Component 25.a. Bread Wheat Activity 25.a.1. Spring bread wheat varieties with Ug99 resistance for irrigated and higher production environments of Africa, Middle East, West, Central and South Asia The partial or fully irrigated areas and those that receive moderate to high rainfall during the crop season constitute about 40 million hectares throughout the developing world where stem rust poses a major threat in its likely migratory path. Due to the higher moisture and application of fertilizers to enhance productivity, the environmental conditions are optimal for major epidemics caused by rust pathogens that are obligate parasites and enjoy healthy plants and lush growth for rapid multiplication. These areas are also the bread baskets for many countries. Field tests conducted during 2005-2008 in Kenya and Ethiopia have identified wheat materials such as Kingbird, Pavon 76, Kiritati, and Juchi that have displayed high levels of adult plant resistance (APR) despite seedlings being susceptible in greenhouse tests. Kingbird had the highest level of APR and was amongst the cleanest materials under the most severe disease pressure observed in 2008 in field nurseries in Kenya with less than 5% severity rating. In addition, wheat lines that carry at least six different race-specific resistance genes conferring high to moderate levels of resistance to Ug99 were also identified. However, these race-specific resistance genes were not present in combinations of two or more genes. The Irrigated Bread Wheat Improvement Program of CIMMYT has breeding materials from new crosses made for transferring durable, adult plant and diverse race-specific stem rust resistance to a small number of high yielding advanced lines. About 80% of program resources will be allocated to breeding durable adult plant resistance and 20% to incorporate multiple race-specific resistance genes in high-yielding backgrounds through marker-assisted selection. The flow of breeding materials from crosses to variety release is shown in Table 25.a.1. Because breeding for this objective was initiated in 2005, materials at all stages of development are available.

Wheat improvement is a continuous process at CIMMYT since the program was commenced in 1944 by Dr. N. E. Borlaug. Advances made at the end of each breeding cycle are captured when initiating the next breeding cycle each year. CIMMYT has also maintained a well structured International Nursery System, initiated in early 1960s by Dr. Borlaug, for free international distribution of germplasm and capture of data generated by the participating institutions worldwide. By the 3rd year (2012) of Phase II, we expect to distribute only TTKSK resistant materials through the CIMMYT international yield trial ESWYT (Elite Spring Wheat Yield Trial), and at least 80% of the lines will be resistant to the Ug99 lineage in the IBWSN (International Bread Wheat Screening Nursery) nursery targeted for irrigated and other higher production environments that are growing white grain wheat varieties. For areas where red grained varieties are preferred, all accessions distributed through HRWYT (High Rainfall Wheat Yield Trial) and 80% of accessions in the HRWSN (High Rainfall Wheat Screening Nursery) will be resistant to the Ug99 lineage by 2014. Modifications in crossing and selection schemes (from lessons learned)

Breeding for complex adult plant resistance. Making simultaneous progress for accelerated improvement in grain yield potential, end-use quality and APR to stem rust is a major challenge, especially when considering that the annual progress in yield potential through breeding has been

240


less than 1% in recent years, and that the best sources of germplasm with APR (as well as most race-specific resistance genes) to stem rust have at least 15-20% lower yield potential than the best yielding improved wheat lines. Of the 3500 new advanced lines tested for yield performance in replicated trials during the 2008-2009 crop season at Cd. Obregon, only 53 (1.5%) yielded 105-115% of the mean of the two recently released, commercial check cultivars. An additional 157 (4.5%) entries yielded between 100-105% of the check cultivars. The two checks used in yield trials in Mexico have a 10% higher yield potential than the cultivars currently grown in most target countries, indicating that it is possible to identify Ug99 resistant varieties superior to even the most competitive check varieties. However, the percentage of superior lines identified in these first year yield trials has dropped to about 60% of the previous two years, likely because some 40% of the crosses were targeted for stem rust resistance breeding and involved a stem rust resistant parent that had relatively lower yield potential. Moreover we relied more on simple crosses to maintain a high frequency of plants with APR is segregating generations. To continue making simultaneous progress for yield potential and resistance to stem rust, we propose the following adjustments in our crossing and selection approach: Specifically, we plan to incorporate high levels of APR in a set of about 100 new high-yielding, diverse genotypes (identified annually) through a single-backcross approach with large BC1 and subsequent segregating populations. Crosses made since 2005 have involved mainly confirmed APR sources such as Kingbird, Kiritati, Pavon, and Juchi. We need to continue depending on these sources until 2010 (the first year of Phase II of the DRRW project). New advanced lines from shuttle breeding are now emerging, and we expect that by 2010 lines with yield potential similar to or better than the checks, but with high levels of APR, will become available. These will then be used in the crossing program from 2011 onwards. To develop superior yielding lines we plan to reduce the number of cross combinations by half our previous number, but to double the size of BC1 and F1 top-cross populations to about 800 plants. The BC1 will be grown in Cd. Obregon, and plants with desired agronomic characteristics and resistance to leaf rust (and Mexican stem rust races) will be selected, harvested, and bulked. About 300 F2 populations from simple crosses retained in El Batan will also be grown in Obregon. The BC1 and F1-Topcross derived F2 populations will be grown at Toluca where we expect to increase the size of each F2 population to about 2000 plants. F3 populations from simple crosses will also be grown at Toluca. Plants will be selected for agronomic characteristics, resistance to yellow rust and Septoria tritici blotch, harvested and bulked.

The selected-bulk selection in BC1, F1-Topcross and F2 generations in Mexico allows selecting very large numbers of plants with good phenotype while reducing undesirable variation such as height, maturity and other agronomic traits. Furthermore, selection for agronomic characteristics in early generations in Mexico confers adaptation to a broader array of production environments throughout our target environments. Plants susceptible for leaf rust (Obregon) and yellow rust and Septoria tritici (Toluca) are also discarded. When selecting for minor gene based additive adult plant resistance, the frequency of plants with high resistance levels is low in the F2 generation due to higher heterozygosity. As homozygosity of alleles increases in subsequent F3 and F4 generations the frequency of resistant plants also increases, and those plants will then be retained.

A sample of about 1000 seeds of F3 and F4 populations will be shipped to Njoro, Kenya for planting in the off-season under stem and yellow rust pressure. Selected plants in Kenya will be

241


bulk-harvested and the resulting F4 and F5 populations of about 500 plants derived from plump grains grown in the main season for the second round of selection where the selected-bulk scheme will be applied again. Two successive generations of selection in Kenya for minor APR genes is required because the selection process allows the retention of favorable alleles with an increasing frequency from generation to generation. If selection were to be based on F3 plants in Kenya only, there will be an increased risk that heterozygous plants will continue to segregate for APR with the risk that a higher frequency of susceptible plants will be retained in F4 and subsequent generations in Mexico. Selection during two segregating generations therefore increases the possibility of retaining plants where sufficient minor genes needed to confer high level of APR are fixed. This crop cycle also ideally fits the following crop cycle in Mexico, resulting in no loss of time. A parallel population will also be advanced in Mexico for 2 or 3 cycles of selection to compare the effect of shuttle breeding on grain yield potential and resistance to stem rust. Once it’s established that the Mexico-Kenya shuttle breeding has no or little effect in recovering wheat lines with high yield potential and in fact enhances the recovery of lines with high levels of APR to stem rust, maintaining parallel populations in Mexico will be discontinued.

Populations in the F5 or F6 generation with approximately 500 plants/cross are returned to Mexico to be grown at Cd. Obregon under leaf rust pressure with selected plants being harvested individually. After selection for grain characteristics, small F6 plots of retained plants will be established at El Batan (for leaf rust screening) and Toluca (yellow rust and Septoria tritici screening). Approximately 3000 F6 lines selected at both sites based on agronomic characteristics and disease resistance will be promoted to replicated yield trials in Cd. Obregon where they will again be characterized simultaneously for resistance to leaf rust (in Cd. Obregon), yellow rust (Ecuador2) and stem and yellow rust (Kenya in the off-season). Lines that are retained based on grain yield performance and resistance to various diseases will be phenotyped for stem and yellow rusts in Kenya during the main season, for yellow rust and Septoria tritici at Toluca and for leaf rust at El Batan and end-use quality analysis conducted in the grain-quality laboratory of CIMMYT. Small quantity seed multiplication at El Batan will also have been achieved, should rapid international germplasm distribution be warranted. Approximately 400 selected lines will be tested for a second year of yield performance in Obregon under five or six environments which are created through full and reduced irrigation regimes, late sown heat-stress, and planting under zero-tillage and stubble. Seed multiplication at Mexicali (Mexico) will be done in preparing for distribution of international yield trials and screening nurseries. All data will be compiled and used in finalizing the international trials that will be distributed for worldwide evaluation by cooperating institutions. Incorporating multiple race-specific resistance genes with exceptional yield performance. There are a limited number of effective race-specific resistance genes available today that are also tightly linked to molecular markers. As a result, only genes such as Sr22, Sr25 and Sr26 can be used in gene pyramids in breeding programs. Other uncharacterized genes are available, though their respective markers are not. These genes have been used in our crossing program and we expect to obtain new high-yielding lines carrying these genes within the next few years.

2 CIMMYT, in partnership with the national program at Quito, Ecuador, screens germplasm for yellow rust at this location, considered a global hot-spot for this pathogen.

242


The efficiency and success of utilizing race-specific resistance genes in pyramid combinations depends on the availability of markers for these genes. Objective 26.c is expected to deliver markers for these genes, as well as identify new sources of resistance (Obj. 26.a) along with their associated markers in this phase of the proposal. . We propose following two strategies that will facilitate the development of varieties with combinations of current and new sources of resistance:

1) Backcross an additional effective Sr gene in existing and forthcoming high-yielding wheat materials that already carry an effective resistance gene. As an example, there are a number of high-yielding wheat lines available that carry Sr25, SrTmp, SrND643, SrHUW234, and new productive lines are expected to emerge in the next two years carrying Sr26, SrSha7, Sr1A.1R and Sr22. We propose to backcross Sr22, Sr25 and Sr26 in selected wheat lines that already carry one of the above resistance genes. It should be noted that while there is virulence to Sr25 in India, CIMMYT lines carrying the gene are resistant to this race, indicating they carry additional genes effective against this race, and inferring that Sr25 can be effectively used in combination. Molecular markers available for these three genes will facilitate their back-crossing. As new genes with markers become available from Activity 26.c.3, they will be introgressed in these materials. The gene management strategy is closely coordinated with scientists working on Objective 26.

2) Back-crossing combinations of resistance genes, Sr22+Sr25, Sr22+Sr26 and Sr25+Sr26 (and any new sources as they become available) in a selected group of wheat lines with APR to stem rust. We propose to use new wheat lines that have at least moderate levels of resistance to Ug99 and are candidates for release and promotion in target countries for this purpose. New wheat lines will be added as they emerge as potential varieties. Both activities will be undertaken in close collaboration with scientists participating in Objective 26. In most cases we propose to make 2 or 3 backcrosses with the high-yielding parents followed by selection. This is specifically important when dealing with alien translocations as background selection is often important in offsetting the frequently negative effects of the translocation. BC2 and BC3 derived F3 or F4 lines will be phenotyped for resistance to stem rust in Kenya, with markers being used to ensuring that specific combinations are achieved. Selected advanced lines will then be evaluated for yield and agronomic performance, end-use quality, and pathology before distributing internationally. By the end of Phase II, high-yielding lines with four or five combinations of major resistance genes in lines with APR will be available, and additional combinations will be in various stages of development.

243


Table 25.a.1 Sequential flow of germplasm and generations through the Shuttle Breeding Scheme used by the Irrigated Bread Wheat Improvement Program, CIMMYT, Mexico.*

Year Months Location Activity

Nov – Apr Obregon, MX About 400 simple crosses made. 1

May – Oct El Batan, MX F1-simple grown; about 200-top and BC (backcross) made (with about 800 seeds per cross).

Nov – Apr Obregon 300 F2-simple and 200 F1-top/BC grown; selected-bulk method used.

2 May – Oct Toluca, MX F3-simple and F2-top/BC grown; selected-bulk method

used.

Nov – Apr Njoro, KE and Obregon

F4-simple and F3-top/BC grown; selected-bulk method used. Parallel populations grown in Obregon.

3 May – Oct Njoro and Toluca F5-simple and F4-top/BC grown at Njoro and Toluca;

selected-bulk method used.

Nov – Apr Obregon F6-simple and F5-top/BC originating from Njoro and Toluca grown; pedigree selection applied. Grain selection conducted on selected plants. 4

May – Oct El Batan & Toluca Advanced lines grown, selected for agronomic traits and yellow rust, leaf rust, etc.

Nov – Apr Obregon, Njoro, Quito, EC

1st year of yield performance; leaf rust, stem rust and yellow rust.

5 May – Oct El Batan, Toluca,

Njoro Seed multiplication; quality analysis; 2nd year leaf rust, yellow rust, Septoria tritici, and stem rust testing.

Nov – Apr Obregon, Mexicali, MX

2nd year of yield performance, quality analysis, seed multiplication for international shipment.

6 Jun – Sep El Batan International yield trials and screening nurseries prepared

and distributed.

7 Oct – Jun National Programs**

Yield trials and screening nurseries grown, best entries selected.

8 Oct – Jun National Programs** Variety registration trials-1st year, seed multiplication.

9 Oct – Jun National Programs**

Variety registration trials-2nd year, seed multiplication, variety release.

*The germplasm flow will begin each subsequent cycle that simple crosses are made. **Targeted NARS include: Afghanistan, Azerbaijan, Bangladesh, Chile, China, Egypt, Ethiopia, India, Iran, Iraq, Kenya, Libya, Mexico, Morocco, Nepal, Pakistan, Syria, Sudan and Turkey. Outputs

• Between 30–50 high yielding, rust-resistant potential replacement varieties tested annually in replicated yield trials in various countries at more than 50 field sites.

244


• Between 100–150 additional high yielding, multiple rust resistant lines distributed annually for evaluation and selection as small plots at more than 100 sites worldwide.

• About 5-10 new multiple rust resistant varieties with >5% higher yield potential than current cultivars released officially in various countries each year.

Activity 25.a.2. Spring bread wheat varieties with Ug99 resistance for drought-stressed and low production environments of Africa, Middle East, West, Central and South Asia.

About 10 million hectares of spring wheat is cultivated in non-irrigated rainfed areas of North Africa, Sub-Saharan Africa and West Asia. Another three million hectares is grown on receding moisture in Central India. On the 8.5 million hectares of wheat in North Africa and West Asia, rainfall during the wheat growing season is highly variable from year to year, ranging from 200 mm in a dry year to more than 600 mm at the same location in a wet year. Due to this climatic variation, breeding germplasm with specific adaptation is quite difficult if not impossible, and wheat cultivars released for these areas must combine excellent drought tolerance with the ability to respond to sporadic or seasonal moisture availability. Cultivars must have resistance to the three rusts: stripe, leaf and stem rust, and to Septoria tritici. This is due to the fact that all of these diseases opportunistically attack wheat when conditions are favorable for yield performance, as is the case during higher rainfall seasons. Rainfed areas of North Africa, West Asia, Ethiopia and Central India are in the predicted migration path of Ug99. Since Ug99 arrived in Iran in 2008, the risk of migration to Afghanistan, Pakistan and Turkey has become very high.

CIMMYT’s Rainfed Wheat Breeding Program, based in Mexico, adds stress tolerance to high-yielding and disease resistant germplasm to enhance adaptation to rainfed areas. Marker assisted selection allows the efficient integration of those genes conferring tolerance to biotic soil stresses such as nematodes, which cause serious yield reductions in rainfed areas. Physiological information on specific drought-adaptive traits, such as canopy temperature, is used to make informed crosses between elite materials and to select new genetic resources (land-races and primary synthetics) for introgression into elite materials. The Rainfed Program started breeding for resistance to Ug99 when Phase I of the DRRW project began. At that time, a few elite lines with good to moderate resistance to TTKSK were identified in existing materials. The best lines were multiplied for distribution to targeted countries, with larger quantities sent to Afghanistan. This process will continue with the generation of new candidate lines for CIMMYT’s international SAWSN nursery (Semi-Arid Wheat Screening Nursery), targeted for semiarid areas. However, by year 2010, the frequency of Ug99 resistance lines is expected to increase to about 65%.

Crosses are currently made with three sources of elite lines for rainfed areas. We use both APR sources and combinations of major genes. The priority is to make cross combinations to maximize the probability of combining good yield performance and Ug99 resistance. Crosses made for this project can be classified into the following three types:

• Two-way, back-, and top-crosses between new elite rainfed materials showing good performance in Mexico and good to moderate resistance to Ug99 and its derivatives. Back- and top-cross parental lines will have good Ug99 resistance.

245


• Back- and top-crosses between new elite rainfed materials (above) and elite lines coming from the irrigated program with good yield potential and good resistance to Ug99.

• Back- and top-crosses with germplasm from the above two approaches, and with elite lines showing good performance in the Semi Arid Wheat Yield Trial (SAWYT), but otherwise susceptible to Ug99 and its derivatives.

International yield performance data for stem rust resistant lines from the Rainfed Program are not available at present. When these data become available from the SAWYT, a combination of major genes will be incorporated into the best elite materials that exhibit good performance and broad adaptation. One of the priorities will be to test elite Ug99 resistant materials at selected rainfed testing sites in target countries and use this information to promote seed multiplication while continuing the testing. The choice of parental materials is obviously critical. Selection is based on resistance to Ug99 and its derivatives from Njoro, Kenya, and multiple environment performance at Cd. Obregon, Mexico. Population size has been increased in the F3 generation to 1000 plants per cross population. For crosses involving progeny with confirmed international performance, population size will be increased to 2000 plants in F2 and F3 generations to increase the probability of finding good recombinants. Additional information, including physiological information, will be used to plan new elite x elite crossing combinations.

Major genes used in the breeding program are Sr1A.1R, Sr25, Sr26, SrSharp, in addition to genes from Chinese sources, such as Shangai7. Markers are available for 1A.1R, Sr25 and Sr26. Recently three major QTLs were identified at CIMMYT originating from two Chinese, and one synthetic derived line, with markers for these new genes becoming available soon. The number of major genes available with DNA marker should increase during the course of the project. Marker Assisted Selection (MAS) will be conducted in F1 top cross populations and in F3 bulks to select only plants with the desired combinations. Activity 25.a.2 will closely liaise with Objective 26 to gain access to new major gene+marker combinations from translocations with reduced linkage drag (at the moment Sr35, Sr32 and SrR). MAS will be conducted in F1 Top-cross and in F3 bulk populations. For F1 Top-cross populations, if parent A carries the major gene, and if the marker used is codominant, we will select homozygous plants and fix this gene in the population. Otherwise, if parent B carries it, heterozygous plants will be selected, and the cross enriched once more in the F3. In theory, 80% of the advanced lines should carry the gene.

The shuttle breeding Mexico – Kenya – Mexico follows a similar scheme as described in the irrigated program. Two consecutive cycles of selection are necessary in Njoro, Kenya to increase the frequency of plants with APR resistance. For all crosses sent to Njoro, parallel selection is done in Mexico, to compare performance of advanced lines selected in Kenya versus those selected in Mexico. Once there is evidence that selection in Njoro has no negative effect on yield performance, good adaptation, and disease resistance in Mexico, selection will only be carried out in Njoro. The method is described in Table 25.a.2.

246


Table 25.a.2 Breeding scheme employed by the Rainfed Bread Wheat Improvement Program, CIMMYT, Mexico, for stem rust resistant germplasm.*

Year Months Location Activity

Nov – Apr Obregon, MX 150 simple crosses.

1 May – Oct Toluca, MX

150 simples, 100 top- or backcrosses.

Nov – Apr Obregon F2, F1 Top and BC1; selected bulk method. MAS in F1 top/backcrosses on major resistance genes when marker available 2

May – Oct Toluca F3 and F2 bulks; selected bulk method Nov – Apr Njoro, KE F3 and F4 bulks; selected bulk method

3 May – Oct Njoro, KE F5 and F6 bulks. Selected bulk method Nov – Apr Obregon F6 and F7 bulks. Pedigree method

4 May – Oct El Batan, MX; Toluca Advanced lines. Screened for leaf rust (Batan), yellow

rust (Toluca).

Nov – Apr Obregon; Quito, EC; Njoro

1st year yield trial Obregon; leaf rust, yellow rust and stem rust data generated.

5 May – Oct Toluca; El Batan; Njoro Elite advanced lines: quality tests, observation plots for

leaf rust and yellow rust.

Nov – Apr Obregon; Quito; Njoro; Izmir; Aleppo, SY; Izmir, TK

2nd year of yield trials Obregon; leaf rust, yellow rust and stem rust, quality analysis data generated. Seed multiplication in Mexicali for international shipment. 6

Jun – Sep El Batan Selection of lines for international yield trials and international screening nurseries.

7 Oct – Jun National Programs** Yield trials and screening nurseries grown, best entries selected.

8 Oct – Jun National Programs** Variety registration trials-1st year, seed multiplication.

9 Oct – Jun National Programs** Variety registration trials-2nd year, seed multiplication, variety release.

*The germplasm flow will begin each subsequent cycle that simple crosses are made. **Targeted NARS include: Afghanistan, Algeria, Ethiopia, India, Iran, Iraq, Kenya, Mexico, Morocco, Nepal, Pakistan, South Africa, Syria, Tanzania, Tunisia, and Turkey. Outputs

• 15-20 lines with multiple rust resistance, good drought tolerance and yield potential sent every year to NARS for evaluation in replicated yield trials.

• 50 to 70 lines with multiple rust resistance, good drought tolerance and yield potential sent annually to NARS for observation and selection in small plots.

• 3–4 stem rust resistant varieties selected for release by NARS by the end of this Phase of the project.

247


Component 25.b. Africa and South Asia Activity 25.b.1. Durum wheat varieties for Ethiopia, South Asia, and North Africa with resistance to Ug99 and its derivatives. Background, achievements to date, and lessons learned.

The situation regarding stem rust resistance of durum wheat is made more complicated by the fact that it not only needs to address the issue of TTKSK and recently identified new Ug99 variants, but also the complex set of races specifically virulent on durum wheat in Ethiopia. Most modern durum wheat germplasm, as well as most Ethiopian landraces, are believed to be highly susceptible to these races. This prompted us to initially adopt various strategies to maximize our opportunities for success in the short and long terms.

Our initial approach was to cross Ethiopian germplasm with known sources of stem rust resistance to CIMMYT elite materials in an attempt to introgress this resistance into backgrounds that were agronomically more competitive for leaf and yellow rust resistance, better agronomic type and acceptable quality attributes. This approach unfortunately resulted in very few acceptable advanced lines (currently only 43 F5 lines made it through selection from our first set of such crosses) because of the Ethiopian lines’ extreme height, and susceptibility to leaf and yellow rust. As we were trying to combine genes from these sources of resistance with those from elite materials recently identified, we concluded that we need to use much larger populations (starting with 3000 plants in F2 populations as opposed to the 1000 that we used) in order the end up with a higher number of advanced lines to send to Ethiopia for final screening against Ug99 and other stem rust variants. The second approach employed was to transfer major genes for resistance from bread wheat to durum wheat, using marker-assisted selection, with the ultimate goal of pyramiding several genes together. While this approach had a higher likelihood of success in the short term, its disadvantage was that only the few known resistance genes could be used and a significant pre-breeding effort was necessary. Nevertheless, the approach was carried out successfully, and we are now in the final stage of developing durum lines carrying Sr25 and Sr22 allowing the pyramiding of both genes into elite durum wheat backgrounds, which will be achieved in Phase II. A disadvantage of this approach is the breaching of the species divide between hexaploid bread wheat and tetraploid durum wheat. This evolutionary divide has resulted in species-specific effective resistance genes. Use of wide interspecies crosses must consider both the advantages of available genetic diversity for resistance, as well as the risks of bridging single gene resistance sources between species. The preferred approach is to identify as many sources of acceptable resistance as possible through an aggressive screening program at Debre-Zeit, Ethiopia, and inter-cross these with the goal of accumulating as many different resistance genes as possible into elite backgrounds. This approach was started in 2007 at Debre-Zeit. While we were fortunate to have good durum wheat stem rust epidemics in 2007, the information collected in 2008 was deemed less reliable as a drought prevented the establishment of a discriminating epidemic. Since screening at Debre-Zeit is critical to our activities, we need to ensure proper and reliable screening conditions at this location. The recent focus placed on Ethiopia as part of the “critical infrastructure” component of the DRRW project (Objective 24) will provide that capacity. The establishment of an irrigation system to make epidemics independent of rainfall, and the exchange of visits and visions

248


between the durum researchers in Ethiopia and at CIMMYT is critical for the success of this Activity.

An excellent screening of durum germplasm occurred in the 2009 season and a common vision guides our breeding and research strategies. Considering the results of 2007-2009, we are now confident that we can rely on some 12 sources of useful resistance within CIMMYT elite germplasm (infection below 20S) with another 10 sources from other germplasm pools (European and ICARDA). This frequency is unacceptably low, and we need to understand whether these resistances are based on different genes. For the short term, we have identified one promising line with adequate levels of resistance to all rusts and greatly improved quality from which 100 kg was provided to EIAR to expedite through their national registration trials and seed multiplication system. Based on this background information, the following sections provide a proposal of activities for follow up during the second phase of the DRRW project for durum wheat. Breeding Strategy

A total of 250 crosses, with 80% top- or backcrosses, will be made each year. Stocks with recently introgressed Sr25 and Sr22 will be used in some of these crosses in combinations with genes identified in CIMMYT and non-CIMMYT elite lines. In addition, new sources of resistance discovered in Objective 26 (primarily from wild tetraploid relatives with putative novel genes) and transferred into adapted durum wheat backgrounds will be used as they become available.

In terms of the selection scheme used, we are opting for (1) a preliminary selection in Mexico for leaf and yellow rust resistance and plant type, through 2 cycles of “shuttle-breeding” between Obregon (F2 and F4 generations) and Toluca/Batan (F3 and F5 generations), followed by (2) a selection for stem rust resistance of selected F6 lines at the Debre-Zeit Agricultural Research Center in Ethiopia. As this material is tested in Debre-Zeit, it is evaluated in Obregon for yield potential and industrial quality in preliminary yield trials. During the second season of evaluation in Ethiopia for stem rust and adaptation to local conditions, the material selected by the Ethiopian NARS will be evaluated in parallel for yield and quality in replicated yield trials in Obregon under full irrigation and drought. Finally, lines will be selected for CIMMYT’s international nurseries based on at least two seasons of stem rust data from Ethiopia, and at least two years of yield/quality data in Mexico. Stem rust resistant material from these new crosses will be identified by the mid-point of Phase II, which will enable resistant cultivar candidates to be considered for release by the end of the project. Rust resistant germplasm for local evaluation and selection will be available only towards the end of this phase of the project. If new sources of resistance are identified within the current CIMMYT elite germplasm, information and seed will be made available to all NARS partners on an annual basis for their crossing programs or evaluation for direct release. The breeding strategy for this objective is set out in Table 25.b.1.

249


Table 25.b.1. Breeding strategy to develop spring durum wheat germplasm, resistant to stem rust, targeted towards end-use requirements of Ethiopia and other NARS. Year Months Locations Activity

Nov – Apr Obregon, MX Simple and top crosses between SR resistant and elite CIMMYT and NARS durum germplasm.

1 May – Oct Batan, MX F1 from Simple crosses and top-crosses populations (400 plants),

MAS in crosses where appropriate

2 Nov – Apr Obregon F2 individual plant selection for leaf rust and agronomic type from large populations (2000-3000 plants), and bulking of selected plants, MAS in crosses where appropriate

May – Oct Toluca, MX

F3 single plant selection for leaf and yellow rust and agronomic type from bulk populations of 300-400 plants, bulking of selected plants; MAS in crosses where appropriate. Selected bulks sent to Debre-Zeit for next year’s off-season*.

3 Nov – Apr Obregon; F4 selection for leaf rust and agronomic type of individual plants (threshed individually here, no bulking) from populations of app. 300 plants.

Jan - May Debre-Zeit Selected F4 seed bulks sent to Ethiopia for mass selection for stem rust resistance during the off-season. *

May - Oct Debre-Zeit Second round of selection of selected F5 bulk during the main season. *

May – Oct Toluca

F4-derived F5 plant row families selected for leaf and yellow rust resistance and agronomic type in Toluca and El Batan; Selected F6 families sent to Ethiopia for Sr screening during the off season and Obregon for preliminary yield and quality testing.

Nov – Apr Obregon

F6 preliminary yield trials under full irrigation. Selected lines screened for relevant industrial quality traits. Communication of results to Ethiopian collaborators to facilitate selection of the same material planted in Ethiopia.

Jan-May Debre-Zeit Selection of F6 lines from Mexico; resistant lines will be yield tested in Mexico and Ethiopia.

4

May – Oct Batan F7 head-row purification/multiplication.

Nov – Jun Obregon Advanced yield trials under full irrigation and terminal drought leaf rust, quality; multiplication for international nurseries.

Jan - May Debre-Zeit Verification of stem rust resistance of advanced lines and yield trial.

5

May-Oct El Batan, Toluca Lr, Yr, verification, seed multiplication. Nov – April

Obregon, Mexicali

2nd year yield performance, quality analysis, seed multiplication for international nurseries.

Jan-May Debre-Zeit Verification of stem rust resistance of advanced lines and yield trial; submission of best lines for registration trials.

6

Jun-Oct El Batan International nurseries prepared and distributed.

250


7 Year long National Programs

Selection for local adaptation and market acceptance of lines from CIMMYT international nurseries.

8 Year long National Programs

Selection for local adaptation and market acceptance of lines from CIMMYT international nurseries. Cultivar release of SR resistance germplasm.

*Applicable with the approval from Ethiopia allowing seed to be sent to Mexico for further evaluation and breeding. Outputs

• Two to three stem rust resistant candidate varieties for release in Ethiopia by the end of this phase of the project.

• 20–30 stem rust resistant durum varieties with >5% higher yield than current varieties distributed worldwide for yield/adaptation testing by NARS.

• Approximately 50 additional high yielding, stem rust resistant durum wheat lines distributed worldwide in CIMMYT screening nurseries.

Activity 25.b.2. Kenyan wheat improvement for East Africa and South-Asia The origin of virulent races of stem rust and other rust pathogens in the highlands of East Africa is well known. In order to mitigate and control the development and further distribution of these pathotypes to wheat growing regions of Africa and Asia, it is important that the wheat being produced in Kenyan wheat fields be resistant to the extant races of rust in that country. The establishment of a wheat breeding program that works seamlessly with the international community in evaluating and developing germplasm that provides this protection to Kenya is an important contribution to controlling rust epiphytotics that can affect wheat crops in other parts of the world. Details of this activity will be developed in concert with CIMMYT and Cornell scientists in establishing a breeding program that will benefit Kenya with durably resistant wheat cultivars. Funding appropriate to the activities will be justified. Outputs

• Durably resistant varieties on Kenyan farms. • Trained and engaged technical staff.

• In-country capacity for plant breeding expertise is improved. Activity 25.b.3. South Asia hub for Ug99 wheat improvement

With more than 26M hectares of wheat under production, more than 50M farm families whose sustenance and economic welfare is dependent on the crop, and a population of more than one billion people for whom the crop is a primary staple, India has much at risk in the face of Ug99 and its variants emanating from East Africa. Indian scientists have the ability to meet their own needs and much to contribute to the global collaborative effort but they are constrained by their lack of resources to travel internationally. This activity is aimed at facilitating the participation of Indian scientists in the BGRI including collaborative activities with the DRRW project, especially the evaluation of breeding material in East Africa, short-term training in advanced breeding technologies, and consultation in connection with collaborative activities. In addition,

251


India is a major resource for the South Asia region, so some funding is provided for the training of Afghan, Bengali, and Nepali scientists at the Flowerdale Station.

Outputs: • Indian breeding material evaluated annually in East Africa

• Training of Afghan, Bengali, and Nepali scientists in rust evaluation techniques • Training of two scientists in marker assisted breeding, gene identification, and allele

mining

Component 25.c. Family Variety Selection Activity 25.c.1. Foster the engagement of the entire household in participatory variety selection through “Family Variety Selection” in India and Ethiopia. Men and women farmers may exhibit different preferences for various traits of cultivars of wheat grown on their farm or in their community. When growing crops that are immediately sold post-harvest (often referred to as “men’s crops”) the primary concern is yield. However, crops grown for home consumption (“women’s crops”) are selected on the basis of storage, processing, taste, and cooking qualities (Doss, 1999).

Whole family training was found to be an effective way to train wheat-producing families in Bangladesh (Meisner et al, 2003). The approach accounts for the fact that, in Bangladesh, all members of the household are engaged in wheat production and all are affected by production decisions. Families are trained as “wheat producing units” as opposed to divided by gender or task. In order to understand the potential differences in trait preferences among the “wheat producing units” and to address the omission of women family members from some varietal selection activities, we propose to engage all members of the household in participatory variety selection—what we call Whole Family Variety Selection. We will test this more inclusive method of participatory variety selection in Ethiopia and India. We will work with our CIMMYT collaborators to implement this approach in Nepal through other, non-DRRW, BGRI projects as has been done previously through a DFID funded PPB (Participatory Plant Breeding) project in the Eastern Gangetic Plains Zone (EGPZ) in India with Banaras Hindu University (BHU) at Varanasi (the PIs from CIMMYT were Drs. Guillermo Ortiz Ferrara (based in Nepal) and Arun Joshi (now also with CIMMYT in Nepal). In Ethiopia we will take advantage of the Farmer Field Days already in place through EIAR and seek consultancy from the EIAR gender specialist Yeshi Chiche. In India we will work with our collaborators at Sathguru to implement this approach within the existing extension system in India.

Key steps to be considered before Milestone 25.c.1 is achieved:

All NGO, NARs and DRRW partners convened to discuss the main objectives, metrics and implementation workplans for the FVS activities, namely:

• Objectives for Family Variety Selection agreed upon by researchers and implementing partners. Objectives could include:

252


— to have a harmonious flow of the variety development and release process, by maintaining research extension continuum

— enhance the feedback mechanism which is inherent in the PVS methodology; a process which would have otherwise been lost due to separation

— to ensure all members of the household, women and men alike, have access to improved varieties and can each influence varietal characteristics.

• Decide if WFVS will be a researcher led or extension led approach. • Site selection and target population selected.

• Key success metrics identified, including a target for women’s meaningful participation in field activities within the household unit.

• Consider data needs through a light touch, participatory appraisal to be done with the whole household. Develop or adapt appraisal tool from previous FVS activity.

• Design elements and steps considered through two country-specific workplans. Workplans will be developed by EIAR and Sathguru and submitted to administration and BMGF for review prior to implementation.

• A plan for disseminating and communicating findings to DRRW is developed and included in the Workplans.

• Composition (skills, sex of field workers if relevant) and size of teams agreed upon.

• MOUs are agreed, drafted and signed between teams. Outputs

• Two workplans for gender-responsive Whole Family Varietal Selection are submitted prior to implementation.

— Appraisal tools for Whole Family Varietal Selection — MOUs signed by all partners

• Results captured and shared with DRRW; changes made to the dissemination objective if FVS proves “successful.”

25.d. Strengthened national program capacity

Activity 25.d.1. Foster a new generation of wheat pathologists and breeders in contemporary wheat improvement with emphasis on adult plant resistance to stem rust.

This new activity fosters a new generation of agricultural scientists from the crescent extending from East Africa to South Asia, which will be realized through training and capacity building. To build a successful cereal improvement program with long-term impact, a cadre of scientists must be able to design and conduct research that addresses current and projected needs. While the concepts of adult plant disease resistance using minor genes is accepted, its application in research programs has been less wide spread due to the nuanced differences in this approach versus the selection and applied practice of major gene resistance which generally has a much cleaner phenotypic expression of host plant resistance.

253


During the Green Revolution, many young researchers from developing countries obtained training at CIMMYT and ICARDA. While this has had lasting impact throughout the developing world, in-the-field expertise has gradually eroded due to promotion and retirement of these individuals. The aim of this activity is to foster a new generation of wheat scientists who are not only experts in wheat pathology and breeding but also are well rounded in their understanding of the broader issues of science and policies for agricultural development. The activity will use regional and CG Center-focused group and individualized training courses and visits. In addition, it will support the implementation of the International Crop Information System across all project partners, at Centers and within NARS. Engagement with the Wheat Atlas component of Objective 23 will provide a comprehensive electronic atlas containing relevant, readily accessible information related to wheat production, markets and research, and is particularly relevant in the developing world. It is essentially, a one-stop, fast access data resource for wheat scientists, policy makers and business leaders. Outputs

• A cadre of young research technicians and scientists (40) will be trained, enabling uniform reporting of global wheat rust surveillance data and knowledge by the end of this phase of the project.

• Senior scientists (10-12) trained at CIMMYT and ICARDA on wheat pathology and breeding, particularly regarding the use of minor gene resistance in pathology research and variety development.

• IWIS3 (an ICIS application) implemented across all Objective 25 DRRW partners, enabling improved sharing of germplasm phenotypic data and information, and deployment of molecular breeding platform tools to enable broader use of marker assisted selection.

• In conjunction with the Wheat Atlas project in Objective 23, an internet-based data hub populated with NARS data inputs and validation, is built and used globally.

IV. Management Plan

Name Institution Email Relevant Activities and outputs (ID and Name)

Hans-Joachim Braun CIMMYT [email protected] 25.a.1; 25.a.2; 25.a.3; 25.a.5; 25.a.6; 25.b.1; 25.b.2; 25.c.1 (joint)

Ravi P. Singh CIMMYT [email protected] 25.a.1 Yann Manes CIMMYT [email protected] 25.a.2; Karim Ammar CIMMYT [email protected] 25.b.1 Sridhar Bhavani CIMMYT [email protected] 25.b.2 Bekele Abeyo CIMMYT [email protected] 25.b.2 Roberto Javier Pena CIMMYT [email protected] 25.a.1,2; 25.b.1 Sarah Davidson Cornell [email protected] 25.c.1 Peter Wenzel CIMMYT [email protected] 25.d.1 Pawan Singh CIMMYT [email protected] 25.a.1; 25.a.2 Sukhwinder Singh CIMMYT [email protected] 25.a.1

254


Hans-Joachim Braun is Director of the Global Wheat Program of CIMMYT and Michael Baum is Director of ICWIP (ICARDA-CIMMYT Wheat Improvement Program for CWANA Region). They will be responsible for ensuring the quality of breeding work, evaluation of progress against the milestones, handling of budget, and liaison with National Programs to promote the testing and release of suitable varieties in different environments. Progress and plans will be discussed periodically through conference calls. Braun and Baum will ensure that team members prepare annual reports and share results and relevant germplasm among themselves/other Objective leaders as soon as they are available and with National Programs. Activity leaders will be accountable for delivering the milestones and assessing progress within their domains.

Ravi Singh, CIMMYT, has expertise in rust resistance breeding/genetics/pathology, and will be responsible for Activity 25.a.1 as well as supporting other activities through rust resistant breeding materials and advice. He will also liaise with Objective 6 (marker development) for the breeding group and work with National Programs to promote relevant wheat materials in irrigated and high production environments. Yann Manes, CIMMYT, will be responsible for Activities 25.a.2. He will also work with National Programs working in rain-fed and high latitude environments to promote stem rust resistant wheat materials.

Karim Ammar, CIMMYT, will be responsible for Activity 25.b.1, and will work with National Programs to promote stem rust resistant materials.

Jose Crossa, CIMMYT, will be responsible for experimental design and analysis of multi-site data for various traits.

Javier Peña will be responsible for the quality analysis of advanced breeding materials. Julio Huerta-Espino, seconded to CIMMYT by INIFAP-Mexico, will be responsible for rust pathology support, testing and breeding in Activity 25.a.1. Sridhar Bhavani is a CIMMYT scientist based in Kenya, responsible for conducting and coordinating all field screening for Ug99. Peter Wenzel , is responsible for biometrics and informatics development and application at CIMMYT, including implementation of ICIS for the Global Wheat Program. Pawan Singh, CIMMYT Pathologist, is responsible for providing pathology support to breeding for diseases such as Septoria tritici blotch, Tan spot and Spot blotch. Sukhwinder Singh is a CIMMYT HQ-based breeder who specializes in molecular techniques.

V. Potential Risks

• Political insecurity in partner countries, could disrupt our capacity to implement activities and germplasm exchange

• Instability in IARC and NARS staff participation in this Objective

• Plant phytosanitary restrictions prevent timely germplasm exchange

255


• Field evaluation of segregating and advanced lines is carried out under the assumption that environmental conditions at the test sites will be conducive to the development of the disease.

• Genotypic hindrance to anther/microspore culture used in double haploid production

• Wide geographic deployment of Sr2 in combination with APR genes could lead to genetic vulnerability.

• Acceptance of APR varieties having inconsequential sporulation will be unnecessarily treated with fungicides and/or not accepted by growers.

• Cultural factors disallow Whole Family Participatory Variety Selection approach

VI. Evidenced based rationale for choice of partners

Research Institutes in Kenya and Ethiopia: These have first hand experience in dealing with Ug99 stem rust, and can provide ‘hot-spots’ so that parental material and the breeding lines generated can be tested for resistance to Ug99. The major partners are NARS of Ethiopia Ethiopian Agricultural Research Institute (EIAR) and Kenya Agricultural Research Institute (KARI) Kenya. The phenotyping sites in both Ethiopia and Kenya are known hot spots for stem rust development particularly Ug99. NARS scientists in Ethiopia and Kenya have excellent experience in generating artificial epidemics, evaluation and data collection. CIMMYT: This reputable international center has developed the best available germplasm and confirmed sources of resistance to Ug99 to be used in crosses by national programs. NARS in Winter/Facultative Wheat growing areas (mainly in Turkey and CAC countries): These have been chosen to ensure the supply of best available germplasm to be tested for Ug99 and to evaluate the generated germplasm for agronomic traits and adaptation.

The major partners are NARS of the Ethiopian Agricultural Research Institute (EIAR), the Kenya Agricultural Research Institute (KARI), and Sathguru, India. The phenotyping sites in Ethiopia and Kenya are known hot spots for stem rust development particularly Ug99. NARS scientists in Ethiopia and Kenya have excellent experience in generating artificial epidemics, evaluation and data collection. ARIs from USA: These have been chosen to supply the best available winter wheat germplasm to be used as parental material in the crosses.

256


References

Doss C. R., (1999) Twenty-five years of research on women farmers in Africa: lessons and implications for agricultural research institutions; with annotated bibliography. CIMMYT Economics Program Paper 99-02. Mexico D.F. CIMMYT

Meisner C.A., Sufian A., Baksh E., Smith O’Donoghue M., Razzaque M. A., Shaha N. K. (2003) Whole family training and adoption of innovations in wheat-producing households in Bangladesh. Journal of Agricultural Education and Extension. 9: 165-175.

257

Appendix C: Detailed Descriptions of Proposed Work / Durable Rust Resistance in Wheat Phase II Objective 26: High breeding value wheat lines with two or more marker-selectable stem rust resistance genes


Objective 26: High breeding value wheat lines with two or more marker-selectable stem rust resistance genes

Team Leader for this Objective: Mike Pumphrey, Washington State University


Institution Name (Scientist) Email

International Center for Maize and Wheat Improvement (CIMMYT)

Ravi Singh [email protected]

Cornell University Mark Sorrells [email protected]

Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia

Evans Lagudah [email protected]


Ayele Badebo [email protected]

Free State University, South Africa Zak Pretorius [email protected]

Institute for Cereal Crops Improvement, Tel Aviv University

Adina Breiman [email protected]

Kansas State University Bernd Friebe [email protected]

University of Adelaide Ian Dundas [email protected]

University of California-Davis Jorge Dubcovsky [email protected]

University of Minnesota (Plant Path) Brian Steffenson [email protected]

University of Minnesota Jim Anderson [email protected]

University of Sydney Harbans Bariana [email protected]

USDA-ARS Cereal Disease Lab Matthew Rouse [email protected]

USDA-ARS Cereal Disease Lab Yue Jin [email protected]

USDA-ARS Northern Crops Science Lab

Steven Xu [email protected]



60


258


I. Executive Summary Production of wheat varieties with resistance gene combinations that effectively protect against a pathogen population’s ability to progressively mutate and cause destructive epidemics is recognized as the most promising avenue to mitigate the “boom-and-bust” cycles of wheat rusts. Routine deployment of broadly effective stem rust resistance gene combinations has not been possible, practical, and/or sufficiently emphasized in most wheat breeding programs throughout the world to date. Stem rust races in the Ug99 lineage demand an exhaustive and strategic effort to disrupt this cycle and incline the balance of this ancient battle towards wheat resistance. The focus of research and germplasm development efforts proposed within Objective 26 is to fill the “wheat breeder’s toolbox,” via 1) discovery and introgression of new, broadly effective resistance genes, 2) genetic information coupled with robust genetic markers that will enable efficient, cost-effective, and diagnostic selection for stem rust resistance loci, and 3) delivery of high value breeding lines containing combinations of effective genes that enhance the likelihood of developing varieties with durable rust resistance. One area of uncertainty in developing durable disease resistance in wheat (or any other crop) involves deciding which “types” of genes should be combined to yield the greatest chance of durability. An attractive strategy for durable leaf rust and stripe rust resistance breeding in wheat is to use slow rusting/adult-plant/minor gene resistance (hereafter termed Adult Plant Resistance or APR) (Singh et al. 2005). Aggressive breeding efforts employing the same concepts to stem rust resistance breeding have been minimal but encouraging, as elite materials with moderate to high levels of APR to stem rust have been identified. A major limitation to worldwide development of APR varieties at present is the reliance on phenotypic screening of breeding populations or advanced lines throughout their development in nurseries with highly-virulent stem rust populations (e.g. Njoro, Kenya or Debre-Zeit, Ethiopia). APR donor lines identified to date often have a number of hypersensitive response (HR)/seedling resistance/major genes, which are ineffective against stem rust races in the Ug99 lineage, but broadly effective in most parts of the world and hinder selection in alternate screening locations. Development of DNA markers diagnostic for APR loci would provide an efficient method to enrich breeding populations for APR genes without complete reliance on screening nurseries and by minimizing limitations on suitable genetic backgrounds. Unfortunately, genetic mapping and discovery of diagnostic DNA markers for stem rust APR genes are in the early stages of development (with the exception of Sr2). Furthermore, the number of stem rust APR loci documented to date is quite small and identification and genetic mapping of additional sources of APR is a high priority. Deployment of broadly-effective HR genes in combinations, or pyramids, in a single variety is another widely accepted strategy to achieve durable disease resistance (Watson and Singh, 1952; McDonald and Linde, 2002; Bariana et al. 2007). Routine implementation has been impractical in the past due to the small number of broadly effective genes available at any given time and logistical difficulties in pyramiding genes without diagnostic DNA markers/genotyping. More than a dozen HR genes conferring moderate to high levels of resistance to stem rust races in the Ug99 lineage have been documented to date. Unfortunately, relatively few of these genes are “breeder ready” and/or have diagnostic markers available for use in pyramiding/molecular breeding. Also, several of these HR genes are ineffective against one or more stem rust races

259


present in wheat growing regions of the world. Identification of additional sources of seedling resistance genes is a high priority.

The combination of strategies (HR plus APR) targeted in this objective is an effort to maximize diversity of resistance while minimizing the potential for stepwise mutation and acquisition of virulence in pathogen populations. This project aims to identify “new” (including those previously described but not deployed) broadly effective resistance genes and transfer them to elite breeding materials, aided by development of diagnostic DNA markers. High value breeding lines with combinations of useful genes (HR and/or APR) will then be delivered to variety development programs. Short, Medium, and Long Term Outcomes The primary short term outcome of these research efforts will be an increase in the number of elite breeding lines with desirable combinations of resistance genes used in variety development programs throughout the world. “Pre-breeding” research in programs supported through the DRRW project already has directly impacted stem rust breeding activities by providing additional sources of resistance (awareness and germplasm), improved DNA marker information, and the ability to efficiently select for combinations of genes. This effort will continue to expand for the remainder of Phase I and throughout the next five years of this project. The primary medium-term outcome of Objective 26 will be a further enhancement of available genetic diversity for stem rust resistance in global wheat germplasm. The synchronous identification, annotation, and deployment of many resistance genes (APR and HR) will provide the means to combine and strategically deploy stem rust resistance in an unprecedented manner, promoting durable rust resistance and avoiding future vulnerability similar to the present situation. Efforts to derive diagnostic DNA markers via fine-mapping will eventually enable identification of the structure and function of globally important genes, paving the way for long term advances via designed/targeted manipulations and/or biotechnology solutions in wheat breeding. While maintaining a steadfast focus on genetic solutions to the stem rust problem, the genetic resources produced through these efforts will simultaneously introduce additional genetic variation for other traits that contribute to yield potential/protection.

Sustainability of on-farm wheat production (farmers growing high yielding, resistant varieties without using chemicals to control stem rust = increased profitability, income consistency, etc.) is the primary long term outcome expected from this research. This socioeconomic outcome represents a core mission of the Bill and Melinda Gates Foundation, Cornell University, the partner institutions, and individual scientists involved in this effort. Breeding programs based on a foundation of durably rust resistant germplasm can afford greater focus on other important traits contributing to yield, quality, and adaptation (i.e., through heat/drought/salinity tolerance, resistance to diseases caused by other pathogens), a critical transition to reach even higher plateaus in wheat production in the face of a growing population. The synergy fostered by the critical mass of experts and institutions in this team research effort is an immeasurable, but central outcome that will have significant influence on global wheat breeding in the short and medium terms, and wheat production in the long term.

260


Progress to Date Encouraging progress has been achieved in all “pre-breeding” areas (encompassing Phase I research programs in Objectives 6, 7, and 8), including:

1) Discovery of new/potentially new sources of APR and HR resistance in wild relatives and landraces of wheat (Bansal et al. 2008a and 2008b; Bansal et al. 2009; Kaur et al 2009; Rouse et al. 2009; Olivera et al. 2007;Toor et al. 2009; Xu et al. 2009).

2) Introgression and/or manipulation of resistance sources from un-adapted or wild donors (Dundas et al. 2008; Faris et al. 2008; Pumphrey et al. 2009; Xu et al. 2009; Millet et al. 2009); Olson et al. 2010).

3) Development of new genetic stocks/populations for mapping additional resistance genes (see table 26.2 in Detailed Work Plan).

4) Discovery/improvement of DNA markers for several broadly effective HR genes (Sambasivam et al. 2008; Wu et al. 2009; Liu et al. 2009 submitted; Yu et al. 2009).

5) Communication, coordination, sharing of genetic resources, and definition of future needs/goals in the wheat-stem rust research community.

Large collections of the following donor species were screened for HR genes as seedling plants with stem rust races in the Ug99 lineage (and in many cases additional virulent races): Triticum monococcum (1020), T. urartu (205), T. dicoccoides (880), T. dicoccum (359), T. carthlicum (86), T. polonicum (76), T. timopheevii (298), Aegilops speltoides (90), Ae. sharonensis (107) and Ae. tauschii (456). Resistance effective against Ug99 was detected in all species. Screening of collections of T. monococcum and T. timopheevii did not reveal promising levels of diversity for stem rust resistance, but screening of other collections almost certainly revealed new resistance gene donors. Novelty of resistance to Ug99 cannot be fully ascertained until these resistant selections are characterized with diverse stem rust races (a part of ongoing Phase 1 efforts), and some preliminary studies on the inheritance of resistance in new populations that are under development. A large collection of wild tetraploid wheats (>1,500) was screened by scientists at ICARDA and the Ethiopian Institute of Agricultural Research (EIAR), and 200 wheat landraces at the University of Sydney in an effort to identify new sources of HR and APR genes. Based on preliminary data, many of these accessions may have useful levels of APR; ongoing activities in Phase I will more fully characterize this material. Introgression from a subset of donor accessions with potentially new resistance genes from tetraploid wild relatives and Aegilops species is underway.

In addition to the above species, a diverse group of triticale (wheat-rye hybrid) accessions (567) was screened, and a high frequency of seedling resistance against Ug99 was observed. The resistant subset of triticale accessions needs further testing with races available in South Africa and Australia, but new stem rust resistance genes may be present in these accessions. Dr. Bob Graybosch, USDA-ARS Lincoln, NE will further exploit these materials as part of his ARS research program in collaboration with Yue Jin and others. New USDA-ARS funds (FY2010 increase) have very recently been designated for this effort, representing good leverage on the initial DRRW-funded “discovery” effort. Scientists at the USDA-ARS National Small Grains Germplasm Research Facility (NSGC), Yue Jin, and partners at the Njoro, Kenya screening facility have systematically screened bread wheat landraces for HR and APR genes and

261


identified a number of potentially new sources of resistance; population development to determine novelty and introgression work is underway, boosted by the FY2009 $1.5 million congressional appropriation to the USDA-ARS and state cooperators. Several HR genes conferring resistance to Ug99 were discovered in elite breeding lines, amphiploids or other cytogenetic stocks. Three new HR genes were identified in advanced breeding lines and preliminarily genetically mapped by Ravi Singh and collaborators at CIMMYT (SrA, SrB, SrC; Yu et al. 2009). At least six new HR genes conferring resistance to Ug99 were found in alien chromosome addition or translocation lines from donor species Ae. caudata (SrAecC, SrAecD), Ae. geniculata (SrAeg5), Ae. searsii (SrAse3), Ae. speltoides (SrAsp5), Haynaldia villosa (SrHv6), and Thinopyrum spp (Pumphrey et al. 2009). In addition to the alien-derived HR genes specifically targeted in the Phase I proposal for chromosome manipulations to reduce linkage drag, exploitation of these newly discovered genes is underway to develop useful breeding lines by USDA-ARS labs (Manhattan, KS and Fargo, ND) and the University of Adelaide.

Research programs funded under DRRW Phase I have indentified or developed improved DNA makers for several Ug99-effective HR genes, including Sr13, Sr22, Sr25, Sr26, Sr33, Sr35, Sr42, Sr45, SrA, SrB, and SrC. For most of these genes, continued high-resolution genetic mapping is needed to produce more useful or diagnostic markers. DNA markers have also been developed or identified that detect translocations harboring Sr32, Sr37, Sr39, Sr40, Sr43, Sr44, Sr47, SrHv6, and SrAeg5. Non-DRRW funded research efforts have identified DNA markers for Ug99-effective genes SrAC Cadillac (DePauw et al., 2009) and additional DNA markers for Sr2 (Spielmeyer, unpublished results). A number of these genes were selected for marker-assisted backcrossing and pyramiding in durum, and spring and winter bread wheat backgrounds; those efforts are on schedule but somewhat limited in scope.

Mapping of APR loci is a critical component of ongoing Phase I activities. More than a dozen populations developed for APR QTL mapping are now available, though progress has been hindered by insufficient phenotypic data. Screening nursery failures (primarily drought/inadequate moisture) are responsible for this delay. Additional mapping/validation populations are being developed that will strengthen this APR mapping effort. Improvement of critical screening facilities (via Objective 24) will further advance this research.

Promising efforts with direct relevance to Objective 26 have developed in recent months in the pre-breeding area. A large group of wheat scientists in the United Kingdom have developed an ambitious and integrated proposal entitled “Enhancing diversity in UK Wheat through a public sector pre-breeding programme.” If this large project is funded by the Biotechnology and Biological Sciences Research Council, substantial opportunity exists for synergy with DRRW pre-breeding (Objective 26) efforts. Professor Graham Moore (project coordinator) and the co-investigators are enthusiastic about seizing opportunities for beneficial exchange of germplasm and information with DRRW programs. The USDA-ARS has received an increase of ~$2.5 million in annual base funds for Ug99 breeding and genetics from FY2009-2010. Several USDA and university programs involved in global rust collaborations have benefitted from this essential funding. Their active collaboration with DRRW-funded partners provides germplasm, information, and services of direct benefit to the DRRW effort.

262


Narrative of Proposed Work Refinement and expansion of promising, high-priority Phase I activities will largely direct future research and germplasm development. Continued focus on discovery, introgression, and characterization of new HR and APR genes will strengthen the pipeline of useful genes available in wheat breeding programs and enable strategic deployment of gene combinations. Alien-derived genes on reduced chromosome segments will be aggressively moved into elite genetic backgrounds, while newly discovered genes on large alien chromosome segments will be manipulated to recover small translocations. Development of DNA markers that are diagnostic for effective HR and APR genes is a critical need for wheat breeding programs globally and will continue to be a central focus. Systemic emphasis on delivery of high-breeding value lines with desirable gene combinations will ensure translation of research efforts into breeding products. While we will employ modern molecular genetics, cytogenetics, and germplasm development techniques in the activities proposed, we are optimistic and aware of potential contributions from rapid advances in genomics and molecular biology. High resolution genetic mapping and diagnostic marker development for HR and APR genes in Phase II will enable cloning and follow-up manipulation of these loci in the medium to long term. Thus, genetic resources and information developed during this project will help drive future molecular breeding and biotechnology solutions in wheat improvement.

Component 26.a. Gene discovery, postulation, and phenotypic support of genetic mapping and germplasm development. Activity 26.a.1. Seedling stem rust evaluation. Seedling screening of stem rust resistance is an integral component of the global effort to combat stem rust. Programs led by Yue Jin and Matthew Rouse (USDA-ARS Cereal Disease Lab), Brian Steffenson (Univ. of Minnesota), Jacob Manisterski (ICCI, Tel Aviv University), Zak Pretorius (Univ. Free State ), and Harbans Bariana (Sydney Univ.–PBI): 1) provide phenotypic data for genetic mapping of HR genes providing effective levels of resistance to Ug99 lineage-races and other highly-virulent races, 2) postulate genes based on multi-pathotype responses and infection types, 3) enable APR resistance breeding by accounting for HR genes, 4) discover new resistance genes by screening collections, 5) assist in selection of resistant lines resulting from wild relative introgression, parent building, and breeding efforts, and 6) provide critical input on development of new segregating populations for mapping/inheritance studies. Continued support of their efforts is essential, especially as the number lines/populations requiring expert phenotyping grows in the near future. Each program is committed to training the next generation of leaders in this artful, exacting field.

Activity 26.a.2. Precision APR evaluation. A major bottleneck in discovery and genetic mapping of durable rust resistance loci is the lack of knowledge, methodology and expertise to perform routine precision APR phenotyping in controlled or semi-controlled environments (greenhouses, hoop/tunnel houses, plant growth rooms). Precision APR screening will almost certainly be required to fully dissect APR loci, by minimizing environmental variation (or even interference) and controlling for important variables during inoculation, infection, and disease development that quantitatively alter resistance responses. Zak Pretorius is poised to focus his program to more fully develop this priority area. Complimentary controlled screening and validation of APR resistance phenotypes will be undertaken through research efforts led by

263


Ayele Badebo (Ethiopian Institute of Agricultural Research), Sridhar Bhavani (CIMMYT, Njoro Kenya), and Brian Steffenson. In addition to refining and documenting techniques and quantitative measures required for stem rust APR precision phenotyping, these programs will speed gene discovery, APR genetic mapping and germplasm development efforts. Wild relative accessions, landraces, mapping populations, genetic stocks/validation materials, and/or high value breeding parents with seedling susceptibility will be screened in replicated APR experiments in each program.

Component 26.b. Population development and introgression of new sources of resistance Activity 26.b.1. Population development in the primary gene pool. Screening activities included in Phase I and Phase II (Activities 26.a.1,2) have/will provide a number of potentially new sources of HR and APR resistance in the primary gene pool. This activity is focused on the development of mapping populations, allelic tests or other inheritance studies, and transfer of resistance genes to adapted genetic backgrounds; these resources are necessary to characterize additional useful, marker-selectable, resistance genes. Many populations will be characterized (phenotypic and genotypic) during the timeline of the Phase II project, while numerous others will be under development at the end of Phase II and create incentives for post-DRRW project investment in stem rust resistance genetics. High-priority populations will be used for genetic mapping in 26.c.1, based on consultation with the Objective 26 steering committee (Yue Jin, Harbans Bariana, Ravi Singh, Susanne Dreisigacker, Robert Park and Jim Anderson).

Activity 26.b.2. Alien gene population development/transfer. Although alien-derived chromosome segments have provided massive global contributions to on-farm wheat production (such as T1BL·1RS, T1AL·1RS, and T1BL·1BS-3Ae#1L), the historic pace of exploitation of traits from alien donors has been dismal. While previously constrained by the laborious and highly-technical nature of the required cytogenetic techniques, advances in DNA marker technology and application have created a paradigm shift concerning transfer of desirable traits from alien species. Enhanced efforts to introgress broadly-effective resistance genes from existing cytogenetic stocks and secondary and tertiary gene pool accessions will provide even greater diversity of stem rust resistance. Amphiploids, chromosome addition, and/or translocation lines will be produced by crossing spring wheat and durum lines with desirable donors identified during Phase I and through Phase II activities (26.a.1,2). Cytogenetic stocks produced by Bernd Friebe (Kansas State Univ.) Mike Pumphrey (Washington State University), Steven Xu (USDA-ARS), and Ian Dundas (University of Adelaide) with new resistance genes from Ae. bicornis, Ae. longissima, Ae. sharonensis, Ae. speltoides, Haynaldia villosa, and Thinopyrum species will provide additional raw material for longer-term germplasm enhancement activities (26.b.3). Transfer of potentially new HR and APR genes discovered in Ae. tauschii is medium-term strategy due to “normal” homologous recombination of chromosomes. Populations will be developed from promising wild relative accessions in each species to study inheritance/allelism of resistance and enable genetic mapping as part of Activity 26.c.1. High-priority populations will be used for genetic mapping in 26.c.1, based on consultation with the Objective 26 steering committee. Activity 26.b.3. Chromosome engineering to improve alien translocations. Wheat-alien chromosome lines, translocation lines, and partial amphiploids with resistance to multiple stem

264


rust races including Ug99 were recently indentified from Ae. caudata, Ae. geniculata, Ae. searsii, Ae. speltoides, H. villosa, Ae. Sharonensis, Th intermedium, Th. junceum, and Th. ponticum by Steve Xu, Ian Dundas, Eitan Millet and Mike Pumphrey. Cytogenetic manipulation of these stocks to produce translocation lines useful in wheat breeding programs has been initiated, but will require continued efforts to derive useful germplasm. Resistance genes in stocks produced as part of Activity 26.b.2 will provide more targets requiring this effort.

Component 26.c. Mapping, validation, and delivery of marker-selectable resistance genes

Activity 26.c.1. High resolution genetic mapping of Ug99 resistance loci. Defining the chromosomal location of both seedling and adult-plant resistance genes in the primary gene pool will enable the identification of diagnostic markers that are necessary for efficient development/deployment of gene pyramids. Research focused on mapping and fine-mapping of loci with effective resistance genes in existing populations segregating for HR genes, recombinant inbred line or double haploid APR populations, and additional APR and HR populations either being developed or that will be developed by project collaborators (Activities 26.b.1,2 and 26.c.2) will help achieve this goal. The increased emphasis on precision APR phenotyping (Activity 26.a.2 and Objective 24) will accelerate characterization and validation of APR loci.

Activity 26.c.2. Validation of APR loci. As loci contributing to APR are identified, phenotypic effects, epistatic interactions, and consistency need to be validated/determined in different genetic backgrounds. This reliability information provides wheat breeders a means to prioritize target loci in forward breeding efforts. Suitable validation materials (backcross, near-isogenic lines, or near isogenic-populations) contrasting for APR loci in appropriate elite genetic backgrounds will be developed and tested in African screening nurseries and in precision APR phenotyping experiments as part of Activity 26.a.2. Development of mutant resources for APR donors is a complimentary validation strategy that may also aid in identification of diagnostic DNA markers and eventual cloning of APR genes; large mutant populations will be developed and characterized for two or more high-priority donors.

Activity 26.c.3. Marker optimization and parent building. The delivery of high-breeding value wheat lines with four marker-selectable stem rust resistance genes to breeding programs will be enhanced in Phase II by the strategic position and substantial expertise of David Bonnett and Susanne Dreisigacker. Improved communication, better integration, and responsive delivery to breeding programs will ensure adoption of Objective 26 outputs. Gene deployment strategies can be more effectively addressed due to centralized pyramiding efforts and useful markers will be implemented and refined in the CIMMYT genotyping laboratory for routine use in their Global Wheat Program (including Objective 25 breeding).

Component 26.d. Collection, preservation and distribution of genetic resources and information Activity 26.d.1. Conservation of project genetic resources. Valuable genetic stocks, mapping populations, and high value breeding lines produced by Objective 26 efforts will be stored at dual locations. For mapping populations and other stable germplasm, the USDA-ARS National

265


Small Grains Germplasm Research Facility and CIMMYT gene banks will preserve and distribute materials. For genetic stocks requiring cytogenetic expertise for maintenance (amphiploids, partial amphiploids, addition lines, etc.), the Wheat Genetic and Genomic Resources Center at Kansas State University and the Tottori Alien Chromosome Bank of Wheat have agreed to preserve and distribute materials. These centers have long-term missions to maintain and share genetic resources with the wheat genetics community.

Activity 26.d.2. Management and coordination of genetic information. Jorge Dubcovsky will proactively incorporate the genetic mapping, marker information, protocols and germplasm developed in the project into the scope of the wheat marker-assisted selection website (http://maswheat.ucdavis.edu/) developed and maintained by his group at UC Davis. This user-driven site is frequented by wheat geneticists across the globe (~4,500 hits per month) to access information on genes that have supporting DNA marker information. Relevant information categories will include: gene-specific marker information, detailed protocols, donor germplasm available, contact information for germplasm distribution, and contact information for research labs with expertise on specific markers or genes. His group will also coordinate germplasm distribution among DRRW partners.

Component 26.e Evaluation of genomic selection models in breeding for APR

Activity 26.e.1 Recurrent selection scheme yielding lines with high levels of APR while empirically evaluating GS models for APR. Led by Mark Sorrells of Cornell, Activity 26.e.1 will explore improved efficiencies to breeding for durable rust resistance by employing Genomic Selection (GS) in a recurrent selection scheme to simultaneously select for stem rust APR in spring bread wheat germplasm characterized for high agronomic performance. GS is a new selection methodology that is specifically developed to improve genetic gain in selection for quantitative traits. There is an added benefit in that it can reduce the burden and expense associated with phenotyping large populations for traits of low heritability. Given the polygenic nature of APR, the difficulty of phenotypically evaluating resistance to multiple pathogens and races, and the immediate need for durable rust resistance, GS is a strategy that offers considerable appeal.

Activity 26.e.2 Genomic Selection: A Tool to Decrease Work-Life Conflict in Agricultural Research.

This Activity addresses the hypothesis that by shifting some wheat breeding activities from field intensive phenotypic evaluations to genotypic intensive lab work, as enabled by GS, plant breeders may experience less work-life conflict. Lowering professional barriers such as season-long field activities that include travel away from family may result in increased recruitment of scientists to this profession. Women considering a career in plant breeding will especially benefit from decreased work-life conflict.

Component 26.f. Molecular genetics of rust resistance

Activity 26.f.1. Molecular genetics of rust resistance near the Sr9 locus. Led by Matthew Rouse of the USDA-ARS-CDL, Activity 26 f.1 is based on recent data that indicate the presence of a Ug99 resistance locus linked or allelic with the Sr9 locus (resistance

266


genes temporarily designated as SrWeb and SrGabo56). Several stem rust alleles are present at the Sr9 locus, which is also known to be allelic with stripe rust resistance genes Yr5 and Yr7. Scientists at the USDA-ARS, Pullman, WA are conducting studies in order to clone Yr5. The availability of markers and sequence information at the Yr5 locus will enable the development of markers potentially tightly linked with Sr9 and SrGabo56 in available mapping populations. In order to test for the allelism of SrGabo56 and Sr9, populations for testing allelism have been derived. Screening of these populations with both stem rust and molecular markers can determine whether or not SrGabo56 is and allele of Sr9.

The unique phenotypic diversity at the Sr9 locus makes this an appealing candidate for cloning. Understanding the variation responsible for five Sr9 alleles, Yr5, Yr7, and SrGabo56 will uniquely enhance our understanding of the molecular mechanisms of resistance and race-specificity and could provide base knowledge for long-term projects including the development of new resistance alleles and for the deployment of durable resistance. The marker information available from the mapping of Sr9a, SrWeb, SrGabo56, and Yr5, the sequence information available from the Yr5 mapping project, and the plant populations currently available make the molecular dissection of resistance at this locus feasible.

Justification for Proposed Work

Objective 26 is at the center of the DRRW project and global efforts to develop durable rust resistance in wheat. Objective 23-derived information on pathogen movement and virulence (and use of actual isolates collected in screening) is key to identify and target desirable sources of resistance. Objective 24 is an integral component of Objective 26 research by providing essential phenotypic data for mapping and validation of resistance donors/loci and identifying additional sources of resistance that demand genetic mapping work. Objective 25 is the direct customer of Objective 26 research; new sources of resistance, supporting DNA marker information, and pyramided breeding lines are developed to directly enhance variety development programs. The research programs included in this objective are world leaders in stem rust pathology, wheat genetics/germplasm enhancement/molecular genetics, and breeding with career commitments to wheat improvement. The efforts proposed are unique and essential in that in most cases they could not be effectively carried out by others and represent the most obvious path to routine deployment of durable stem rust resistance in wheat (via interactions with Objectives 23, 24 research and Objectives 25, 21 delivery). Routine, reliable, and high-throughput screening with stem rust races in the Ug99 lineage (Objective Component 26.a) is uniquely possible via support of research conducted by Yue Jin, Zak Pretorius, and Brian Steffenson (and Objective 24 collaborators). Large-scale development of genetic resources focused on Ug99 resistance (from both primary and secondary/tertiary gene pools) requires genetics/cytogenetics expertise, readily accessible germplasm, supporting pathology (Components 26.a, b and Objectives 23, 24) and suitable infrastructure. All partners in the proposed 26.b activities are well positioned and have the necessary expertise to deliver these resources. The team responsible for genetic map construction, validation, and delivery of APR and HR loci (Objective Component 26.c) are among the most productive wheat geneticists/breeders in the world. Their combination of existing genetic resources and

267


experience with stem rust, molecular mapping/validation of quantitative trait loci, diagnostic marker development, gene/QTL cloning, and application of QTL information in breeding make them uniquely qualified to conduct this research. The activities in Objective 26 are technical in nature, as they represent the genetics and technology underlying efforts to breed for durable rust resistance. The subsequent development and wide-scale adoption of superior wheat varieties with multiple sources and mechanisms of rust resistance are the cornerstone of a world where the food and livelihood security of the world’s poor is enhanced through cultivation of wheat varieties with durable resistance to the cereal rusts. Production of valuable genetic resources and information in Objective. 26 will enable sustained community focus on development of durable rust resistance.


268


Objective 26: High breeding value wheat lines with two or more marker-selectable stem rust resistant genes



26.a. Gene discovery, postulation, and phenotypic support of genetic mapping and germplasm develop-ment.

26.a.1. Seedling stem rust screening of wild relatives of cultivated wheats, introgres-sion lines, mapping populations, and high breeding value lines.

Identification of Ug99 resistant Triticum/Aegilops spp., Haynaldia villosa, Secale cereale (and derived triticales) accessions, and Thinopyrum spp.-derived amphiploids with potentially new sources of seedling resistance based on multipathotype analysis; 2000 entries tested per year. (Mar 2011, recurring annually)

Identification of Ug99 resistant rye (Secale cereale and derived triticales) accessions and introgression lines with new sources of seedling resistance based on multipathotype analysis: 100 entries per year. (Dec 2011, recurring annually)

Identification of Ug99 resistant Sitopsis accessions (Ae. bicornis, Ae. longissima, Ae. sharonensis, and Ae. speltoides) and Ae. variabilis, Ae. kotschyi and Ae. geniculata with potentially new sources of seedling resistance: • 300 entries tested per year at TAU (Dec 2010,

recurring annually);

• up to 300 entries tested per year at UMN. (Mar 2011, recurring annually)

Seedling phenotypic data for genetic mapping and selection of introgression lines and breeding parents: • 500-1000 entries tested per year at UMN (Mar

2011, recurring annually); • 300 entries tested per year at Free State (Dec

2010, recurring annually);

• 500 entries tested per year at UMN (Mar 2011,

Five Years Seedling resistant accessions provided to both funded and unfunded collaborators for population development, genetic mapping, and germplasm enhancement of new sources of Ug99 resistance. Genetic mapping studies (with populations from both funded and unfunded partners) reveal chromosomal location of new resistance genes.


Fifteen Years Durable rust resistance strategically deployed based on combinations of major genes and/or APR genes.

Y. Jin, USDA-ARS CDL

Z. Pretorius, Free State U


J. Manisterski, ICCI Tel Aviv U

M, Rouse, USDA-ARS CDL

269




recurring annually)

Seedling Phenotyping of Mapping Populations; Pheotyping T. monococcum populations (Mar 2012)

• Einkorn/ PI 272557

26.a.2. Controlled APR screening of seedling-susceptible wild relatives, landraces, mapping populations, and high breeding value lines.

Ug99 resistant Triticeae accessions identified with potentially new sources of adult plant resistance, validation of adult-plant resistance QTL, and confirmation of high-value breeding lines: 100 lines tested per year in greenhouse APR screens with 5 replicates (~500 data points). (Dec 2010, recurring annually)

Adult-plant phenotypic data for QTL mapping. 300 lines tested per year with 5 replicates (~1500 data points). (Dec 2010, recurring annually)

Adult-plant phenotypic data for QTL mapping, validation of adult-plant resistance QTL, and confirmation of high-value breeding lines. 200 lines tested per year with 4 replicates in BL-3 facility. (~800 data points). (Mar 2011)

Tetraploid wheat accessions with potentially new sources of APR; APR phenotypic data for genetic mapping, validation of APR QTL, and confirmation of high-value breeding lines in controlled screen-house. (Dec 2010, recurring annually)

Methods for quantitative infection and measurement of APR are determined, standardized and communicated to the rust community. (Dec 2011)

Five Years APR accessions provided to both funded and unfunded collaborators for population development, genetic mapping, and germplasm enhancement of new sources of Ug99 resistance. Genetic mapping studies reveal chromosomal location of APR loc



Z. Pretorius, Free State U.

B. Steffenson. U Minn

A. Badebo, EIAR


270




26.b. Population development and introgression of new

26.b.1. Intro-gression, population develop-ment, and/or

Recombinant inbred line populations developed for new sources of seedling and APR resistance identified in Watkins collection wheat landraces. At least two populations advanced two generations per year. (Dec 2010, recurring annually)

Five Years Resistant accessions provided to both funded and unfunded collaborators for population development, genetic mapping, and germplasm enhancement of new sources of Ug99 resistance.


S. Xu, USDA-ARS

271




sources of resistance.

allelism testing of primary gene pool sources of seedling and adult plant resistance.

Five or more new doubled-haploid and/or recombinant inbred populations for mapping novel sources of resistance in tetraploid wheats. ~200 DH and/or 400 SSD progeny advanced two generations per year. (Dec 2010, recurring annually)

Genetic mapping studies reveal chromosomal location of APR loci.



26.b.2. Intro-gression, population develop-ment, and/or allelism testing of intractable (secondary/ tertiary gene pool) sources of seedling and adult plant resistance.

New amphiploid and chromosome addition stocks for Haynaldia villosa and Aegilops spp.. Direct introgression lines and synthetic hexaploids with potentially new sources of seedling and APR resistance from Ae. tauschii. Mapping/allelism testing populations for high-priority resistance sources. Five amphiploids, direct introgressions from ten Aegilops accessions, and eight mapping/allelism populations advanced two generations per year. (Dec 2010, recurring annually)

Allelism tests, amphiploids and chromosome addition lines for Sitopsissection species. Six allelism/mapping populations and amphiploids with four Sitopsis accessions produced each year. (Dec 2010, recurring annually)

Backcross introgression/mapping/allelism testing populations with Ug99-resistant Ae. speltoides (4 accessions) and T. dicoccoides (8 accessions)

Five Years Germplasm with new and/or improved alien sources of resistance suitable for development of high breeding value lines. Genetic mapping studies (with populations from both funded and unfunded collaborators) reveal chrom-osomal location of new resistance genes.







272




advanced two generations per year. (Dec 2010, recurring annually)

26.b.3. Targeted molecular-cytogenetic manipu-lation of intractable sources of seedling and adult plant resistance.

Translocation stocks with minimal alien chromatin for four new Ug99-effective resistance genes from Th. intermedium, Ae. caudata, Th. ponticum, and Th. junceum. (Dec 2014)

Translocation stocks with minimal alien chromatin for new Ae. sharonensis-derived stem rust resistance genes. (Dec 2013)

Translocation stocks with minimal alien chromatin for four Ug99-effective resistance genes from Ae. geniculata, Ae. searsii, Ae. speltoides, H. villosa (7/2011) and additional resistance genes identified in via 26.b.2. (Dec 2014).

Translocation stocks with minimal alien chromatin for Ae. speltoides and Th. ponticum derived resistance genes. (Dec 2014)

Five Years Germplasm with new and/or improved alien sources of resistance in variety development programs.



S. Xu, USDA-ARS



B. Friebe, Kansas State U



26.c. Mapping, validation, and delivery of marker-selectable resistance genes.

26.c.1. Mapping rust resistance loci toward development of diagnostic markers for effective genes.



High-resolution genetic maps of two or more Ug99-effective stem rust resistance loci. Robust

Five Years Efficient pyramiding of diverse stem rust resistance loci in breeding lines.

Ten Years Identification of allelic sources of resistance. Development of diagnostic markers or marker combinations for prediction of Sr genes in germplasm collections. Elite breeding lines with APR in variety development programs.


J. Anderson, U Minn


U. Bansal and

273




DNA markers that are tightly linked or diagnostic for stem rust gene detection. (Dec 2014)

Chromosomal location two or more new sources of stem rust resistance (Ug99-effective) through molecular mapping and and identification of linked markers. (Dec 2014)


Mapping populations suitable for APR mapping, phenotypic data, and framework genetic maps for three APR populations (Dec 2012)

High-resolution genetic maps of the Ug99-effective stem rust resistance loci in durum wheat. Robust DNA markers that are tightly linked or diagnostic for stem rust gene detection. (Dec 2014)

Enhanced diversity of stem rust resistance available in wheat breeding.

Fifteen Years Identification of molecular basis of APR resistance loci. Strategic manipulation of APR loci for routine durable rust resistance deployment (including biotechnology solutions).


E. Lagudah, CSIRO


S. Xu, USDA-ARS

26.c.2. Validation of effective APR genes conferring resistance to the Ug99 lineage.

Backcross near-isogenic populations for APR loci in Kingbird, Juchi, and Kiritati. Heterogeneous inbred families suitable for near-isogenic line development. (Dec 2013)

Backcross-derived doubled haploid populations contrasting for APR loci in multiple genetic backgrounds. (Dec 2013)

Near-isogenic lines/populations for two or more APR loci in two or more spring wheat backgrounds (Dec 2013)

Near-isogenic lines/populations for two or more APR loci in two or more spring wheat/durum backgrounds (Dec 2013)

Five Years Reliability information concerning expression of APR QTL in different genetic backgrounds and flanking markers that guides variety development efforts. Stocks for fine mapping and development of diagnostic markers/cloning

Ten Years Determine the effectiveness of different APR genes in different genetic backgrounds. Determine the epistatic interactions among different APR genes. More durable resistance based on Sr2



J. Anderson, U Minn


274




Study of epistatic interactions among APR genes (Dec 2014)

Mutant populations for Kingbird and appropriate parent. Single QTL backcross isolines from Parula (Dec 2013)

Backcross-derived isolines of two APR loci derived from wheat landraces. (Dec 2013)

Near-isogenic lines/populations for two or more APR loci in two or more CWANA winter wheat backgrounds (Dec 2013)

+additional well defined APR loci or genes

Fifteen Years

Durable rust resistance routinely deployed based on APR genes. Integrated APR strategies that incorporate a better understanding of the epistatic interactions among APR genes and their interactions with different wheat genetic backgrounds.

E. Lagudah, CSIRO



26.c.3. Parent building and delivery to breeding programs.

High breeding value lines homozygous for two or more effective marker-selectable stem rust resistance genes distributed in International Stem Rust Screening Nursery. Twelve elite genotypes used as recurrent parents (Dec 2011, recurring annually)

Optimized screening conditions for DNA markers linked to Ug99-effective resistance loci and marker-assisted pyramids in high-breeding value lines. (Dec 2010, recurring annually)

Five Years Enhanced diversity of stem rust resistance available in wheat breeding. Pyramided donor lines for CGIAR and National Program breeding efforts. Introgression of resistance genes in germplasm adapted to the targeted regions.

Ten Years Elite breeding lines with new sources of Ug99 resistance in variety development programs worldwide.

Fifteen Years Efficient crossing blocks with multiple resistance genes fixed in the parental lines, which will eliminate the need of additional MAS in these lines.


S. Dreisigacker, CIMMYT Mexico

275




26.d. Collection, preservation and distribution of genetic resources and information.

26.d.1. Preservation and distribution of germ-plasm.

Genetic stocks, amphiploids, mapping populations, resistance donors, validation, and high-value breeding lines preserved and distributed to international wheat breeding community; Preservation: H.Bockelman/ NSGC Aberdeen, H. Tsujimoto/NBP Japan, B.S. Gill/WGGRC (in-kind collaborators); Additional distribution via International Stem Rust Screening Nursery. (Dec 2010, recurring annually)

Five Years Fluid distribution of information an germplasm among participants and target breeding programs

Ten Years Integrated web resources to facilitate rapid access to information about sources of resistance, available germplasm, and detailed protocols for marker implementation. Generation of feedback mechanisms from the users (e.g. wiki)

T. Payne, CIMMYT Mexico

26.d.2.

Manage-ment of genetic information and resources.

Centralized web-accessible information on effective sources of stem rust resistance, including donor germplasm, mapping information, useful DNA markers, detailed protocols, feedback tools, and available high breeding value lines. Coordination of Obj. 26 germplasm distribution and screening nursery entries. Strong international partnerships. (Feb 2011, recurring annually)

Fifteen Years An active research community engaged in the continuous actualization of protocols and information.


26.e. Evaluation of Genomic Selection Models for Breeding for APR

26.e.1. Recurrent selection scheme yielding lines with high levels of APR while empirically evaluating GS models for APR.

Initiation of cycle one of recurrent selection scheme by crossing 10 high performing parents in all possible combinations and intermating the F1s (Jul 2012)

Selection of lines to be intermated in cycle two of recurrent selection scheme using Genetic Estimated Breeding Values (GEBVs) calculated with GS models (Oct 2012)

Selection of intermated cycle two lines using GEBVs calculated with GS models (Apr 2013).

Phenotypic evaluation in Njoro, Kenya of selected

Five Years Advanced breeding materials with high levels of APR combined with good agronomic performance. Evaluation of GS model accuracy and consistency across CIMMYT germplasm.

Ten Years Finished varieties with elite agronomic performance combined with high levels of APR and major resistant genes. Use of GS in breeding for APR in other lines.


276




cycle one and cycle two lines for APR, and empirical evaluation of GS models (Apr 2014).

Fifteen Years Durable rust resistance deployed. Routine use of GS to reduce phenotyping and increase gain from selection per unit time. Gender equity in wheat breeding achieved from the shift from field breeding to molecular breeding using GS.

26.e.2.

Genomic Selection: A Tool to Decrease Work-Life Conflict in Agricultural Research?

Use data from CGIAR and private companies to look at effect of molecular advancements on time spent away from home. (Sep 2011)

Train female graduate student in GS while also testing hypothesis that GS will reduce amount of time spent phenotyping in the field (Jessica Rutkoski). (Sep 2013)

Support publication of paper title “Genomic Selection: A New Tool to Decrease Work-Life Conflict in Agricultural Research.” (Sep 2011)

Five Years Proof of concept that GS shifts the proportion of time spent in lab or data analysis versus field.

Ten Years This technology shifts responsibilities of the scientist from field work to increased management and planning versus field work.

Fifteen Years Gender parity among wheat breeders.


26.f. Molecular Genetics of Rust Resistance

26.f.1. Molecular Genetics of Rust Resist-ance near the Sr9 locus.

Identification of markers tightly linked to Sr9 allelles—DArT derived markers and markers linked to Yr5. (Mar 2012)

Linkage testing between Sr9e and SrGabo 56. (Mar 2013)

Publication of genetics and mapping of stem rust resistnace in Gabo 56/alelism with Sr9. (Mar 2014)

VIGS induced gene silencing of putative Yr5 homologs in wheat lines possessing Sr9 alleles.

Five Years

Molecular and functional genetics of the Sr9 locus is molecularly characterized and understood.

Ten Years Efficient pyramiding of diverse stem rust resistance loci in breeding lines. Diverse resistance available in wheat breeding.

M. Rouse, USDA-ARS CDL

277




(Mar 2015)

Molecular characterization of SrGabo56 / Yr5 homologs

Fifteen Years SrGabo56 and homologs are deployed in combination with other resistance genes in CIMMYT germplasm

278


III. Detailed Work Plan Component 26.a. Gene discovery, postulation, and phenotypic support of genetic mapping and germplasm development Activity 26.a.1. Seedling stem rust screening of wild relatives of cultivated wheats, introgression lines, mapping populations, and high breeding value lines.

Research programs led by Yue Jin, Zak Pretorius, Jacob Manisterski, Harbans Bariana, and Brian Steffenson will conduct seedling phenotypic screening of large Triticeae wild collections, potentially novel resistance donors in the primary gene pool, mapping populations, and introgression lines with multiple pathotypes (including Ug99-lineage) in order to identify and characterize new resistance genes. Phenotypic screening of mapping populations will be divided among these programs based on capacity, pathotype considerations, and feasibility. Potentially new sources of resistance identified through non-DRRW funded research programs (i.e. USDA-ARS NSGC) will require the phenotyping expertise and capacity of supported DRRW research programs, and their research products will be available for parent building. Although thousands of accessions of wild relatives in the Triticeae tribe have been screened with stem rust races in the Ug99 lineage since the start of Phase I, this number is a fraction of the available genetic resources present in gene banks throughout the world. Resistant accessions identified to date need continued characterization with diverse stem rust races to identify selections that are likely novel for Ug99 resistance and have broad resistance to other important stem rust races. While wheat geneticists begin to exploit materials with potentially new resistance genes, additional collections of several wild relatives in the secondary gene pool are available and represent rich sources of additional broadly-effective HR genes. For example, several species in the Aegilops genus are known to have Ug99 resistance genes, but have not been the focus of extensive gene discovery and introgression efforts to date. Identification of Ug99 resistant Sitopsis accessions (Ae. bicornis, Ae. longissima, Ae. sharonensis, and Ae. speltoides) and Ae. variabilis, Ae. kotschyi and Ae. geniculata-Manisterski and Steffenson

The Harold and Adele Lieberman Germplasm bank at the Institute for Cereal Crops Improvement (ICCI, Tel Aviv Univ.) has an invaluable collection of Sitopsis group relatives (closely related to the B genome of cultivated wheats). The frequencies and levels of resistance to North American races of stem rust in representative collections of Sitopsis species Ae. bicornis, Ae. longissima, Ae. sharonensis, and Ae. speltoides are quite encouraging (Anikster et al. 2005; Olivera et al. 2007). Comprehensive screening of ICCI Sitopsis collections will identify donor accessions with new resistance genes for follow-up inheritance and genetic mapping studies, introgression and parent building. Approximately 300 accessions will be screened per year with three stem rust races at ICCI, followed by testing of resistant accessions with TTKSK and other highly-virulent races at UMN. Phenotypic data will be added to the existing web-accessible database of these accessions maintained by ICCI. Identification of Ug99 resistant Triticum/Aegilops spp., Haynaldia villosa, Secale cereale (and derived triticales) accessions, and Thinopyrum spp.-Jin Complimentary collections of potential donors of new resistance genes in secondary and tertiary gene pools (alien donors), including other Aegilops species (>1,000 accessions), Haynaldia

279


villosa (>100), Secale cereale (and derived triticales) (>500), and Thinopyrum species (>300), are housed in CIMMYT, ICARDA, and USDA-ARS NSGC, and WGGRC gene banks. Additional unique collections (tetraploid and hexaploid landraces, wild relatives) will be accessed from the Vavilov Institute Gene Bank. These alien and landrace collections will be systematically screened with multiple races to identify new sources of resistance. Screening results will enable geneticists with expertise in each species/complex to develop populations for inheritance studies, produce targeted transfers to the wheat genome, and begin cytogenetic manipulation to make genes useful in wheat breeding. An impressive number of amphiploids/partial amphiploids (~50) derived from diverse crosses between wheat and Thinopyrum spp. have been produced by the Land Institute as part of their efforts to develop perennial grain crops. Thinopyrum species are considered rich sources of disease resistance genes in wheat, including Ug99-effective genes Sr25, Sr26, Sr43, and Sr44. The Land Institute will contribute these materials for stem rust gene discovery and introgression efforts. Activity 26.a.2. Controlled APR screening of seedling-susceptible wild relatives, landraces, mapping populations, and high value breeding lines. Adult plant resistance in mapping populations- Pretorius, Steffenson, Badebo

Research efforts led by Zak Pretorius (emphasis on high-priority APR populations and Ae. tauschii), Brian Steffenson (emphasis on high-priority APR populations), Ayele Badebo (emphasis on tetraploid wheats), and Sridhar Bhavani (emphasis on high-priority APR populations via Objective 24) will refine precision APR phenotyping methods, identify components of APR, provide critical precision phenotypic data to discover new APR sources, map in existing high-priority populations, and validate resistance genes.

Adult plant resistance in tetraploid wheat- Badebo Wild tetraploid wheat species are promising sources of additional APR genes and continued characterization of materials identified during Phase I and enhanced discovery efforts are warranted. Dr. Badebo will continue APR screening of tetraploids in a controlled lathe-house in Debre-Zeit, Ethiopia. Populations derived from tetraploid accessions, with APR and HR identified during Phase I, will be phenotyped in replicated experiments. Additional tetraploid populations and derived germplasm developed as part of 26.b.1 and 26.c.2,3 activities will also be screened.

Adult plant resistance in diploid relatives of wheat-Pretorius Given the challenges of clearly defining stem rust APR genes (apart from Sr2) in hexaploid wheat, diploid relatives are also attractive targets to search for new APR loci. Preliminary screening of a large number of seedling-susceptible accessions of Ae. tauschii, the “D” genome donor of bread wheat, for additional sources of leaf rust APR have been encouraging to date (B.S. Gill, unpublished data). We plan to explore the wide genetic variation available in Ae. tauschii to discover new stem rust APR loci by adult-plant phenotyping of seedling-susceptible accessions. USDA-ARS labs have already screened approximately 500 accessions of Ae. tauschii as seedlings with Ug99 and other important stem rust races. This existing data set allowed for selection of seedling-susceptible accessions (particularly emphasizing those with moderate susceptibility as seedlings). More than 200 seedling-susceptible accessions have already been preliminarily screened as adult plants in a greenhouse test and ~8 accessions with

280


moderately resistant-moderately susceptible reactions were indentified. These and additional seedling-susceptible accessions will be rigorously tested by Zak Pretorius to confirm APR and promising accessions will then be used for introgression into bread wheat (26.b.2) and genetic mapping (26.c.1). If sufficient APR screening capacity exists, seedling-susceptible T. monococcum and T. urartu collections will be screened in a similar manner and provided to funded and unfunded collaborators for further characterization and introgression work.

Component 26.b. Population development and introgression of new sources of resistance Activity 26.b.1. Introgression, population development, and/or allelism testing of primary gene pool sources of seedling and adult plant resistance.

Population development for new resistance genes from landraces of wheat-Bariana University of Sydney Plant Breeding Institute scientists have screened a collection of landraces collected in the 1920s from over 30 nations. These lines predate deployment of Rht (dwarfing) genes in wheat breeding, an event that may have resulted in a considerable loss of genetic variation. Seedling and field tests revealed yet uncharacterized sources of HR and APR stem rust resistance. Development of over two dozen mapping populations has been initiated by Harbans Bariana and colleagues. After validation of the effectiveness of each resistance source to stem rust races in the Ug99 lineage (26.a.1, 2), continued development of mapping populations and transfer to elite wheat cultivars through backcrossing will be aggressively advanced. At least two high-priority populations will be targeted for genetic mapping in 26.c.1 based on consultation with the Objective 26 steering committee. Development of doubled-haploid and/or recombinant inbred populations for mapping novel sources of resistance in tetraploid wheats-Xu Five tetraploid wheat (Triticum turgidum L.) accessions were found to be resistant to multiple stem rust races including Ug99 races (Yue Jin, unpublished). Steven Xu will produce five or more DH or recombinant inbred line populations to identify new resistance loci in tetraploid wheat. High-priority populations will be used for genetic mapping in 26.c.1 based on consultation with the Objective 26 steering committee. Durum wheat (T. turgidum subsp. durum) “Rusty,” a genetic stock that is a near universally susceptible to stem rust (Klindworth et al., 2006), will be used as susceptible parent. The five tetraploid wheat accessions will be crossed as female with Rusty. The F1 hybrids from these crosses will be used to develop DH or RI populations. At least 200 DH or RI lines will be developed from each of the crosses. The DH populations will be developed using the wheat-corn hybridization method successfully used in Dr. Xu’s lab as described by Chu et al. (2008).

Because wheat-corn hybridization is highly affected by the genotypes of wheat, we will first make crosses between half the number of plants from each of the five F1 hybrids and corn in the first season. For the F1 hybrids for which adequate haploid plants have been obtained, we will proceed with DH population development. Otherwise, the remaining plants of the F1 hybrids will be allowed to self-pollinate to produce F2 seed, which will be used to develop RI populations. At least 200 F2 individuals will be advanced to F5:6 generation using single seed descent (SSD).

281


Activity 26.b.2. Introgression, population development, and/or allelism testing of intractable (secondary/tertiary gene pool) sources of seedling and adult plant resistance.

Introgression of resistance from Ae. speltoides-Dundas Ae. speltoides accessions AEG363-5, AEG818-4, AEG874-60, AEG2106-38 will be used for HR gene introgression work. These accessions have been tested with multiple races, including TTKSK, and have shown near-immunity. Introgression into bread wheat of two resistance genes derived from diploid Ae. speltoides AEG357-4 and amphiploid CS/ Ae. speltoides TA8026 has been underway for several years. Several putative recombinants with short 2S chromosomes produced from AEG357-4 and a confirmed translocation of 2S chromosome segment from TA8026 will be further characterized. All have been confirmed with in situ hybridization as carrying reduced Ae. speltoides chromatin. All lines are resistant to all known pathotypes of Ug99 and resistance genes in these lines will be transferred into the Indian cultivar HUW234 or another suitable susceptible spring wheat background. Allelism tests, amphiploids and chromosome addition lines for Sitopsis section species.

Brian Steffenson and Eitan Millet will produce populations and amphiploids for Sitopsis section relatives with effective resistance. Resistant accessions will be crossed with two or more susceptible wheat genotypes. Chinese spring will be included because additional genetic stocks for continued chromosome manipulation are in a Chinese Spring (CS) background. Amphiploids will be developed by colchicine doubling. Amphiploid stocks are generally stable and may be transferred to gene banks and available for long term germplasm enhancement efforts (including desirable variation for other traits). For Ae. sharonensis, continued backcrossing in CS Gc2mut and/or CS ph1b Gc2mut backgrounds will produce chromosome addition and translocation stocks for further manipulation in 26.b.3. Ae. sharonensis accessions have selfish genetic elements, known as gametocidal genes (Gc), that may be circumvented via the Gc2mut mutant stock (Friebe et al. 2003). Resistant by susceptible Sitopsis populations will be developed for genetic mapping and marker development using existing genetic mapping data (Olivera et al. 2007). Tests for allelism between resistant accessions of Ae. sharonensis (or other Sitopsis species accessions) will be produced and phenotyped for their response to inoculation by TTKSK. This broad approach will allow for systematic determination of potential gene numbers and selection of new sources of resistance. Development and characterization of chromosome addition and introgression lines for new resistance genes from existing Thinopyrum species partial amphiploids-Xu Thinopyrum species are excellent sources of genes for stem rust resistance. Among the 18 Sr genes derived from the progenitor and related species of wheat, at least five (Sr24, Sr25, Sr26, Sr43, and Sr44) were derived from Thinopyrum species (McIntosh et al. 2008). A recent evaluation showed that most of the 22 partial amphiploids derived from crosses between bread wheat and several Thinopyrum species (Th. junceum, Th. intermedium, Th. bessarabicum, and Th. ponticum) were resistant to multiple stem rust races including the races in the Ug99 lineage (Xu et al. 2009). The partial amphiploids Zhong 4 (wheat-Th. intermedium) and 784 (wheat-Th. ponticum) are of particular interest (Banks et al. 1993; Zhang et al. 1996). Both Zhong 4 and 784 showed immune or flecking reactions to three races in the TTKS lineage (TTKSK, TTKST, and

282


TTTSK) (Xu et al. 2009). When Zhong 4 was tested with six North American races (QFCS, QTHJ, RCRS, RKQQ, TTTT and TPMK), it also showed near-immunity to all of these races. To characterize and transfer these resistance genes to wheat, we will develop the chromosome addition lines in a CS background. In this procedure, Zhong 4 and 784 will be crossed and backcrossed with CS. The BC1 plants will be tested with a less virulent race (i.e. LBBL) of stem rust. The resistant plants will be cytologically studied for identification of plants with 2n = 43 chromosomes. The plants with 2n = 43 will be self-pollinated and their progenies will be cytologically examined for selection of disomic addition lines (2n = 44). The disomic addition lines will be tested with the multiple races mentioned above. The alien chromosomes in disomic addition lines will be identified using protein and DNA marker analysis as described by Faris et al. (2008). The rust reaction data and the molecular characterization of the addition lines will provide key information on the novelty of the resistance genes. The chromosome addition or introgression lines developed in this work will be the excellent genetic stocks for further introgression of novel genes for stem rust resistance through chromosome engineering.

Direct introgression lines and synthetic hexaploids with potentially new sources of seedling and APR resistance from Ae. tauschii-Pumphrey

Deployment of genes from Ae. tauschii is straightforward due to normal homologous recombination and the diploid genome facilitates genetic mapping of useful traits. Screening of Ae. tauschii accessions in USDA and WGGRC collections revealed accessions with seedling resistance to TTKSK (65), TRTTF (36), TTTTF (24). Although only eight accessions had seedling resistance to all races (tested with TTKSK, TRTTF, TTTTF, TPMK, RKQQ, and QTHJ), new genes are likely present in those eight and additional accessions based on differential seedling responses (Rouse et al. 2009). These accessions/new genes conferring resistance to TTKSK will be useful for strategic deployment in gene combinations. Ae. tauschii accessions with measurable levels of APR are also expected from screening activities in 26.a.2. The effectiveness of HR and APR donor resistance will be verified at the hexaploid level by creating synthetic hexaploids via crosses with the susceptible durum lines and seedling and adult-plant phenotyping (Activities 26.a.1, 2). Direct crosses with hexaploid wheat will also be produced for all accessions with potentially novel genes to speed transfer into adapted backgrounds (both HR and APR accessions). Synthetic wheat production and direct hexaploid transfer procedures (embryo rescue and colchicine doubling) are well established in the Pumphrey lab. The increasing genomics resources available for Ae tauschii will allow rapid marker development for new sources of stem rust HR and APR. High-priority populations will be produced and contributed for mapping in Activity 26.c.1 based on consultation with the Objective 26 steering committee. Evans Lagudah will pursue population development and QTL mapping of promising APR donor accessions.

Amphiploids, chromosome addition stocks, and mapping/allelism populations for new resistance genes from Haynaldia villosa-Pumphrey

Among the ~49 named stem rust resistance genes, none were discovered or transferred from wheat relative Haynaldia villosa. Encouragingly, seedling stem rust resistance evaluation of 95 accessions of H. villosa revealed that this species is a potentially rich source of resistance genes. Infection types were recorded as “0” or “0;” for all 95 accessions after a minimum of 15 plants per accession were inoculated with a mixture of three North American races in replicated experiments [a single accession, TA10270, was found to be heterogeneous for stem rust

283


resistance, where two susceptible plants were identified and saved]. Inoculation of a small set of these accessions with TTKSK showed the same near-immunity. Using an existing set of chromosome addition lines available for H. villosa, we identified TTKSK-effective resistance on chromosome 6V and have since produced a T6AS.6VL translocation line (a current chromosome engineering target, Pumphrey et al. 2008, 2009). Four populations were developed by crossing TA10270 (susceptible) by other geographically diverse accessions of H. villosa (all with 0 or 0; infection types). To date, only one of these populations has been phenotyped in the F2 generation, where the segregation ratio and distinct infection types supported a three-gene model of inheritance for resistance to RKQQ. Thus, it is highly likely this out-crossing species has additional broadly-effective resistance genes. The co-linearity of H. villosa and wheat chromosomes makes production of translocation lines and further homoeologous recombinants feasible. Because additional amphiploid/chromosome addition lines are unavailable, five or more amphiploids of H. villosa will be produced each year to produce genetic stocks for manipulation of new, broadly effective resistance genes. Amphiploids will be backcrossed to wheat (with characterization by stem rust screening, marker analysis and cytology) in an effort to produce chromosome addition lines, compensating translocation lines, and eventually small translocations with new stem rust resistance genes. H. villosa populations segregating for single distinctive genes will also be isolated by screening large F3 families and/or single backcross populations to derive populations for future genetic mapping.

Activity 26.b.3. Targeted molecular-cytogenetic manipulation of intractable sources of seedling and adult plant resistance.

Traditional hybridization and chromosome engineering methods are coupled with development of robust DNA markers, stem rust phenotyping (Activities 26.a.1, 2) and genotyping of large populations to identify recombinant progeny with compensating translocations, and/or small, marker-selectable translocations. The following recently discovered genes confer seedling resistance to TTKSK and other races tested and will require continued chromosome manipulation during Phase II using standard population development procedures and techniques (Figure 26.1). Homoeologous recombination and an efficient selection procedure to reduce linkage drag associated with the stem rust resistance genes is used to produce chromosome translocations. We will closely follow this procedure to minimize the size of the alien segments carrying the resistance genes in the compensating translocations developed in this activity. In this procedure, CS ph1bph1b plants will be identified among the progeny of CS Ph1bph1b plants using the markers PSR128, PSR574, and PSR2120 (Roberts et al., 1999). DNA markers such as AWJL3 (Roberts et al., 1999), Xedm80, or GDM108 (Qi et al., 2007) will be used as a positive control for PCR amplification and marker analysis.

284


Figure 26. 1. Generalized diagram of the procedure to reduce the size of an alien segment in a wheat-alien translocation line.

Translocation stocks with minimal alien chromatin for four Ug99-effective resistance genes from Ae. geniculata, Ae. searsii, Ae. speltoides, H. villosa (Friebe and Pumphrey) Translocation lines T5MgS·5MgL-5DL (SrAge5), T5DS·5S#3L (SrAsp5), T6AS·6V#3L (SrHv6), and T3AL·3SS#1S, T3BL·3SS#1S, T3DL·3SS#1S (SrAse3) were targeted/produced during Phase I because they have new TTKSK-effective resistance genes (Pumphrey et al., 2009). Each translocation is large and shortening by ph1b-induced homoeologous recombination and further marker development is needed. Broadly-effective resistance genes from new H. villosa amphiploids (26.b.2) will then be identified by molecular-cytogenetic screening and populations designed/developed to transfer these additional genes.

Molecular-cytogenetic manipulation of new sources of resistance gene derived from Thinopyrum and Aegilops species-Xu

Four wheat-alien species addition lines were recently identified with resistance to multiple stem rust races including Ug99 lineage (Xu et al., 2009; P. J. Larkin, personal communication). They include wheat-Th. intermedium 2Ai (a group 2 chromosomes from Th. intermedium) disomic addition line Z6 (Larkin et al., 1995; Tang et al., 2000), Alcedo/Ae. caudata disomic addition lines AII (C) (Bluethner et al., 1988; Friebe et al., 1992), CS/Th. junceum disomic addition line HD3505 (Charpentier, 1992), and CS/Th. bessarabicum//Genaro 7J disomic addition line W5336 (Zhang et al. 2002). These five addition lines are novel sources of Sr resistance genes because Sr resistance genes have not been reported in Ae. caudata, Th. junceum, Th. bessarabicum, and

F1 Ph1bph1b Sr__ × CS ph1bph1b __ __

Chinese Spring (CS) Ph1bph1b

Self and screen progeny with markers PSR128, PSR574, PSR2120, and AWJL3

CS ph1bph1b __ __ × Translocation line Ph1bPh1bSrSr

BC1

ph1bph1b Sr __ × CS

Screen for rust resistance and discard susceptible; Screen for reduced alien translocation size among the resistant plants using molecular markers for the chromosome of interest.

1000-2000 F1 plants

Select ph1bph1b Sr _ by testing >50 BC1 plants with stem rust and Ph1 molecular markers.

285


group 2 chromosomes of Th. intermedium. In this project, the resistance genes in the five disomic addition lines will be transferred into the wheat genome through chromosome engineering. The first step in this work is to induce primary translocations between wheat chromosomes and their homoeologs carrying the resistance genes from alien species. We will use the monosomic approach described by Friebe et al. (2005) to induce compensating translocations involving the known alien chromosomes. The wheat-Th. intermedium 2Ai addition line Z6 and CS/Th. bessarabicum//Genaro 7J addition line W5336 will be crossed with CS monosomic for chromosomes 2A and 7A, respectively. About 300-400 F2 plants from each cross will be tested with stem rust. The resistant plants will be analyzed by molecular markers to identify the plants with putative translocations. Chromosome banding and fluorescent genomic in situ hybridization (FGISH) will be further used to confirm compensating centromeric translocations (Robertsonian). The alien chromosomes in the lines AII (C) and HD3505 are currently being characterized. Once their homoeologous groups are determined, the addition lines will be used to develop Robertsonian translocations using the procedure described above. Meanwhile, the the addition lines will also be crossed with CS ph1b mutant or Ph1 inhibitor and the F2 populations from these crosses are expected to produce chromosome translocations. We will test about 300 F2 plants from each cross with stem rust and then identify the desirable translocations among the resistant plants with 2n = 42 chromosomes by molecular marker analysis, chromosome count, and FGISH. The CS ph1bph1b plants will be crossed to the translocation lines carrying the Sr genes and the F1 plants will then be backcrossed to CS ph1bph1b plants. Because Ug99 will not be available for use in all locations and Ug99 screening at the USDA-ARS Cereal Disease Laboratory and University of Minnesota Biolevel-3 Containment Facility is currently limited to only a few months of the year, stem rust races other than Ug99 will be used to detect each alien gene. Most of North American races are virulent to stem rust resistance genes present in CS. Six North American races, including QFCS, QTHJ, RCRS, RKQQ, TPMK, and TTTT, are avirulent to the resistance genes in the addition lines (Xu et al. 2009) and thus any of these races may be used. At least 50 BC1 plants will be inoculated with stem rust to detect the presence of the alien segment. Resistant BC1 plants will then be analyzed with the molecular markers used to detect Ph1. The resistant BC1 plants that are homozygous for ph1b and hemizygous for the translocated alien segment will be selected and backcrossed to CS. About 1,000 to 2,000 crossed seeds from each backcross will be produced. These hybrids will be tested with stem rust and the resistant plants will be tested with molecular markers for the chromosome of interest. Approximately 6-10 markers which are polymorphic between the parents, and which span the alien segment will be chosen for initial study. If the alien segment has recombined, it will be evident by haplotype changes in the recombinant chromosomes. After identifying lines with reduced alien segments, each line will be examined by FGISH to determine the size of the alien segment. The smallest alien segments retaining each Sr gene will be selected.

286


Translocation stocks with minimal alien chromatin for Ae. speltoides and Th. ponticum derived resistance genes-Dundas

Ian Dundas will transfer alien chromosome segments carrying potentially new stem rust resistance genes from Ae. speltoides AEG874-60 and CS/ Ae. speltoides TS01 (Israel), Th. ponticum partial amphiploids OK7211542 or Th. ponticum decaploid species TA12099, TA12100, TA12101 or TA12102. Stem rust resistance in the Ae. speltoides lines has already been isolated to the “2S” chromosomes. Chromosomes with new resistance genes will be identified and populations produced for ph1b-induced homoeologous recombination and markers developed in collaboration with Bernd Friebe and Mike Pumphrey. Translocation stocks with minimal alien chromatin for new Ae. sharonensis-derived stem rust resistance genes-Millet/Steffenson Eitan Millet will continue to transfer Ae. sharonensis-derived HR genes conferring resistance to TTKSK. Experience suggests that relatively large chromosome segments will be transferred but this will be verified by analyzing different translocation lines using markers developed by Brian Steffenson. Plants with a translocated segment distally to the resistance gene will be crossed with plants with a proximal translocation to allow the alien segments to recombine and produce progenies with smaller translocations. Complimentary attempts to reduce the translocation size will be carried out using a method similar to that presented in Figure 1. Selection for minimal size segments with the resistance gene will be aided by molecular markers. To facilitate more routine A. sharonensis introgression work in the future, a genetic stock will also be produced that is ph1b ph1b Gc2mut Gc2mut. Potential assembly of an Sr13/Sr26 linkage block-Dubcovsky

Dr. Dubcovsky’s lab will do detailed comparative mapping of Sr13 and Sr26 (both located on the distal portion of the long arm of chromosome 6) to determine if they correspond to homoeologous loci or if they can be combined in a single chromosome. If possible, recombinants will be targeted based on ph1b-induced homoeologous recombination and selected for using appropriate stem rust pathotypes and molecular markers resulting from high-resolution genetic/comparative mapping efforts. The derived germplasm would be desirable for gene pyramid deployment.

Component 26.c. Mapping, validation, and delivery of marker-selectable resistance genes Activities involving CIMMYT (Singh, Bhavani, Bonnett, Dreisigacker, Payne) are essential to realize Objective 26 impact (and long term food security impact). The originally proposed activities have been left intact in this proposal revision, but the funding requested for these activities has been removed. Funds are actively being sought from the Biotechnology and Biological Sciences Research Council and Department for International Development, UK, the Federal Ministry for Economic Cooperation and Development (BMZ), Germany, and the US Agency for International Development. Preferably, one (or a combination) of these agencies will direct funding to this critical effort. If sufficient funds are not realized, DRRW Phase II Objective 26 activities will require further prioritization. Funding decisions/outcomes are expected by Fall 2010.

287


Activity 26.c.1. Mapping rust resistance loci toward development of diagnostic markers for effective genes.

High-resolution genetic maps Ug99-effective stem rust resistance loci Jim Anderson, Urmil Bansal, Jorge Dubcovsky, Yue Jin, Evans Lagudah, Ravi Singh, Mark Sorrells, Brian Steffenson, and Steven Xu will continue efforts/initiate genetic mapping towards development of diagnostic markers for Ug99-effective APR and HR genes. Where appropriate, each collaborator will pursue mapping of high-priority loci with the perspective of fine-mapping towards map-based cloning to maximize the likelihood of developing diagnostic markers. In most cases, each lab will focus on at least one APR locus (QTL) and one HR gene. Criteria for prioritization of project genotyping resources and efforts are presented in the Management Plan section. A promising stem rust APR QTL on chromosome 7A was recently mapped by Harbans Bariana’s group from Indian wheat cultivar “HD2009” (Kaur et al. 2009). This effectiveness of this QTL against Ug99 races will be determined (26.a.2) and higher-resolution mapping and validation in other backgrounds pursued if effective. As QTL maps are produced for resistance donors such as Kingbird, Kiritati, Pavon, and Juchi (preliminary maps expected through Phase I efforts by Summer 2010), 26.c.1 collaborators will divide responsibility for higher-resolution mapping of promising QTL based on communication with the Team Leader and the Objective 26 steering committee. The saturation of QTL regions is expected to be complex, requiring development of suitable fine-mapping populations and refinement of QTL positions. These populations will include near-isogenic lines from heterogeneous families and backcrossing of individual QTL into a recurrent susceptible parent for at least two generations to reduce genetic variability and facilitate precision phenotyping. We have used these strategies successfully to clone wheat QTLs for high grain protein content (Uauy et al. 2006), partial stripe rust resistance (Fu et al. 2009), and to clearly define the Fusarium head blight resistance locus Fhb1 (Liu et al. 2006). The required level of backcrossing depends on the strength of the QTL and the number of genes segregating in the population. Considering the previous factor and the step-wise nature of the QTL dissection process, the timelines associated with these efforts will be variable and require some flexibility.

Until the APR QTL are identified the labs listed above will concentrate their efforts in the fine-mapping of HR loci, either already identified or resulting from 26.b.1 and 26.b.2 which should be more straightforward. Detailed maps for these genes will be useful to predict the alleles present in germplasm collections (haplotype analysis), to reduce linkage drag, to suggest allelism, and for marker-assisted backcrossing/pyramiding. A list of current populations, target genes, or type of resistance and status are presented in Tables 26.1 (next page) and 26.2.

TTKSK-effective HR genes on homologous chromosomes (wheat origin), such as SrA, SrB, SrC (Yu et al., 2009), SrTmp and Sr42 (Y. Jin and J. Anderson, unpublished), are particularly difficult targets to derive diagnostic flanking DNA markers due to their moderate phenotypic effects and the rate/nature of polymorphism in bread wheat. This situation is unfortunate given their immediately and proven value in wheat breeding. Each of these genes will likely require development of multiple mapping populations and persistent marker development efforts in order to derive robust DNA markers (similar to QTL mapping efforts). Population development

288


efforts for these genes will be led by Ravi Singh and Yue Jin and their mapping will be in collaboration with 26.c.1 labs.

Because phenotyping of several large populations in both greenhouse and field tests would overwhelm screening capacity, genotyping of fine-mapping populations with flanking DNA markers will be conducted first to identify potentially informative recombinants. Only this small subset of recombinant progeny will need phenotypic screening. Similarly, high-density mapping of HR and APR genes will be done with surrogate races (and at other locations) when suitable pathotypes are available to discriminate between parents and segregation of Ug99 resistance has been confirmed.

Table 26.1. Summary of populations developed at CIMMYT for mapping uncharacterized sources of APR to stem rust and planted for phenotyping at Njoro during 2009

No. PBW343 x Parents with Adult Plant Resistance Generation RIL (No.)

1 JUCHI F6 225 2 KIRITATI F6 225 3 PAVON76 F6 225 4 DUCULA/2*PRINIA F6 225 9 PGO/SERI//BAV92 F6 225 5 Kenya Nyangumi F6 225 6 Kenya Kudu F6 225 7 Kenya Swara F6 225 8 Kenya Fahari F6 225 9 KINGBIRD F5 200

10 CNDO/R143//ENTE/MEXI_2/3/AEGILOPS SQUARROSA(TAUS)/4/WEAVER/5/2*KAUZ/6/FRET2 F5 150

11 PFAU/WEAVER*2//KIRITATI F5 150

12 PGO//CROC_1/AE.SQUARROSA (224)/3/2*BORL95/4/CIRCUS F5 150

13 BABAX/3/OASIS/SKAUZ//4*BCN/4/PASTOR F5 150 14 HE1/3*CNO79//2*SERI/3/ATTILA/4/WH 542 F5 150 15 HPO/TAN//VEE/3/2*PGO/4/MILAN/5/SSERI1 F5 150

289


Table 26.2. Additional populations available/under development (phenotyping in early generations and mapping initiated for race-specific resistance genes) for mapping APR and HR genes

Population Type Lines (No) Gen. Source

Susceptible Parent: CANADIAN/CUNNINGHAM//KENNEDY KIRITATI/2*TRCH APR 200 F3 CIMMYT CHONTE APR 200 F3 CIMMYT PAURAQUE#1 APR 200 F3 CIMMYT KIRITATI APR 200 F3 CIMMYT Kingbird APR 200 F3 CIMMYT Parula APR 200 F3 CIMMYT YANAC/3/PRL/SARA//TSI/VEE#5/4/CROC_1/AE.SQUARROSA (224)//OPATA

Race-specific 200 F3 CIMMYT

NING MAI 9558//CHIL/CHUM18 Race-

specific 150 F4 CIMMYT

ND643/2*WBLL1 Race-

specific 150 F4 CIMMYT SHARP/3/PRL/SARA//TSI/VEE#5/5/VEE/LIRA//BOW/3/BCN/4/KAUZ


Susceptible Parent: PBW343 MILAN/SHA7/3/THB/CEP7780//SHA4/LIRA/4/SHA4/CHIL


NING MAI 9415.16//SHA4/CHIL/3/NING MAI 50 Race-

specific 150 F5 CIMMYT

CHEN/AE.SQ//2*WEAVER/3/OASIS/5*BORL95 Race-

specific 150 F5 CIMMYT CHEN/AEGILOPS SQUARROSA (TAUS)//BCN/3/CMH81.38/2*KAUZ


NING9415/3/URES/BOW//OPATA/4/NINGMAI 7 Race-

specific 225 F6 CIMMYT AUS12/Yitpi APR - F3 PBI Cobbity India 2/Yitpi APR - F2 PBI Cobbity India 232/Yitpi APR - F3 PBI Cobbity India 316/Yitpi APR - F3 PBI Cobbity Smyrna 3/Yitpi APR - F2 PBI Cobbity Varna 6/Yitpi APR - F2 PBI Cobbity

Morocco 30/Yitpi Race-

specific - F2 PBI Cobbity

90RN2491/WL711

Race-specific Plus

APR - F8 PBI Cobbity

290


Population Type Lines (No) Gen. Source

T. dicoccum PI193883/Rusty Race-

specific >200 F1 2010 Jin/Xu

T. carthlicum PI387696/Rusty Race-


T. polonicum CItr14803/Rusty Race-


T. turgidum PI387336/Rusty Race-


T. dicoccoides PI466979/Rusty Race-


Ae. tauschii TA10081 (Azerbaijan)/Susceptible Race-

specific >200 F1 2010 Jin/Pumphrey

Ae. tauschii TA1718 (Iran)/Susceptible Race-


Ae. tauschii TA10147(Kazakhstan)/Susceptible Race-


Ae. tauschii TA1675 (Turkmenistan)/Susceptible Race-


Ae. tauschii TA10124(Uzbekistan)/Susceptible Race-


Kofa /UC1113 (Durum) Sr13 93 F6 and BC4F2 Dubcovsky

DV92/G3116 (T.monococcum) Sr35 150 F7 Dubcovsky CS sub[1D RL5406] /CS Sr45 >500 F3 Lagudah Schomburgk/Yarralinka Sr22 - RIL Lagudah Schomburgk/Westonia Sr22 - RIL Lagudah Sr22Tb/Lakin Sr22 291 F3 Pumphrey Sr22Tb/2174 Sr22 392 F3 Pumphrey T. monococcum Sr22/susceptible Sr22 >500 F3 Jin/Lagudah LMPG-6/Norin 40 Sr42 237 F3 Jin/Anderson Chinese Spring/CS SrTmp SrTmp 120 F3 Jin-CDL Rusty/Sceptre Sr13 120 F3 Jin-CDL

LMPG-6/CI15685 Race-

specific 120 F3 Jin-CDL

Chinese Spring/CI14035 Race-

specific 120 F3 Jin-CDL Saturation mapping of Ug99-effective stem rust resistance loci Currently, the most efficient molecular marker strategy for whole genome mapping of wheat consists of using a combination of DArT markers (Akbari et al. 2006; Semagn et al. 2006) provided by Triticarte (http://www.triticarte.com.au/) and SSR markers, most of which are publicly available. Triticarte’s wheat DArT service is based on a survey of about 40,000 loci,

291


and about 5,000 markers have been characterized in a broad selection of germplasm. Typically, about 300-500 markers will be polymorphic in a cross between two wheat cultivars. Supplementation of the map with SSR markers is necessary to fill gaps and to cross reference the DArT map with previously published maps. Microsatellite markers can be selected from the map alignment provided by Triticarte at their website or from consensus maps available on GrainGenes (http://wheat.pw.usda.gov/). A major project funded by the National Science Foundation titled “Haplotype Polymorphism in Polyploid Wheats and their Diploid Ancestors” http://wheat.pw.usda.gov/SNP/new/project.shtml has produced about 1,700 SNP markers, a portion of which may be useful to this project. The Wheat SNP project also generated a set of PCR primers (so called “genome-specific primers”) that allow targeted amplification of gene fragments from each of the homoeologous genomes of polyploid wheat, thereby providing a means to overcome the complexity of polyploid genomes. The Wheat SNP project also showed that SNPs could be reliably genotyped in tetraploid and hexaploid wheat utilizing the Illumina genotyping platform.

Eight CIMMYT APR donors and elite breeding lines will be included in a large-scale SNP discovery/development project recently funded by a USDA-AFRI competitive grants program (PI-E. Akhunov, Kansas State University). Funding from the Phase I DRRW project to include these parents has been committed to significantly enhance the likelihood of recovering SNPs that will be useful in the mapping populations/germplasm used in the DRRW project. This AFRI project started September 2009 and improved SNP resources will be online in the form of a refined Illumina platform by 2011. The throughput and low cost of genotyping make this platform an excellent tool for construction of high-density genetic maps and genotyping of a large number of lines for allele mining and detecting marker-trait associations. Populations targeted in DRRW Phase II will also utilize this platform as appropriate.

Fine-mapping will be advanced by using various sources of markers in wheat (SSRs; physically mapped ESTs; synteny-based mapping information from rice, Brachypodium and other cereals; SNP markers under development through other projects, etc.). The ability of newly developed markers to discriminate resistance donor alleles from alleles in breeding parents will be evaluated by applying tightly-linked markers to a panel of 12 parental lines used in 26.c.3, as well as additional relevant germplasm/genetic stocks. This polymorphism information will be made available to wheat research community (via 26.d.2) and specifically provided to 26.c.3 partners for parent building.

Activity 26.c.2. Validation of effective APR genes conferring resistance to the Ug99 lineage. Near-isogenic lines/populations and backcross-derived isogenic populations for APR loci

New APR genes must be validated in breeder-relevant germplasm before breeders will have confidence to deploy the genes in their cultivars. Near-isogenic lines (NILs) will be developed and tested for the APR genes discovered from each population that explains at least 5% of the phenotypic variation. NILs will be developed from heterogeneous head rows (F4 generation) following the methods of Pumphrey et al. (2007). This method is particularly efficient because the NILs are developed from pre-existing breeder germplasm, thereby reducing both the development time and cost. Alternatively, APR genes will be backcrossed into common susceptible backgrounds using markers. The effect of the APR genes will be assayed based on the results of at least two

292


phenotypic screenings in at least 10 different genetic backgrounds. Development of BC1 (Susceptible parent/Resistant parent//Susceptible parent) derived mapping populations is underway for Pavon, Kingbird and Kiritati. Backcrossing will allow further breakdown of the combination of APR genes and higher frequency of lines then are expected to carry genes singly. We will grow about 250 BC1 derived F2 lines in Kenya to identify BC1F2 populations that appear to segregate for a single APR gene. Selected BC1F2 populations will be advanced to F3 and higher generation to verify the segregation ratio, derive near isogenic lines and further mapping work (26.c.1).

Development of mutant resources for high-priority APR donors-Lagudah CIMMYT cultivar Kingbird predicted to carry at least 3 APR genes in addition to Sr2 (RP Singh, CIMMYT unpublished observations), is now at the foundation of APR breeding efforts, as well as Kiritati, Juchi and Parula. Extensive QTL mapping efforts will be advanced to dissect loci contributing to the high levels of APR in these lines and continued fine-mapping efforts will strive for diagnostic marker identification (26.c.1). Mutant populations/lines for high-priority donors/loci may be useful for fine-mapping and phenotypic validation of APR loci (when large deletion mutants are targeted, i.e. by gamma irradiation), and invaluable for gene identification as map-based cloning efforts progress. Mutant progeny in a highly resistant APR background lacking a single APR locus with a minor effect conceivably allow for easier validation and more accurate determination of the QTL effect than near-isogenic lines for the same locus in a moderately resistant-susceptible background. [as an oversimplified example, assume a single APR locus confers a 5% lower disease severity rating. Kingbird is rated as 5MR in the harshest of Ug99 screening nurseries. If mutant progeny lacking the single APR locus are 10MR, this difference would be readily observed/quantified. On the other hand, if the same locus is in an isogenic background with a score of 50MR, the isoline with the APR locus expected to be 45MR would be difficult to reliably differentiate due to increased scoring and biological variation associated with intermediate reactions]

Seed of at least two APR donors will be mutagenized by EMS and gamma irradiation to produce mutant populations (~5,000 M1 progeny will be initially produced and advanced to the M2 generation) that will be phenotypically screened to identify altered phenotypes with varying levels of stem rust severity. A subset of selected mutants may be associated with corresponding APR gene regions by marker screening. By combining phenotypic data with deletion variants (gamma irradiation-derived) detected by marker screening for known QTL, a focused effort can be made towards developing selectable markers for the multiple APR genes (Spielmeyer et al., 2008). At the same time, remnant seed of mutant populations will be available for future targeted identification of candidate APR genes (e.g. TILLING). A similar approach has been used successfully for the validation of the partial stripe rust resistance gene Yr36 (Fu et al. 2009).

Activity 26.c.3. Parent building and delivery to breeding programs. Optimized screening conditions for DNA markers linked to Ug99-effective resistance loci-Dreisigacker Efforts to convert the most frequently used markers into high throughput forms amenable to use in the CIMMYT marker lab is anticipated, as well as development of protocols for multiplexing. Susanne Dreisigacker will oversee marker screening activities including refinement of protocols for high throughput screening and multiplexing where appropriate. A proactive shift toward

293


SNP-based genotyping methods (i.e. Taqman assays) will be undertaken to ensure genotyping capacity and costs are conducive to enhanced molecular breeding in CIMMYT’s Global Wheat Program. Collaborating mapping labs (Activity 26.c.1) will test the ability of newly developed markers to discriminate resistance donor alleles from alleles in breeding parents by applying tightly-linked markers to the panel of 12 parental lines used for parent building (next section). Provided with this information and detailed protocols, Dr. Dreisigacker will select appropriate polymorphic markers and optimize their use at CIMMYT. High breeding value lines homozygous for two or more effective marker-selectable stem rust resistance genes-Bonnett Project collaborators will provide useful HR and APR donor lines and supporting DNA marker information to David Bonnett for systematic parent building in twelve elite genetic backgrounds (scheme below). Backcross introgression and pyramiding of four resistance loci into twelve backgrounds (3 spring wheats, 3 facultative/winter/photoperiod sensitive bread wheats, 4 durum wheats, and 2 East Asian spring wheats) will be initiated in each year of the project. The backgrounds will be selected and updated by Objective 25 breeding programs. The durable resistance locus, Sr2, will be included in every pyramiding effort, along with at least two HR genes (initial candidates could include Sr13, Sr22, Sr25, Sr26, Sr32 (new, small translocation), Sr35, Sr39 and Sr40 (new, small translocations), Sr42, Sr45, SrR, and Sr1A.1R. Durable leaf/stripe rust resistance locus Lr34/Yr18 is also associated with stem rust APR, at least in the Thatcher background, and represents another likely component of many four gene pyramids. Additional useful genes originating from 26.a,b,c activities will be included as they are available.

Limited backcrossing to BC2 with marker-assisted selection (Dreisigacker) of the resistance genes and a small number of key background genes will be followed by intercrossing to combine multiple sources of resistance. Two cycles of crossing will be performed each year. Doubled haploids will be produced from intercrossed populations to quickly develop homozygous lines in elite backgrounds with combinations of genes giving resistance to TTKSK and derivatives. Gene pyramids that already exist (from Phase I efforts, from DRRW breeding programs, and from other collaborators) will be combined with new Objective 26 genes and moved into the range of elite backgrounds; the time required to produce lines for validation and distribution to breeders will be reduced from four years to three. Introgression and pyramiding of four genes into the twelve backgrounds will be initiated in each year of the project. Population sizes will be large enough to recover 5 or 6 DH lines combining the 4 introgressed resistance genes and additional lines carrying 0-3 loci for APR validation studies.

The deployment of HR genes (combinations) will be based on consultation between the target breeding programs and Objective 23/24/25/26 Team Leaders. Lines developed from this backcrossing and selection scheme will be transferred to CIMMYT/ICARDA breeders and National Programs for evaluation/use as parents and for validation of the effectiveness of the resistance genes and gene combinations (Activities 26.a.1,2 and 26.c.2). Pedigree and genetic information will be maintained in ICIS so that these efforts share a common information platform when transferred to Objective 25 breeders. These efforts are complementary to marker-assisted breeding activities in Objective 25 by focusing on transfer of new resistance genes into pyramided lines, or rapid introgression into adapted backgrounds. A selected set of derived lines

294


will be included for worldwide distribution in annual International Stem Rust Resistance Screening Nurseries.

Scheme for Activity 26.c.3: Parent building and delivery to breeding programs.

Season Gene 1 (Sr2)

Gene 2 (SrX)

Gene 3 (SrY)

Gene 4 (SrZ)

Winter 2010 F1 x F1 F1 X F1

↓ ↓ Summer 2010 X Elite X Elite

↓ MAS ↓ MAS Winter 2011 X BC1F1 X BC1F1

↓ MAS ↓ MAS

Summer 2011 → BC2F1 (2 gene) X BC2F1

(2 gene)

MAS ↓

Winter 2012 → IC1F1

MAS ↓

Summer 2012 DH start

MAS ↓

Winter 2013 DH end

↓ Summer 2013

Increase, breeders, validation

Component 26.d. Collection, preservation and distribution of genetic resources and information Activity 26.d.1. Preservation and distribution of germplasm.

Project collaborators will send valuable cytogenetic stocks, mapping populations, donor lines, and improved germplasm to gene banks lead by Dr. Tom Payne (CIMMYT), Dr. Harold Bockelman (NSGC, Aberdeen), Dr. Hisashi Tsujimoto (Chairperson of the National Bioresource Project-Wheat in Japan, Tottori University, Japan), and Dr. Bikram Gill (WGGRC, Kansas State University). These centers have dedicated staff for increase, maintenance, and distribution of genetic resources. Dual storage of stable germplasm at CIMMYT and NSGC and cytogenetic

295


stocks and valuable resistance donors at Tottori University and WGGRC will ensure long-term conservation and availability of these technical materials.

Deposition of materials into each gene bank will be communicated to the objective coordinator (26.d.2) by each collaborator. Whenever practical, collaborators will maintain and increase seed of the exact parent genotypes (single plant) with new genes used for mapping population development, gene introgression, validation, etc. These high-fidelity sources will be the source of germplasm stored at each gene bank. Activity 26.d.2. Management of genetic information and resources.

Advances in gene discovery, genetic mapping, and germplasm development will be communicated to an objective coordinator supervised by Jorge Dubcovsky at UC Davis. This coordinator will facilitate centralized web-accessible information on effective sources of stem rust resistance targeted in this objective, including: donor germplasm, mapping information, protocols for recommended DNA markers, and available high breeding value lines. This coordinator will serve as the point person on requests for Objective 26-derived entries to be tested in Njoro (Objective 24) and Debre-Zeit (26.a.2) field nurseries, and seedling testing by Free State University and USDA-ARS/UMN labs (26.a.1 and 26.a.2). Coordination of the phenotyping of mapping populations, validation and distribution of enhanced germplasm developed via MAS, pyramiding and chromosome engineering will ensure materials are tested and validated in appropriate screening nurseries (and multi-pathotype seedling resistance). Communication between the objective coordinator, Mike Pumphrey (Team Leader), Sridhar Bhavani (Objective 24 Team Leader), Ayele Badebo, Brian Steffenson, Yue Jin, and Zak Pretorius will be essential to ensure materials are adequately prioritized if screening capacity is limited and that timely distribution is achieved. The MASwheat web site: Eight years of marker assisted information for wheat breeders

In January 2001 the MASwheat site (http://maswheat.ucdavis.edu) went on-line. This web resource was one of the activities of the USDA-funded IFAFS project “Bringing Genomics to the Wheat Field” and its initial goal was to provide breeders with detailed protocols for using molecular markers in wheat breeding. Later it became the official site of WheatCAP, a second project ran by the same consortium of wheat breeders and funded by a Coordinated Agricultural Project (CAP) grant from USDA-CSREES.

In contrast with the static nature of the information provided in a journal article, the protocols in MASwheat are updated as new information is available. This occurs, for example, when minor modifications are introduced to a procedure that would not justify a new peer-reviewed publication. Also, collaborators are encouraged to communicate laboratory tips or negative results that are important for successful marker application and rarely informed in a paper. The site is open to contributions from anyone working in wheat, there is no restriction to non-WheatCAP collaborators or scientists outside the US and several pages have been contributed by researchers in other countries. The authorship of each web page is properly acknowledged.

Today the site still focuses on marker assisted selection in wheat, but has a broader scope. In addition to the specific marker protocols, the site contains general laboratory protocols, guidelines to submit data to GrainGenes (a public database of genetic information on cereals) and an education section. Table 26.3 shows the traits or genes for which the site has at least one

296


protocol. In many cases a trait can have more than one gene and some of these genes can have more than one protocol associated. For example, the Hessian fly resistance page (http://maswheat.ucdavis.edu/protocols/HF/) includes five genes; one of these, H9, has procedures for site specific, RAPD and microsatellites markers.

The education and outreach section (http://maswheat.ucdavis.edu/Education/) has Adobe-Flash animations, fact sheets and MS-PowerPoint presentations on DNA handling procedures (extraction, PCR, gel electrophoresis), marker assisted breeding, disease resistance and quality improvement. This section also hosts presentations and other materials for an introductory molecular breeding class (“CSI Plant Style”) and for a genetic mapping course. Most of the visits to the web site originate in the US, but it has an audience in other countries and regions too, mainly China, India, Europe, Canada and Argentina. Figure 26.2 shows the monthly rate of visits and pageviews between April 2008 and 2009.

The MASwheat web site is hosted at the Plant Sciences Department of the University of California, Davis. It has a close working relationship with GrainGenes. Both sites exchange information, their curators hold weekly conference calls for coordination and GrainGenes provides support with more specialized database tasks.

Figure 26.2. Number of visits and pageviews between April 2008 and April 2009

297


Table 26.3. Traits and genes with pages in MASwheat

Fungi resistance genes Leaf rust resistance gene Lr19 Leaf rust resistance gene Lr21 Leaf rust resistance genes Lr29 and Lr25 Leaf rust resistance gene Lr34, stripe rust resistance gene Yr18 Rust resistance genes Lr35 (leaf rust), Sr39 (stem rust) Rust resistance genes Lr37 (leaf rust), Yr17 (stripe rust), Sr38 (stem rust) Leaf rust resistance gene Lr39 Leaf rust resistance gene Lr46, stripe rust resistance gene Yr29 Leaf rust resistance gene Lr47 Leaf rust resistance gene Lr50 Leaf rust resistance gene Lr51 Stripe rust resistance gene Yr5 Stripe rust resistance gene Yr15 Stripe rust resistance gene Yr36 Stem rust resistance genes Sr25, Sr36 Powdery mildew resistance gene Pm34 Powdery mildew resistance gene Pm35 Resistance to fusarium head blight Eyespot resistance Resistance to septoria tritici blotch Insensitivity to the toxins produced by Pyrenophora tritici-repentis and Stagonospora nodorum

Viruses resistance genes Wheat streak mosaic virus resistance gene Wsm1 Barley yellow dwarf virus resistance gene Bdv2 Resistance to wheat spindle streak mosaic bymovirus.

Insects resistance genes Resistance to hessian fly Resistance to russian wheat aphid Resistance to wheat stem sawfly Greenbug resistance

Abiotic stress and agronomic traits Aluminum tolerance Drought tolerance and root biomass Dwarfing genes Vernalization requirement

Quality related genes High grain protein content (HGPC) gene. Pre harvest sprouting (PHS) tolerance Starch properties: waxy mutants. Grain texture Gluten strength Semolina color

298


Component 26.e Evaluation of Genomic Selection Models in Breeding for APR.

Activity 26.e.1. Recurrent selection scheme yielding lines with high levels of APR while empirically evaluating Genomic Selection (GS) models for APR.

We propose to explore improved efficiencies to breeding for durable rust resistance by employing Genomic Selection (GS) in a recurrent selection scheme to simultaneously select for stem rust APR, yellow rust APR, and leaf rust APR in spring bread wheat germplasm characterized for high agronomic performance. GS, introduced by Meuwissen et al (2001), is a new selection methodology that is specifically developed to improve genetic gain in selection for quantitative traits. There is an added benefit in that it can reduce the burden and expense associated with phenotyping large populations for traits of low heritability. Given the polygenic nature of APR, the difficulty of phenotypically evaluating resistance to multiple pathogens and races, and the immediate need for durable rust resistance, GS is a strategy that offers considerable appeal.

Genomic selection (reviewed by Heffner et al. 2009) consists of two components; model training and selection. In model training, a training population of relevant germplasm having reliable phenotypic and genotypic data is used to estimate marker effects. The GS models are applied to a companion population under selection using only genotypic data to calculate genomic estimated breeding values (GEBV). GS accurately predicts breeding values according to simulation studies in animals (Meuwissen et al. 2001, VanRaden et al. 2009) and plants (Bernardo and Yu 2007; Zhong et al. 2009). Empirical studies in animals have reported high accuracies and increased gains from selection per unit time using GS (Hayes et al. 2009). In plants, empirical studies have yet to be conducted. GS models for stem rust APR will be developed using a training population consisting of 200 lines expressing APR and two Recombinant Inbred Line (RIL) populations segregating for APR. Collection of phenotypic data on the training population is already underway in the stem rust screening nursery in Njoro, Kenya. Model training and cross-validation will be completed by 2012.

We will begin recurrent selection using 10 parents with high agronomic performance and acceptable levels of APR. To begin cycle one; the parents will be recombined by performing all 45 possible combinations of crosses. The F1s will be intermated by crossing each F1 to at least four other randomly selected F1 individuals, for 180 total crosses. These inter-mated F1s will then be pre-selected using SSR markers for important major genes. 470 individuals randomly selected from the inter-mated F1s will then be genotyped with DArT markers. Lines to be intermated in cycle two of the recurrent selection scheme will be selected based on GEBVs calculated using GS models and DArT data. Intermated lines from cycle 2 will be (DArT) genotyped and selected based on GEBVs calculated using GS models and DArT data. Cycle 1 and cycle 2 lines selected using GS will be phenotypically evaluated in Njoro, Kenya for stem rust APR response. Performance of the selected cycle 1 vs. cycle 2 lines will be compared to a random sample of lines from cycles 1 and 2 to empirically evaluate accuracy and efficiency of the GS model when incorporated in a recurrent selection scheme. The protocol for recombining, pre-selecting, and recurrently selecting inbred lines based on GEBVs is outlined in Table 26.4.

299


This project will be the first application of GS in an applied plant breeding program and will be the first study of GS for disease resistance in a plant species. The results of this recurrent GS scheme will not only generate lines with high levels of APR combined with good agronomic performance, but it may also provide evidence for the routine use of GS in plant breeding programs. Table 26.4. Recurrent GS breeding scheme to combine stem rust APR, resistance to leaf and yellow rust, and good agronomic performance Year Month Activity

Jan Identify 10 lines to be used as parents that have high agronomic performance and acceptable levels of APR for stem rust.

Jan – Apr Initiate cycle one of recurrent selection scheme: cross parents in all possible combinations (45 crosses).

Apr- Jul Plant the F1s and intermate (180 crosses). Jul Plant intermated F1s and extract DNA. Jul – Aug Pre-select intermated F1s with SSR markers for important major genes. Aug-Oct DArT Genotype pre-selected lines (470 individuals).

1

Oct Select lines to be intermated in cycle two of recurrent selection scheme using Genomic Estimated Breeding Values (GEBVs) calculated with GS models.

Nov- Feb Plant selected cycle two lines and intermate. Feb Plant intermated cycle two lines and extract DNA. Feb-April DArT genotype cycle two lines. April Selection of final lines using GEBVs calculated with GS models. Self all

selections 2 generations to generate homozygous lines.

2

Nov Plant selected and random lines from cycles 1 and 2 in Njoro, Kenya. 3 March Evaluate APR of all lines in Njoro, Kenya and analyze data.

Activity 26.e.2. Genomic Selection: A New Tool to Decrease Work-Life Conflict in Agricultural Research?

Throughout history, the development of small, but significant, technologies has fostered women’s entrée into traditionally male dominated careers. The number of women engaged in agronomy, breeding, and other professions that require significant field based activities remains low when compared to other professions that do not have the same level of this type of activity. Understanding this gender asymmetry should be addressed if we are to attract more women scientists to wheat breeding.

This activity addresses the hypothesis that by shifting some of the wheat breeding activities from field intensive phenotypic evaluations to genotypic intensive lab work, as enabled by genomic selection, plant breeders may experience less work-life conflict. Lowering professional barriers such as season-long field based activities that include travel away from family, may result in increased recruitment of scientists to this profession. We suggest that women considering a career in plant breeding will especially benefit from decreased work-life conflict.

300


Genomic Selection eliminates many of the burdens associated with wheat breeding research that may have traditionally deterred women from this career. The intense demands of carrying out large-scale field trials and the phenotypic screening of potential lines in remote locations, such as the screening nursery at Njoro, Kenya, have likely negated this career path for women from many cultural backgrounds. Genomic selection is a technology that can significantly lessen the burdens associated with phenotypic selection, such as travel and time away from family and household responsibilities. Enabling women to competitively participate in world-class wheat breeding programs will have long-term impact on gender equity in plant breeding and agricultural development.

We believe a gender initiative embedded within the scientific activities of Phase II of the DRRW proposal will have impact in the short and long-term. Genomic selection is an evolutionary approach to plant breeding and holds potential for gender parity since the selection for a trait in any environment can be done locally once the prediction models have been established.

Through this activity, the DRRW project has the opportunity to advance the cause for gender equity and lead plant genetics into a new era through genomic selection, while simultaneously moving wheat breeding for stem rust resistance forward. Outputs

• Proof of concept that GS shifts the proportion of time spent in lab or data analysis versus field.

• This technology shifts responsibilities of the scientist from field work to increased laboratory work, management and planning.

• Use data from CGIAR and private companies to look at effect of molecular advancements on time spent away from home.

• Train female graduate student in GS while also testing hypothesis that GS will reduce amount of time spent phenotyping in the field (Jessica Rutkoski).

• Support publication of a paper titled “Genomic Selection:A New Tool to Decrease Work-Life Conflict in Agricultural Research?”

Component 26.f. Molecular Genetics of Rust Resistance Activity 26.f.1. Molecular Genetics of Rust Resistance near the Sr9 locus

Led by Matthew Rouse of the USDA-ARS-CDL, Activity 26.f.1 is based on recent data that indicate the presence of a Ug99 resistance locus linked or allelic with the Sr9 locus (resistance genes temporarily designated as SrWeb and SrGabo56). Several stem rust alleles are present at the Sr9 locus, which is also known to be allelic with stripe rust resistance genes Yr5 and Yr7. Scientists at the USDA-ARS, Pullman, WA are conducting studies in order to clone Yr5. The availability of markers and sequence information at the Yr5 locus will enable the development of markers potentially tightly linked with Sr9 and SrGabo56 in available mapping populations. In order to test for the allelism of SrGabo56 and Sr9, populations for testing allelism have been derived. Screening of these populations with both stem rust and molecular markers can determine whether or not SrGabo56 is and allele of Sr9.

301


The unique phenotypic diversity at the Sr9 locus makes this an appealing candidate for cloning. Understanding the variation responsible for five Sr9 alleles, Yr5, Yr7, and SrGabo56 will uniquely enhance our understanding of the molecular mechanisms of resistance and race-specificity and could provide base knowledge for long-term projects including the development of new resistance alleles and for the deployment of durble resistance. The marker information available from the mapping of Sr9a, SrWeb, SrGabo56, and Yr5, the sequence information available from the Yr5 mapping project, and the plant populations currently available make the molecular dissection of resistance at this locus feasible.

IV. Management Plan Travel funds have been included for project collaborators to attend annual project meetings (such as the Borlaug Global Rust Initiative 2010 Technical Workshop at the 8th International Wheat Conference); Objective 26 scientists will hold additional planning/coordination/discussion meetings at those times. Many of the team members have extensive professional connections and attend other common meetings, including Plant and Animal Genome meetings, Australian wheat meetings, and other international wheat genetics meetings. These frequent encounters encourage additional face-to-face communication. Many of the members of this team have been collaborating actively during the last 10 years as part of the ITMI activities, which provides a useful base of confidence among participants.

The objective coordinator position will enhance overall project management and foster within- and between-objective communication. Prioritization of 26.c.1 genotyping resources for genetic mapping (DART, Illumina-SNP, etc.) and selection of genes for parent building efforts will largely be facilitated by a steering committee composed of Yue Jin, Harbans Bariana, Ravi Singh, Susanne Dreisigacker, Robert Park and Jim Anderson. These members directly represent Objectives 23, 25, and 26, are closely involved in Objective 24, and are global leaders in wheat breeding and rust research. Objective collaborators will coordinate genetic mapping plans with Mike Pumphrey (Team Leader), which will then be evaluated by this committee. Criteria for prioritization will include: 1) demonstrated data on likelihood of uniqueness of source (based on haplotyping, allelism, preliminary or low-resolution genetic mapping, and/or multipathotype infection response), 2) perceived phenotypic value/breeding importance of resistance donor/locus, 3) strength of existing or preliminary population phenotypic data, and 4) willingness to share germplasm and information publicly within a lapse of 1 year after genotyping was completed. In Phase II, Cornell will administer access to these resources (Activity 26.c.1). Additional funds representing a “retreat” budget are included for steering committee members to hold an in-depth convening during year 2 of the project.

Team Leader, Mike Pumphrey, is responsible for ensuring that project resources/activities maintain honest focus on developing information and genetic resources that promote durable rust resistance and will translate to on-farm benefits for the resource poor. The Team Leader will communicate with the objective coordinator/Dr. Dubcovsky, the genetic mapping steering committee, programs conducting phenotypic screening, individual investigators, other Team Leaders, and DRRW management to document and maintain collaboration, momentum, and progress. The Team Leader will review annual technical reports and provide feedback to Cornell and individual collaborators. As breakthroughs demanding additional emphasis (or advocacy) or

302


“no-go” situations may evolve in Objective 26, the Team Leader will consult and coordinate with leading scientists, other objective team leaders and DRRW project management to facilitate the best possible science.

Name Institution E-mail Address Relevant Activities and Outputs

Mike Pumphrey Washington State Univ. [email protected] 26.b.2, 26.b.3

David Bonnett CIMMYT [email protected] 26.c.3 Susanne Dreisigacker CIMMYT [email protected] 26.c.3

Ravi Singh CIMMYT [email protected] 26.a.2, 26.b.1, 26.c.1, 26.c.3

Mark Sorrells Cornell Univ. [email protected] 26.c.1, 26.e.1, 26.e.2 Evans Lagudah CSIRO [email protected] 26.c.1, 26.c.2 Ayele Badebo EIAR [email protected] 26.a.2 Zak Pretorius Free State Univ. [email protected] 26.a.1, 26.a.2 Eitan Millet ICCI [email protected] 26.b.2, 26.b.3 Jacob Manisterski ICCI [email protected] 26.a.1 Bernd Friebe Kansas State Univ. [email protected] 26.b.3 Ian Dundas Univ. of Adelaide [email protected] 26.b.2, 26.b.3

Jorge Dubcovsky Univ. of California-Davis [email protected] 26.c.1, 26.d.2

Jim Anderson Univ. of Minnesota [email protected] 26.c.1

Brian Steffenson Univ. of Minnesota [email protected] 26.a.1. 26.a.2, 26.b.2, 26.c.1

Harbans Bariana Univ. of Sydney [email protected] 26.b.1, 26.c.1 Urmil Bansal Univ. of Sydney [email protected] 26.c.1

Yue Jin USDA-ARS Cereal Disease Lab [email protected] 26.a.1, 26.b.1, 26.c.1

Matthew Rouse USDA-ARS Cereal Disease Lab [email protected] 26.a.1, 26.f.1

Steven Xu USDA-ARS North Dakota [email protected] 26.b.1, 26.b.2, 26.b.3,

26.c.1 V. Potential Risks and Unintended Consequences • Redundancy is a major concern when a large group of scientists are aggressively pursuing a

common goal without reasonable coordination (e.g., discovery and characterization of the same resistance genes). This risk is addressed in Phase II by 1) dividing resistance gene discovery by donor species, 2) by creating a committee to prioritize genetic mapping investments, 3) the overall collaborative structure and 4) inclusion of a project coordinator and Team Leader to maintain communication channels.

303


• Significant effort will be invested in assembly of elite breeding parents with combinations of resistance genes. It is possible, even probable, that subsequent breeding efforts will not maintain these strategic gene combinations. In the long term, HR genes deployed singly will suffer a significantly greater risk of defeat. Development of robust diagnostic markers and proactive delivery of that information to programs throughout the world are promoted in this objective to address this risk. The support and involvement of wheat molecular breeding personnel at CIMMYT in Objective 26 (and Objective 25) will strengthen their institutional expertise for marker-assisted selection and adoption of diagnostic DNA markers for pyramiding.

• Even combinations of broadly effective HR genes (and possibly APR loci) have the potential for defeat. The proposed assembly of a combination durable APR loci Sr2 (and Lr34/Yr18), along with at least two HR genes in high breeding value lines provides an additional level of insurance.

• Access to essential resources is assumed for the proposed work based on community experience to date. However, interruption or loss of these resources may delay progress, potentially via 1) restricted access to adequate screening capacity and quality in both field and greenhouse screening (i.e. nursery failures or new policies restricting pathogen use), 2) poor exchange of germplasm and data, 3) regulatory restrictions on seed movement (inability to import seed, etc.), and 4) greenhouse or chamber failures (over-heating/cooling, natural disasters, etc.).

• Inheritance/genetics studies in polyploid wheat are not always predictable, or easily explained. Erratic behavior of alien chromosomes (based on unknown structural rearrangements, gene interactions, etc.) is possible and documented in wheat, and can delay or block production of targeted materials. Inversions or deletions may limit the extent of homoeologous recombination limiting the reduction of some alien segments by ph1b-induced homoeologous recombination. Silencing of resistance genes has also been documented in several cases when developing hybrids between wild relatives and polyploid wheat. Resistance in some accessions may not be recovered when amphiploids or introgession lines are developed. Similarly, it is not likely that APR loci will have universal effects in different genetic backgrounds. We will maintain adequate experimental designs and materials to minimize and better understand these contingencies.

• Use of highly-virulent races in Minnesota is an activity that creates some risk of escape, and potential for establishment of Ug99 in North America. This risk has been carefully evaluated by APHIS, USDA-ARS, and the University of Minnesota, and practices to prevent accidental introduction are accepted and in place. The new Biolevel-3 (BL-3) Containment facility at the University of Minnesota offers an additional layer of safety against possible pathogen escape in addition to the time restriction of only working with exotic pathogen races during the bitter cold winter months. Moreover, the isolation of this research location from major cereal production areas has made it an ideal place for stem rust screening for nearly 100 years.

304


VI. Evidenced based rationale for choice of partners (including current and potential funds) Yue Jin provides global leadership on stem rust resistance phenotyping, gene discovery and postulation, and genetics. The USDA-ARS Cereal Disease Lab has been a key institution with long-term commitment to leaf and stem rust epidemiology, population genetics, resistance screening and genetic characterization. Dr. Jin strengthens links between objectives 23, 24, 25, and 26 due to his contributions to each of these areas. The CDL has recently been targeted to receive “Ug99 resistance breeding” funds via a recent government appropriation. While the language concerning the use of funds specifically designates enhancement of US readiness for the threat of Ug99 introduction, their efforts will be strengthened by this increase and retain global perspectives. From the same funding increase, USDA-ARS Regional Genotyping Laboratories and geneticists in Aberdeen, ID, Pullman, WA, and Raleigh, NC are increasing molecular mapping research and germplasm development focused on resistance to Ug99. Dr. Jin has strong collaborative relationships with these programs and will continue to coordinate activities to minimize redundancy and maximize output. Zak Pretorius, University of Free State, South Africa, has 30 years experience in wheat rusts. His program is uniquely engaged in refining greenhouse tests on adult plant stem rust response. He has successfully applied for rust research funding from FRD/NRF and the Wheat Board/Winter Cereals Trust in South Africa, and recently the BBSRC in the UK. His expertise and available collection of stem rust races provide critical capacity for both seedling and adult plant phenotyping. Brian Steffenson, University of Minnesota, is another world-class cereal geneticist/pathologist with an active program focused on Ug99. The BL-3 screening facility available for Ug99 is an invaluable asset for both seedling and future APR screening. Dr. Steffenson’s long-term collaboration with Eitan Millet and others at Tel Aviv University will enhance coordination of activities.

Eitan Millet, Tel Aviv University has wide experience in cytogenetic manipulations in general and in transferring genes from wild cereals, including Ae. sharonensis, to wheat. The Institute for Cereal Crops Improvement (ICCI) at TAU holds a large collection of wild cereals, most of which were collected in Israel, including Aegilops spp. and Triticum dicoccoides. Jacob Manisterski, Institute for Cereal Crops Improvement (ICCI), Tel Aviv University, is a highly skilled pathologist with 40 years of proven experience with cereal rusts. He isolates and maintains Israeli rust races and wild wheat accessions in The Harold and Adele Lieberman Germplasm Bank. He has authored many papers dealing with different aspects of rust fungi. Ayele Badebo and collaborating scientists at the Ethiopian Institute for Agricultural Research have extensive experience in nursery establishment, screening, and assessment of resistance to stem rust. The strategic location of a screening nursery at the Debre-Zeit location is critical to evaluate resistance in wild tetraploid accessions, mapping populations, and high breeding value lines.

Harbans Bariana (Geneticist/Pre-breeder) and Urmil Bansal (Molecular Geneticist) are located at the University of Sydney Plant Breeding Institute (PBI), which has a long history of breeding for stem rust resistance in Australia. Since its inception, the PBI-based Australian Cereal Rust

305


Control Program (ACRCP) is a model of integration of basic research, germplasm development and interaction with breeding companies to deliver rust resistant cultivars to growers. PBI has expertise in plant pathology, molecular genetics and germplasm development at one place to assure delivery of rust resistant germplasm together-with validated molecular markers for implementation in breeding programs. Postgraduate training is a major component of the program. PBI has trained scientists who are currently working in CIMMYT, ICARDA and several other organizations. Excellent greenhouse, field (irrigated) and molecular laboratory facilities are available for project work. Of A$1.4 m per annum funding of the Australian Cereal Rust Control Program, a significant proportion is spent on pathology, genetics, germplasm development and marker development aspects of stem rust research. An Australian Centre for International Agricultural Research (ACIAR) funded project with India (Trethowan and Bariana) deals with implementation of markers linked with stem rust resistance genes in two Indian wheat breeding programs. An Australia India Strategic Research Fund project attracts A$310,477 from Australia (Bariana) and about INR 2.2 m from the Indian government (Gupta). This project started in July 2008 and will finish in 2011 and is focused on molecular mapping of adult plant stem rust resistance in wheat.

CIMMYT has a global mandate for bread and durum wheat improvement for the developing world. They are well connected with breeding and research programs in developing countries. A key component is a well-established international nurseries system in which promising new wheat lines are distributed for evaluation all around the world. In addition to this, training of scientists from the National Agricultural Research Systems from developing countries and collaborative projects with many provide strong mechanisms for transfer of new knowledge and technology, particularly marker technology in this case. CIMMYT has the appropriately skilled research scientists, breeders, technical staff, management and leadership capabilities to successfully implement this project. Selection of recurrent parent backgrounds will make use of the expertise of CIMMYT and ICARDA breeders who are best placed to understand adaptation across diverse environments around the world. David Bonnett is responsible for many of the wheat pre-breeding activities at CIMMYT. He has a strong track record in development of germplasm carrying novel traits in adapted backgrounds. He has put a lot of emphasis on use of DNA markers in germplasm development and is recognized internationally for development and implementation of marker-assisted selection strategies. Many germplasm lines he has produced have been used by wheat breeders in Australia and at CIMMYT; some are undergoing evaluation for direct release as varieties and several are under consideration for release in Australia. Dr. Bonnett will oversee development of the germplasm delivery strategy and it’s implementation. Susanne Dreisigacker is the leader of CIMMYT’s wheat molecular marker group. She is responsible for marker development and screening in CIMMYT’s Global Wheat Program. She has extensive experience in diversity analysis, marker development and marker-assisted breeding and a strong publication record in this area. Dr. Dreisigacker will oversee marker screening activities including refinement of protocols for high throughput screening and multiplexing where appropriate for 26.c.3 efforts. Ravi Singh is the world leader in development/identification of APR for rust diseases in wheat. He has been involved in discovery and mapping of several genes and cloning of Lr34/Yr18. Resistance to Ug99 and its derivatives is an important target in all of CIMMYTs wheat breeding

306


activities and Dr. Singh has been responsible for rapidly selecting resistance in elite backgrounds and fast-tracking release and increase of seed of resistant varieties in key environments under threat from Ug99. Steven Xu, USDA-ARS, Fargo, ND has unique expertise and capacity required for robust chromosome engineering, population development, genetic mapping, and trait introgression. His program is well-funded by the USDA-ARS, the United States Wheat and Barley Scab Initiative and other competitive grants. Dr. Xu is a highly productive wheat geneticist, efficiently integrating diverse aspects of trait discovery and improvement, and leveraging considerable resources and collaborations at both North Dakota State University and the USDA-ARS Cereal Crops Research Center.

Mike Pumphrey (Washington State University) has an active program with heavy emphasis on germplasm enhancement focused on rust resistance. Dr. Pumphrey has a unique combination of experience in molecular cytogenetics, wide-crossing, genetic mapping and map-based cloning, wheat germplasm enhancement, cereal rust pathology, and wheat breeding. Prior to appointment as Spring Wheat Breeder at WSU, he was an integral member of the Wheat Genetic and Genomic Resources Center (led by Bikram Gill) as the USDA-ARS Research Geneticist in Manhattan, KS, and remains a strong collaborator from WSU. The critical mass of wheat research at WSU is also recognized worldwide, particularly in wheat breeding and pathology research. Bernd Friebe (Research Professor at Kansas State University) is internationally recognized for his expertise in wheat cytogenetics, and has a career commitment to chromosome engineering of agronomically important traits. Dr. Friebe works with Bikram Gill in the Wheat Genetic and Genomic Resources Center. A gene bank (>2,500 wild accessions and >10,000 genetic/cytogenetic stocks), USDA-ARS regional genotyping lab, supporting rust pathology expertise, and extensive greenhouse facilities are actively leveraged to achieve project goals. Additionally, the USDA-ARS Hard Winter Wheat Genetics Research Unit in Manhattan focuses significant resources on stem rust germplasm enhancement and genetics research in collaboration with the WGGRC. Drs. Friebe, Gill, and Pumphrey have a strong relationship that has already produced translocations harboring several new broadly-effective stem rust resistance genes, as well as several other genes of agronomic importance on small alien translocations.

Evans Lagudah (CSIRO Plant Industry) has a program dedicated to basic and strategic research in rust biology, molecular genetics and molecular breeding applications. The scope of CSIRO programs span fundamental research in the model system of the flax gene for gene, effector biology through to applied research in robust marker development to facilitate pyramiding resistance genes to achieve more durable resistance. Under the auspices of the Australian Cereal Rust Control Program, CSIRO in conjunction with the University of Sydney, Adelaide and CIMMYT bring together complementary skills from the laboratory to the field in rust research. Dr. Lagudah has availability of a cobalt source for generating gamma irradiation. He successfully demonstrated the use of gamma irradiation in generating overlapping set of interstitial deletion and point mutations and eventual cloning of the Lr34/Yr18 adult plant resistance. Well established knowledge base and genetic resources on the diploid D genome, Ae tauschii are also strategic advantages.

307


The CSIRO group currently has a $1million/year-five year project funded from the Grains Research and Development Corporation. Part of the phase I activity of the Cornell DRRW on non host resistance from rice is based at CSIRO. The group is in the process of finalizing a new $250,000 per year project for four years ($1million) in collaboration with the University of Sydney through the Australian Centre for International Agricultural Research-ACIAR in conjunction with partners from the Indian Council for Agricultural Research (ICAR) on Ug99 rust research. Jim Anderson (Professor, University of Minnesota) has been working in the areas of wheat breeding and genetics for 20 years. He has contributed to the development of 14 released wheat cultivars. His major research effort is the genetic investigations of complexly inherited traits including grain quality and disease resistance. Recent research has focused on Fusarium head blight, leaf and stem rust resistance and incorporating resistance into new cultivars using marker-assisted selection. Recent publications include those describing diagnostic DNA markers for stem rust resistance genes Sr6, Sr9a, and Sr36, the high molecular weight glutenins, a QTL validation strategy, and marker-assisted selection strategies. His close proximity to Drs. Brian Steffenson and Yue Jin facilitates frequent communication and collaboration on project activities. Matthew Rouse, Research Plant Pathologist, is a recent hire at the USDA-ARS Cereal Disease Laboratory in St. Paul, Minnesota. Rouse studies under DRRW collaborator, Yue Jin, and was heavily involved with DRRW Phase I while earning his PhD. He is a skilled pathologist as well as a talented molecular biologist. The USDA recently created a position for Rouse so that he can continue to work for the USDA-ARS at the CDL where he is now running his own laboratory.

Mark Sorrells is a wheat breeder and pioneer of molecular mapping and genetic analysis of complex traits in wheat. His lab has developed or contributed to the development of extensive molecular marker resources over the past 20 years. His program has expertise in QTL mapping, comparative mapping, association analysis and genomic selection methodology.

Jorge Dubcovsky is a world leader in map-based cloning in wheat. His lab has cloned four wheat genes that regulate vernalization and frost tolerance (Yan et al. 2003, 2004, 2006; Knox et al. 2008) and two QTLs for high grain protein content (Uauy et al. 2006) and APR resistance genes for stripe rust resistance (Fu et al. 2009). Dr. Dubcovsky has provided leadership during the last eight years for the implementation of MAS in public wheat breeding programs in the US (IFAFS and CAP programs) and developed the MASwheat site that summarizes and distributes MAS in wheat. This web portal will be used to distribute the information generated by this project. Dr. Dubcovsky’s lab has developed four gene pyramids of seedling and APR resistance genes for stripe rust that will be useful to develop germplasm combining multiple stripe rust and stem rust resistance genes. Dr. Dubcovsky has recently established an active collaboration with the Ethiopian wheat breeding program and initiated MAS backcrossing projects in tetraploid and hexaploid wheat. The postdoc in charge of this activity at Dr. Dubcovsky’s laboratory (Zewdie Abate) was a member of the Ethiopian Wheat National program, which enormously facilitates the communication between these two groups. Dr. Zewdie Abate is interested in continue working in the Phase II of this project. Ian Dundas, Cereal Cytogenetics laboratory at the University of Adelaide, Australia has succeeded in producing many new candidate lines with shortened alien chromosome segments

308


carrying stem rust resistance genes SrR, Sr26, Sr32, Sr37, Sr39, Sr40, SrTt3, Sr2S#1, Sr2S#3, Sr2S#4 and Sr2S#5 from Imperial rye, Thinopyrum ponticum, Triticum speltoides and T. timopheevii. Lines with SrR, Sr26, Sr32, Sr2S#1 and Sr39 genes have already been sent to all major wheat breeding programs around Australia and wheat lines with genes Sr40, SrTt3, Sr2S#3 and Sr2S#4 will soon be available. Dr. Dundas has extensive connections to other Australian programs through the Australian Cereal Rust Control Program, including CSIRO and University of Sydney Plant Breeding Institute.

309


References Cited

Anikster, Y., Manisterski, J., Long, D.L., and Leonard, K.J. 2005. Resistance to leaf rust, stripe rust and stem rust in Aegilops spp. In Israel. Plant Dis. 89: 303-308

Banks, P.M., S.J. Xu, R.R.-C.Wang, and P.J. Larkin. 1993. Varying chromosome composition of 56-chromosome wheat × Thinopyrum intermedium partial amphiploids. Genome 36:207-215.

Bansal U.K., E. Bossolini,, H. Miah., B. Keller., R.F. Park, and H.S. Bariana. 2008a. Genetic mapping of seedling and adult plant stem rust resistance in two European winter wheat cultivars. Euphytica 164: 821-828.

Bansal U.K., D. Singh, H. Miah, R.F. Park, and H.S. Bariana. 2008b. Revisiting old landraces of wheat for stem rust resistance. . In : R. Appels, R. Eastwood, E. Lagudah, P. Langridge, M. Mackay, L. McIntyre, and P. Sharp (Eds.) Proc. 11th International Wheat Genetic Symposium, Sydney University Press, Sydney, Australia.

Bansal U.K., M. Hayden., B. Keller, C.R. Wellings, Park R.F., Bariana H.S. 2009. Genetic relationship between Yr1 with a new stem rust resistance gene Sr48 and the marker stm673acag.. Plant Pathology (accepted).

Bariana HS, G.N. Brown, U.K. Bansal, H. Miah, G.E. Standen, and M. Lu. 2007. Breeding for triple rust resistance wheat cultivars for Australia using conventional and marker assisted selection technologies. Australian Journal of Agricultural Research 58, 576-587.

Bernardo R., Yu J.M. (2007) Prospects for genome-wide selection for quantitative traits in maize. Crop Science 47:1082-1090. DOI: 10.2135/cropsci2006.11.0690.

Bluethner, W.D., V.Schubert, and D.Mettin. 1988. Instability in amphiploids and backcross derivatives of a Triticum aestivum × Aegilops caudata cross. P. 209-213. In: T.E. Miller and R.M.D. Koebner (ed.) Proc. 7th Int. Wheat Genet. Symp. Institute of Plant Science Research, Cambridge, England.

Charpentier, A. 1992. Production of disomic addition lines and partial amphiploids of Thinopyrum junceum on wheat. C.R. Acad. Sci. Paris 315:551-557.

Chu, C.-G., S.S. Xu, T.L. Friesen, and J.D. Faris. 2008. Whole genome mapping in a wheat doubled haploid population using SSRs and TRAPs and the identification of QTL for agronomic traits. Molecular Breeding 22:251–266.

DePauw, R., T. Fetch, J.B. Thomas, R.E. Knox, C.J. Pozniak, A.K. Singh, H. Randhawa, D.G. Humphreys, S.L. Fox, P.D. Brown, F.R. Clarke, and A. Comeau. 2009. Sources of resistance to Ug99 variants in Canadian germplasm. Borlaug Global Rust Initiative Technical Workshop, CIMMYT Ciudad Obregon, March 16-20, 2009.

Dundas IS, Verlin DC, Park RF, Bariana HS et al (2008) Rust resistance in Aegilops speltoides var. ligustica. In: Proc 11th Int Wheat Genet Symp, Brisbane, Australiahttp://ses.library.usyd.edu.au/handle/2123/3372

Faris, J.D., S.S. Xu, X. Cai, T.L. Friesen, and Y. Jin. 2008. Molecular and cytogenetic characterization of a durum wheat - Aegilops speltoides chromosome translocation conferring resistance to stem rust. Chromosome Res. 16:1097-1105.

310


Friebe, B., V. Schubert, W.D. Blüthner, and K. Hammer. 1992. C-banding pattern and polymorphism of Aegilops caudata and chromosomal constitutions of the amphiploid T. aestivum-Ae. caudata and six derived chromosome addition lines. Theor. Appl. Genet. 83:589- 596.

Friebe, B., P. Zhang, S. Nasuda and B.S. Gill. 2003. Characterization of a knock-out mutation at the Gc2 locus in wheat. Chromosoma 111:509-517.

Friebe, B., P. Zhang, G. Linc, and B.S. Gill. 2005. Robertsonian translocations in wheat arise by centric misdivision of univalents at anaphase I and rejoining of broken centromeres during interkinesis of meiosis II. Cytogenet. Genome Res. 109:293-297.

Fu, D.,C. Uauy, A. Distelfeld, A. Blechl, L. Epstein, X. Chen, H. Sela, T. Fahima, and J. Dubcovsky. 2009. A Kinase-START Gene Confers Temperature-Dependent Resistance to Wheat Stripe Rust. Science 323:1357-1360.

Hayes B.J., Bowman P.J., Chamberlain A.J., Goddard M.E. (2009) Genomic selection in dairy cattle: progress and challenges. Journal of Dairy Science 92:433-443. DOI: 10.3168/jds.2008-1646.

Heffner E.L., Sorrells M.E., Jannink J.L. (2009) Genomic selection for crop improvement. Crop Science 49:1-12. DOI: 10.2135/cropsci2008.08.0512.

Kaur, J., U.K. Bansal, R. Khanna, R.G. Saini, and H.S. Bariana. 2009. Molecular mapping of stem rust resistance in HD2009/WL711 recombinant inbred line mapping population. Int. J. Plant Breeding: 3: 28-33.

Klindworth, D.L., J.D. Miller, and S.S. Xu. 2006. Registration of Rusty durum wheat. Crop Sci. 46:1012-1013.

Klindworth, D.L., S.S. Xu. 2008. Development of a set of stem rust susceptible D-genome disomic substitutions based on rusty durum. In: The 11th International Wheat Genetics Symposium Proceedings Edited by R. Appels, R. Eastwood, E. Lagudah, P. Langridge, M. Mackay, L. McIntye, and P. Sharp. Sydney University Press. URI: http://hdl.handle.net/2123/3522. ISBN: 9781920899141

Larkin, P.J., P.M. Banks, E.S. Lagudah, R. Apple, X. Chen, Z.Y. Xin, H.W. Ohm, and R.A. McIntosh. 1995. Disomic Thinopyrum intermedium addition lines in wheat with barley yellow dwarf virus resistance and with rust resistances. Genome 38:385–394.

Liu, S., X. Zhang, M. O. Pumphrey, R.W. Stack, B. S. Gill, and J. A. Anderson. 2006. Complex microcolinearity among wheat, rice and barley revealed by fine mapping of the genomic region harboring a major QTL for resistance to Fusarium head blight in wheat. Funct. Integ. Genomics. 6:83-89.

Liu, S. et al. 2009. Co-dominant markers for Sr25 and Sr26. Crop Science, submitted. McDonald, B. A. and Linde, C. 2002. Pathogen population genetics, evolutionary potential, and

durable resisitance. Ann. Rev. Phytopathol. 40:349-379. McIntosh RA, Wellings CR, Park RF. 1995. Wheat Rusts: An Atlas of Resistance Genes.

Kluwer Academic Publishers, The Netherlands.

311


McIntosh RA, Yamazaki Y, Devos KM, Dubcovsky J, Rogers J, Appels R (2008) Catalogue of gene symbols for wheat. MacGene 2008. http://www.shigen.nig.ac.jp/wheat/komugi/genes/download.jsp.

Meuwissen T.H.E., Hayes B.J., Goddard M.E. (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.

Olivera, P., Kolmer, J. A., Anikster, Y., and Steffenson, B. J. 2007. Resistance of Sharon goatgrass (Aegilops sharonensis) to fungal diseases of wheat. Plant Dis. 91:942-950.

Olson, E. L., G. Brown-Guedira, M. Rouse, E. Stack, Y. Jin, R. Bowden, and M. O. Pumphrey. Development of wheat lines having a small introgressed segment carrying stem rust resistance gene Sr22. Crop Science, in press.

Pumphrey, M.O., R. Bernardo, and J.A. Anderson. 2007. Validating the Fhb1 QTL for Fusarium head blight resistance in near-isogenic wheat lines developed from breeding populations. Crop Science 47:200-206.

Pumphrey, M.O., Y. Jin, M. Rouse, L.L.Qi, B. Friebe, and B.S. Gill. 2008. Resistance to Stem Rust Race TTKS in Wheat Relative Haynaldia villosa. Proceedings of the 11th International Wheat Genetics Symposium, Brisbane, Queensland, AU, R. Appels et al (eds.) Sydney University Press.

Pumphrey, M.O., I.S. Dundas, S.S. Xu, Y. Jin, J.D. Faris, X. Cai, W.X. Liu, L.L. Qi, B. Friebe, B.S. Gill. 2009. Cytogenetic manipulation to enhance the utility of alien resistance genes. Borlaug Global Rust Initiative Technical Workshop, CIMMYT Ciudad Obregon, March 16-20, 2009.

Qi, L., B. Friebe, P. Zhang, and B.S. Gill. 2007. Homoeologous recombination, chromosome engineering and crop improvement. Chrom. Res. 15:3-19.

Roberts, M.A., S.M. Reader, C. Dalgliesh, T.E. Miller, T.N Foote, L.J. Fish, J.W. Snape, and G. Moore. 1999. Induction and characterization of Ph1 wheat mutants. Genetics 153:1909-1918.

Rouse, M., E. Olson, M. Pumphrey, B. Steffenson, and Y. Jin. 2009. Stem rust resistance in Aegilops tauschii germplasm. Borlaug Global Rust Initiative Technical Workshop, CIMMYT Ciudad Obregon, March 16-20, 2009.

Sambasivam P. K., U. K. Bansal, M. J. Hayden, J. Dvorak, E. S. Lagudah, and H. S. Bariana. 2008. Identification of markers linked with stem rust resistance genes Sr33 and Sr45. In : R. Appels, R. Eastwood, E. Lagudah, P. Langridge, M. Mackay, L. McIntyre, and P. Sharp (Eds.) Proc. 11th International Wheat Genetic Symposium, Sydney University Press, Sydney, Australia.

Singh, R. P., Huerta-Espino, J. and William, H. M. 2005. Genetics and breeding for durable resistance to leaf and stripe rusts in wheat. Turk. J. Agric. For. 29:121-127.

Spielmeyer, W. R. P. Singh, H. McFadden, C. R. Wellings, J. Huerta-Espino, X. Kong, R. Appels and E. S. Lagudah. 2008. Fine scale genetic and physical mapping using interstitial deletion mutants of Lr34/Yr18: a disease resistance locus effective against multiple pathogens in wheat. Theor Appl Genet, 116: 481-490.

312


Tang, S.X., Z.S. Li, X. Jia, and P.J. Larkin. 2000. Genomic in situ hybridization (GISH) analyses of Thinopyrum intermedium, its partial amphiploid Zhong5 and disease-resistant derivatives in wheat. Theor. Appl. Genet. 100:344–352.

Toor, A.K., U.K. Bansal, and H.S. Bariana. 2009. Identification of new sources of adult plant stem rust resistance in tetraploid wheats. Proc. of the 14th Australasian Plant Breeding and 11th SABRAO Conference, Cairn, Australia (accepted).

Uauy, C. A. Distelfeld, T. Fahima, A. Blechl, J. Dubcovsky. 2006. A NAC Gene Regulating Senescence Improves Grain Protein, Zinc, and Iron Content in Wheat. Science 314:1298-1301.

Watson I.A., D. Singh. 1952. The future for rust resistant wheat in Australia. J. Aust. Inst. of Agri. Sci. 18. 190-197

Wu, S., M.O. Pumphrey, and G.H. Bai. 2009. Molecular mapping of stem rust resistance gene Sr40 in wheat. Crop Science, in press.

Xu, S.S., Y. Jin, D.L. Klindworth, R.R.-C. Wang, and X. Cai. 2009. Evaluation and characterization of seedling resistance to stem rust Ug99 races in wheat-alien species derivatives. Crop Sci. (in press).

Yu, L. X., Z. Abate, J. A. Anderson, U. K. Bansal, H. S. Bariana, S. Bhavani, J. Dubcovsky, E. S. Lagudah, S. Liu, P. K. Sambasivam, R. P. Singh, M. E. Sorrells. Developing and Optimizing Markers for Stem Rust Resistance in Wheat. Borlaug Global Rust Initiative Technical Workshop, CIMMYT Ciudad Obregon, March 16-20, 2009.

Zhang, J.Y., X.M. Li, R.R.-C. Wang, A. Cortes, V. Rosas, and A. Mujeeb-Kazi. 2002. Molecular cytogenetic characterization of Eb-genome chromosomes in Thinopyrum bessarabicum disomic addition lines of bread wheat. Int. J. Plant Sci. 163:167-174

Zhang, X.Y., A. Koul, R. Petroski, T. Ouellet, G. Fedak, Y.S. Dong, and R.R.-C. Wang. 1996. Molecular verification and characterization of BYDV-resistant germ plasms derived from hybrids of wheat with Thinopyrum ponticum and Th. intermedium. Theor. Appl. Genet. 93:1033-1039.

Zhong S.Q., Dekkers J.C.M., Fernando R.L., Jannink J.L. (2009) Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics 182:355-364. DOI: 10.1534/genetics.108.098277.

313

Appendix C: Detailed Description of Proposed Work / Durable Rust Resistance in Wheat Phase II Objective 27: Optimized wheat improvement system in Ethiopia

Summary Information (Objective Level)

Objective Name: Objective 27: Optimized wheat improvement system in Ethiopia.

Team Leader for this Objective: Bedada Girma

E-mail [email protected]

Collaborating Institutions with budgeted activities (add more rows if necessary):

Institution Name (Scientist) email


Dr. Bedada Girma Buta [email protected]

International Center for Maize and Wheat Improvement (CIMMYT), Mexico

Hans Braun [email protected]



60

314



In Ethiopia, wheat is the second most important cereal crop, accounting for 19% of the total annually planted hectares (10.7 million hectares), and 25% of the gross annual grain production of some 19.9 million tons. Wheat stands second in productivity (2.41 tons per hectare, FAO Special Report, 2008) to maize (2.44 tons per hectare). Bread wheat (Triticum aestivum L.) and durum wheat (Triticum durum) are the two species predominantly grown, and serve as a source of food and income, as well as raw materials for Ethiopian agro-industries. Ethiopia is also considered as a center of diversity for tetraploid wheat species, two of which are currently grown by farmers (Triticum durum Desf. and Triticum dicoccon Schrank). For most of the country, wheat production comes from resource-poor small-scale farmers, while emerging large-scale farmers and state commercial farms occupy only two percent of the total wheat area and contribute three percent to the total wheat production.

Major constraints to production include low inherent yield potential of varieties under widespread cultivation, prevalence of diseases (leaf rust, yellow rust, stem rust, Septoria), poor agronomic and cultural practices, poor soil fertility, moisture stress (low and high), frost, and other biotic and abiotic stresses.

Given the importance of the wheat crop to the food security and economy of Ethiopia, and in particular to small-scale farmers, and given the additional threat imposed by Ug99, it is important to continue the development of the research infrastructure currently in place and evolving before and during Phase I of the DRRW project. Ethiopia has established ten wheat-based research centers in different agro-ecological zones, and has established collaborations with a number of international and national research institutes. The result of a continued investment will be a contribution to the continuing growth and maturity of Ethiopia’s wheat research programs, and result in an increasing contribution to the alleviation of poverty in Ethiopia and sub-Saharan Africa, and to global wheat development and food security.

Summary of Short, Medium, and Long-Term Outcomes Five Years

• Breeding programs, in concert with pathology and agro-industry participants, have breeding objectives prioritized, and research equipment prioritized, purchased, and placed into service. Preventative maintenance and repair is routine.

• On- and off-site trials are mechanically planted, harvested and data analyzed and available to enable selection prior to sowing of the crop in the following cycle.

• Breeding programs have routinely employed two cycles of evaluation per year.

• Spring bread wheat varieties with stem rust resistance and improved yield performance are evaluated at all wheat-based research centers, with seed increases of promising lines being initiated.

• Durum wheat varieties with stem rust resistance and improved yield and agro-industrial performance are evaluated, with seed increases of promising lines initiated.

315


Ten Years

• Improved varieties are routinely developed using advanced marker technologies in durum and bread wheat breeding programs.

• EIAR developed varieties are competitive with introduced varieties, have resistance to yellow and stem rust, and a 5% performance advantage vs. commercial checks.

• Professional staff are routinely contributing to global wheat development through interactions with ARIs, journal publications, released varieties and shared breeding germplasm.

Fifteen Years • Food security and economic livelihoods in Ethiopia are improved as a result of robust

breeding programs delivering agronomically improved and durably resistant cultivars.

Progress to Date

• The acquisition of vehicles and securing of quotations for proposed work projects (irrigation, greenhouse construction, lab equipment) has been problematic. Eight vehicles purchased many months ago have only recently been placed into service. After a lengthy search, contractors have been identified, submitted proposals, and initiated greenhouse construction. An ad hoc technical committee has been set up to look for additional quotes and competitive contractors for investments in seed systems. Initial irrigation projects at Debre-Zeit and Kulumsa have been completed, though more remains to be done.

• Communication can be difficult. Although internet connections have improved significantly, they are still unreliable, often due to electrical power outages or periodic government use of all available bandwidth.

• Three scientists have attended training in rust pathology in South Africa with Dr. Zak Pretorius. Additional training is scheduled in Australia with Dr. Robert Park.

• New candidate varieties from CIMMYT and ICARDA with resistance to Ug99 are in replicated performance trials at multiple locations, and under initial seed increases. Discriminating performance data and significant seed quantities will be available for selection toward continued evaluation, another larger pre-release seed multiplication, and progress toward varietal release.


Optimization of the national wheat improvement program for Ethiopia will involve the integration of resources and ideas from all stakeholders with vested interests in the outcomes of this investment. It will be an ongoing and constantly evolving progression that carefully evaluates solutions to problems and then efficiently utilizes and allocates all human and capital investments as judiciously as possible toward the solution(s).

Breeding targets will be confirmed and agro-ecologies appropriately identified. Human resources will be allocated to various responsibilities and provided with training. Aggressive screening of introduced and extant germplasm will inform the crossing programs in both bread wheat and durum wheat breeding programs. Development and utilization of two cycle

316


observation and selection nurseries will enable accelerated genetic progress. Investments in equipment, irrigation capacity, greenhouses and laboratories will also enable the development of breeding programs that deliver durably resistant wheat varieties with improved agronomic and end-use quality performance characteristics.

Justification for Proposed Work Clearly the best control strategy for the rust diseases of wheat for resource-poor farmers is the development of genetic resistance, which will contribute to a world where the food and livelihood security of the world’s poor is enhanced through cultivation of wheat varieties with durable resistance to the cereal rusts. Ninety-seven percent of the wheat produced in Ethiopia comes from small-scale, resource-poor farmers. It is this production that mainly contributes to the domestic agro-industry and to Ethiopia’s ability to feed its people, and thus investments in this project will deliver improved varieties that help keep the price of wheat and other staple crops affordable. Developing wheat breeding programs with dedicated scientists who have access to adequate resources will enable the development and delivery of new technological innovations as programs and technology evolve.

Investments in Ethiopia in other Phase II objectives include phenotyping work in the field and in the greenhouse as supported at Debre-Zeit by Objective 24: World class stem rust response phenotyping facilities in East Africa (Activities 24.b.1 and b.2). National surveillance of the stem rust population is also included in Activities 24.b.5 and b.6. A seed health unit is also included in Activity 24.b.7, and in-service training opportunities provided in Activity 24.b.8. Additional investments in capacity are included in Activity 24.b.9.

Activities in Objective 25: Durably resistant, high yielding wheat varieties include durum wheat breeding at Debre-Zeit (Activity 25.b.1) and bread wheat breeding and capacity improvements at EIAR’s Kulumsa research station (Activity 25.b.2).

II. Logframe Table

See next page.

317


Objective 27: Optimized wheat improvement system in Ethiopia.



27.a Optimized wheat improve-ment system in Ethiopia (all)

27.a.1 Coordinate DRRW wheat breeding activities in Ethiopia for an integrated wheat improvement program.

An integrated and evolving national wheat improvement program (breeding, plant protection, extension) that serves Ethiopia, Africa, and the world. (Jan 2011, recurring annually)

Collaboration within the National program and between the National program and International programs, Regional programs, and NGOs is coordinated. • CIMMYT • ICARDA • DRRW (Cornell) • AGRA • ARIs • GCP • USDA • Sasakawa Global 2000 • Other NARS

(Apr 2011, recurring annually)

Agro-ecologies and farming systems identified and confirmed as breeding targets. (Apr 2011)

Wheat-based research centers (RARIs) engaged in evaluation and selection. (Apr 2011)

Staffing positions identified and filled, with responsibilities outlined. (May 2011).

Maintenance and repairs to equipment, purchase of budgeted equipment, with equipment being placed into service. (Mar 2011, recurring annually)

Five Years Nucleus of a cohesive national wheat improvement program is established and functioning as a team.

Ten Years Targeted agro-environments with specific adaptation have improved and durably resistant varieties.

Fifteen Years Ethiopian wheat program is contributing to food security in Ethiopia and in SSA. Scientists are contributing to technology achievements and advancements in wheat pathology, breeding and crop management.

Bedada G., EIAR

318




Breeding and replicated testing programs tailored to match resources and budgeted priorities. (May 2011)

Progress and direction of programs Monitored/Evaluated. (Apr and Sep 2011, recurring annually)

27.a.2. Bread wheat breeding.

Two cycles per year Kulumsa-based spring bread wheat breeding program is operating. Program outlined • Holeta (Septoria hot-spot) • Bekoji/Meraro (Yellow rust) • KARI-Njoro (shuttle SR screening) • KU/DZ/Arsi Robe (stem rust)

(Apr 2011)

Agronomic, pathologic and end-use quality objectives prioritized and listed.

• Seed color • Volume weight • Industrial baking quality • Other

(Apr 2011)

10,000 introductions from international nurseries evaluated and promising lines selected for entry into Observation Nurseries at designated sub-centers. (Jun and Dec 2011, recurring annually)


Five Years Varieties released from introduced germplasm and/or the National program are resistant to TTKS and other stem rust variants, to stripe rust, and to Septoria; all wheat based research centers evaluating candidate varieties.

Ten Years Durably resistant lines identified that contribute to NARS and CG center breeding programs. Durably resistant varieties from EIAR program compete with CG varieties, and occupy 20% of the bread wheat area.

Fifteen Years EIAR wheat varieties with specific adaptation to Ethiopian environments occupy 75% of the bread wheat area, are durably resistant, and have superior yield potential.

Bedada G., EIAR

319





Five sets of 200 promising lines evaluated in observation nurseries at two to three locations. (Jun 2011, recurring annually)

Five sets of 20 high yielding, rust resistant entries evaluated annually in replicated trials (NVT) at 4-6 locations for two years. (Jun 2011, recurring annually).

Four sets of variety release verification trials (VVT) with at least one candidate variety planted on-station and on-farm trials. (Jun 2011, recurring annually)

An array of key breeding lines genotyped at CG centers. (Mar 2011, recurring annually).


27.a.3. Durum wheat breeding.

Two cycles per year Debre-Zeit based durum wheat breeding program is operating. Program outlined. (Apr 2011)

Agronomic, pathologic and end-use quality objectives prioritized and listed. (Apr 2011)

International durum wheat nurseries evaluated and promising introductions identified. (Jun and Dec 2011, recurring annually)

Parent lines used in hybridization identified and

Five Years Varieties released from introduced germplasm are resistant to TTKS and other stem rust variants, to leaf rust, and to Septoria; all wheat based research centers evaluating candidate varieties.

Ten Years Durably resistant lines identified that contribute to NARS and CG center

Bedada G., EIAR

320




150 crosses outlined. (Aug and Jan 2011, recurring annually)


Two sets of 200 promising lines evaluated in observation nurseries at 2-3 locations. (Jun 2011, recurring annually)

Two sets of 20 high yielding, rust resistant entries evaluated annually in replicated trials (NVT) at 4-6 locations for two years. (Jun 2011, recurring annually).

Two sets of variety release verification trials (VVT) with at least one candidate variety planted on-station and on-farm trials. (Jun 2011, recurring annually).


breeding programs. Durably resistant varieties from EIAR program compete with CG varieties, and occupy 20% of the durum wheat area.

Fifteen Years EIAR wheat varieties with specific adaptation to Ethiopian environments occupy 75% of the durum wheat area, are durably resistant, and have superior yield and quality potential.

27.a.4 Develop the human resource capacity for wheat research in Ethiopia:

Skills of the EIAR technical staff and assistants are enhanced with short-term training opportunities. (Sep 2011, recurring annually)

Training opportunities for EIAR scientists, such as biotechnology, data management and interaction with ARI counterparts result in progressive breeding programs. (Apr 2011) • Exchange visits with ARIs and sister

institutions. • Long-term training at ARIs (Apr 2011)

Five Years EIAR wheat staff has technical skills, which enable efficient evaluation of introduced germplasm in screening nurseries that fit national agro-ecologies. New and renovated equipment contributes to program efficiencies.

Ten Years Breeding program matures and staff manages genetic diversity and

Bedada G., EIAR

321




Enhanced skills and training in preventative maintenance and repairs to research equipment. • Small engine repair and maintenance. • Preventative maintenance of field and lab

equipment. (Apr 2011)

breeding technologies, driving genetic gains in host resistance and yield performance.

Fifteen Years EIAR wheat research staffs become leaders in SSA and contribute to wheat research and development, and to global food security.

27.a.5 Acquire necessary equipment to modernize and improve efficiencies of EIAR bread wheat and durum wheat improvement programs.

Necessary equipment has been acquired. (Nov 2011)

Irrigation capacity is maximized to meet program requirements. (Nov 2012)

Lab, greenhouse, cold room, and seed health facilities improved or constructed. (Nov 2012)

Essential field equipment has been acquired and / or received necessary repairs to achieve functional use. (Apr 2011)

Five Years Improved efficiencies for all program activities.

Ten Years Progress realized in breeding for resistance to stem and other rust pathogens. Pathology and breeding programs maturing and contributing to EIAR goals of generating and delivering improved technologies, resulting in contributions to food security in Ethiopia.

Fifteen years Durably resistant and increasingly productive varieties result in a viable domestic wheat industry. Contributions also lead to increased food security in SSA in general and particularly for resource-poor farmers and consumers in Ethiopia.

Bedada G., EIAR

322


III. Detailed Work Plan.

Ethiopia is at once home to a large number of wheat-dependent farmers and consumers, and one of the few countries already colonized by Ug99. It is also the likely jumping off point for migration of Ug99 either to west-central Asia, or South Asia. For these reasons, Cornell has embraced the notion that an Ethiopia-specific Objective aimed at supporting Ethiopia per se, is logical for both local (Ethiopia’s population) and global reasons. Overall coordination of EIAR DRRW activities is also supported.

Activity 27.a.1. Manage all the wheat breeding activities in Ethiopia for a coordinated wheat improvement program. The EIAR wheat breeding programs for bread wheat and durum wheat will be coordinated with contributions from plant pathology, agro-industrial stakeholders, seed production stakeholders, and collaborations with many international and regional programs. Wheat-based research centers in Ethiopia will contribute to the evaluation and selection of varieties to be considered as candidates for commercial release. Staffing positions will be identified and responsibilities outlined in contribution to an efficient program that delivers genetic progress on yield performance and protection against endemic pathogens. Progress will be evaluated twice annually.

Activities 27.a.2 and 27.a.3. Bread wheat breeding and Durum wheat breeding.

Both bread wheat and durum wheat breeding programs will evolve a two cycle per year evaluation and selection program. Agronomic, pathologic and end-use objectives will be prioritized, and introductions from international nurseries will be evaluated and selected with these priorities in mind. Various sets of germplasm at different stages of development will be distributed for evaluation at a number of wheat research centers, with this information contributing to decisions leading to promotion of breeding lines and variety release. An array of key breeding lines will be genotyped, and along with phenotypic data collected from the research centers, will inform the crossing programs.

Activity 27.a. Develop the human resource capacity for wheat research in Ethiopia. Research skills of technical staff and assistants will be enhanced with training opportunities in applied field research, including nursery management, data collection, and data entry and compilation. EIAR scientists will have training opportunities through exchange visits with ARIs and sister institutions, as well as longer-term training through visits to ARIs. A needed skill base in routine preventative maintenance and minor equipment/engine repair will ensure that equipment and capital investments are secured and contributing to program efficiencies.

Activity 27.a.5. Acquire necessary equipment to modernize and improve efficiencies of EIAR bread wheat and durum wheat improvement programs. Equipment investments, including continued investments in irrigation capacities that enable two cycle/year breeding programs, will maximize genetic progress. Needed renovations and equipment for laboratories, greenhouses, seed cold storage facilities that were begun in Phase I will need additional investment in the following Phase II. These investments will contribute to efficient breeding programs and allow the necessary delivery of genetic progress that will contribute to improved varieties, resulting in greater food security for Ethiopia.

323


IV. Management Plan Name (or position if to be hired)

Institution Email Relevant Activities and outputs (ID and Name)

Dr. Bedada Girma EIAR [email protected] Coordination

Admin. Assistant EIAR TBD Support staff

V. Potential Risks and Unintended Consequences.

• Success of this Objective relies heavily on the interest and support of EIAR and its scientists to embrace and lead the development of an improved comprehensive and progressive breeding program.

• Without investments in understanding end-use quality, there is a risk that developed varieties may not be adopted by farmers/consumers.

• Effects of weather related problems in managing trials and collecting meaningful data cannot be avoided, but can be mitigated by attention to agronomic principles, by planting of additional nurseries, and with investments in appropriate field and lab equipment.

• Multi-lateral links with Extension agronomists and the delivery of information that results in impact of improved varieties in the many small-holder farmers’ fields may limit adoption of improved cultivars.

• Current strong national and international institutional support will be necessary to establish and sustain progress toward development of a comprehensive and robust program.

VI. Evidenced based rationale for choice of partners (including current and potential funds).

The Ethiopian Institute of Agricultural Research (EIAR) is the government research organization with a history of investments and capacity in agricultural research. There is considerable public support for research and development with over 10 wheat-based research centers established to address production constraints in different agro-ecological zones. There is also considerable collaboration with a number of regional and international NGOs, ARIs, and various development supporting organizations such as the World Bank, FAO, USAID, Sasakawa Global 2000, and others. Drs. Bedada Girma, Getaneh Woledab, Ayele Badebo, Firdissa Eticha and Mr. Solomon Gelalcha have excellent knowledge of the breeding and pathology efforts and resources available in Ethiopia. They also have extensive experience gained from their engagement in Phase I of the DRRW project.

324


References Cited

FAO Special Report, 2008.

Tesemma, T. and G. Belay. 1991. Aspects of Ethiopian tetraploid wheat with emphasis on durum wheat breeding and genetics. In Gebre-Mariam, H., D.G Tanner and M. Hulluka (ed.) Wheat Research in Ethiopia: A Historical Perspective. IAR/CIMMYT, Addis Ababa, Ethiopia.

325

Appendix C: Detailed Descriptions of Proposed Work / Durable Rust Resistance in Wheat Phase II Objective 28: Project management, communication, and coordination

Summary Information (Objective Level) Objective Name: Objective 28: Project management, communication, and coordination

Objective Team Leader:

First name Ronnie Surname Coffman

Title Director, International Programs Telephone 607 255 3035 Fax 607 255-6683 Mobile 607 327 1824

Address

CALS 252 Emerson Hall Cornell University Ithaca NY 14853


Institution Primary Contact Email Cornell University Ronnie Coffman [email protected]

Amount Requested ($USD): Project Duration

(months): 60

326



Phase II of the Durable Rust Resistance in Wheat Project will be administered by the DRRW Project Management Unit (PMU) of the Office of International Programs in the College of Agriculture and Life Sciences (IP/CALS) at Cornell University in Ithaca, New York. IP/CALS has extensive experience with donor-funded projects and has its own Project Management Office. IP/CALS's long and successful donor-funded project experience will ensure timely satisfaction of all BMGF reporting requirements.

Efficient, transparent project management mechanisms specific to the DRRW project are essential to achieving the goals of the DRRW project. The DRRW project has dedicated staff for this purpose, and it also draws on the institutional and human resources of IP/CALS and the Cornell community in the design and implementation of its project management mechanisms.

Summary of Short, Medium, and Long Term Outcomes Five Years

• The DRRW Project has been successfully implemented and administered. • Project goals have been successfully communicated to target audiences.

• Web resources have been developed to serve the wheat rust community and help ensure its sustainability.

• The Global Access Strategy has been developed and implementation is underway to assure that all DRRW innovations will be delivered to the target users.

Ten Years • The wheat rust community has grown and benefitted from the knowledge produced

and models for information sharing developed by the DRRW project. • The livelihoods of millions of wheat farmers and poor consumers worldwide have

been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat varieties.

• Gender equity has been improved as a result of the DRRW project efforts and opportunities to enhance gender parity are continually fostered.

Fifteen Years • The wheat rust community has grown and benefitted from the knowledge produced

and models for information sharing developed by the DRRW project. • The livelihoods of millions of wheat farmers and poor consumers worldwide have

been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat varieties.

Progress to Date In April 2008 Phase I of the project was launched with a wave of favorable publicity and commitments by many key players. Fifteen subcontracts were negotiated and the follow-on task orders issued for Year 1 within the first six months. Staff positions were announced and candidates interviewed and hired to constitute the Project Management Unit. Following

327


submission of a satisfactory annual report and the receipt of Year 2 funding, the second annual set of task orders was issued within two months with revised milestones as determined by Year 1 progress. Regular communication with the BMGF program officer has been maintained, and regular interaction among DRRW management, team leaders and key stakeholders remains an ongoing activity. An External Project Advisory Committee (EPAC) was formed in close consultation with BMGF, and their advice has been well received. Information technology support and equipment were provided as necessary to allow reliable communication with East African collaborators. Communications activities were effectively implemented through all relevant media, including brochures, posters and an effective web presence. The Global Access Strategy as well as gender and diversity issues are addressed in Phase II with particular attention.

Narrative of Proposed Work Description of Proposed Activities and Personnel

Activities will be similar to Phase 1 with refinements based on lessons learned. Cornell staff (all Ithaca-based) collectively will constitute the Project Management Unit (PMU), and will be responsible for Objectives 22 and 28. The PMU will be responsible to BMGF on all Project management issues. Working through IP/CALS, the PMU will also liaise with the Office of Sponsored Programs Services at Cornell University, which will be responsible to BMGF for all financial reporting.

This Objective has four components: project management, communications, global access and impacts, and gender. Activities and key outputs of these components are described in detail in the work plan section of this narrative. Activities under the project management component include the financial, administrative, and legal services necessary to administer the DRRW project, as well as the financial and technical reporting to the BMGF, communication between the PMU and the scientific Objective Team leaders, and interaction with the External Program Advisory Committee (EPAC). Activities under the communications component include the development of outreach materials to inform of events and progress of the DRRW project, and the development of web resources to support learning, communication and collaboration within the DRRW project and in the larger wheat rust community. Activities under the global access and impact component include the development and management of the DRRW project’s Global Access Strategy and an annual review of “project level workflows,” to ensure that innovations and information produced by the DRRW scientific objectives is being passed on within the DRRW project sufficiently and efficiently. Because gender equity needs to be considered at both the professional level as well as the moral level, we propose a range of activities embedded in the scientific objectives so that gender equity is addressed at both levels. In Objective 28, we will manage and monitor project-wide gender activities (22.a.2; 25.c.1; 25.c.2; 25.d.1) as well as be vigilant of additional opportunities to enhance gender with contingency funds. In addition, we have engaged a gender expert as a member of the EPAC in Phase II. The Director of IP/CALS, Dr. Ronnie Coffman, will serve as the Principal Investigator (PI) and Director for the project and supervise the coordinating staff. All positions are described below. PMU staff contributes to both Objective 22 (Advocacy) and to Objective 28 (Project

328


Management) as evidenced in the budget. The PMU is organized as “Action Teams” to achieve the Outputs as outlined in the logframe (see Appendix A). The Action Team concept and construction is discussed in Section IV of this narrative. Briefly, responsibilities of PMU staff will include:

• Director (Ronnie Coffman, 0.44 FTE). Will serve as the Principal Investigator (PI) of the project (an internal requirement of Cornell) responsible for all major contractual, financial and personnel decisions, and the management of all institutional relationships associated with project activities. Leads the Advocacy and Coordination efforts (Objective 22).

• Associate Director (Sarah Davidson, 0.75 FTE). Will facilitate selected project activities with particular emphasis on Objectives 23 and 26. Responsible for programmatic coordination of the Project, including liaising with the Objective Team Leaders described below, leadership of annual reporting to BMGF, and supporting Advocacy and Coordination efforts (Objective 22).

• Associate Director (Gordon Cisar, 0.75 FTE). Will facilitate selected project activities with particular emphasis on Objectives 21, 24, 25, and 27. Serves as a liaison on BGRI seed panel, and works extensively with East Africans to implement all East Africa based initiatives and capacity building.

• Sr. Project Finance Specialist (Tammy Thomas, 0.5 FTE). Responsible for financial management and budgeting, task order and invoice management, and liaison with subcontractor counterparts.

• Project Finance Specialist (Angela Smith, 0.5 FTE). Responsible for financial processing and budgeting and task order invoice processing..

• Assistant Director (TBD 0.50 FTE). Primary contact for communications and project networking, supports development and oversight of web-based digital information system, responsible for coordinating/facilitating meetings and other events, and supports advocacy and project coordination.

• Sr. IT Specialist (Stefan Einarson, 0.5 FTE). Responsible for information technology infrastructure development and maintenance in East Africa and oversight of all aspects of website and Digital Information Systems including software, programming and hardware.

• Website Administrator (John Bakum, 0.50 FTE). Point person for constructing and maintaining the software aspects of the Advocacy Resource and point person for the Web Presence and Virtual Communities action teams, including content updates to our websites.

• IT Specialist (D.H. Goodall, 0.25 FTE). Responsible for aspects of website and digital information systems including software, programming and hardware.

• Communications Specialist (Cally Arthur, 0.35 FTE). Responsible for facilitating quality control, content, and production of all project reports and outreach products into digital and other media.

• Administrative Assistant (Denise Percey, 0.5 FTE). Administrative support of the PMU, facilitation of travel for PMU staff, and support of convenings funded through Objectives 22 and 28.

329


• Administrative Assistant (Nicole Peppin, 0.50 FTE). Administrative support of the PMU, serving as a member on 12 of 14 action teams. Duties include recording notes at action team meetings, facilitation of travel, and support of convenings funded through Objectives 22 and 28.

In addition to the Project Staff listed above, the Project will draw upon the skills and experience of Cornell University’s Faculty and Staff. For instance, Dr. Mark Sorrells, wheat breeder and Chair, Department of Plant Breeding and Genetics, a recognized global leader on molecular markers (and collaborating scientist in Objective 26), will advise on a broad spectrum of issues relating to plant breeding and genetics. Another important asset available to the PMU is the Transnational Learning initiative (http://www.ctl1.com/) based in IP/CALS. This unit has extensive expertise in state-of-the-art technologies and strategies requisite to successful coordination of multi-institutional, transnational partnerships. In addition to digital conferencing and communications, that program advises on innovative, situation-specific strategies to establish and keep lines of communications open in the varied circumstances that our collaborators encounter in the developing world. For instance, in Phase I, this unit facilitated improved Internet access for wheat research stations in Ethiopia and Kenya.

Overall scientific coordination of the Project is the responsibility of the Project Directors, and will be effected through extensive on-site hands-on consultations and communications by PMU staff with scientists and administrators at each of the subcontracting partners, and with target NARS. The Assistant Director will play a strong contributing role to Coordination via her role in establishing and maintaining people and information networks. PMU staff will employ cutting-edge virtual conferencing capacities (facilitated and accessible via the Project website) to maintain close engagement with scientists and administrators at partner institutions. PMU staff will also employ the conferencing and other communications tools of the Project website to foster growth of strong communities of interest (including the teams working on each Objective), and to promote and enable communications within and among such communities. Scientific coordination and expanded partnerships beyond the current scope of the Project will be facilitated by the Project’s role as Secretariat to the Borlaug Global Rust Initiative.

Leadership within the Project Objectives will be provided by Team Leaders identified by the PMU. Team Leaders will foster coordination among scientists funded through their Objective, and also act as point persons in liaison with the Directors and outside partners. The PMU staff will endeavor to foster communications and a collegial relationship among the Objective Team Leaders as well as other scientists and staff engaged in the project. Respectful relations with NARS partners, funded and otherwise, are of extreme importance to the Project leadership. We have a respected and highly effective resource in the permanent and rotating members of the BGRI Executive Committee. One of our responsibilities is to use this resource to achieve effective coordination of activities and to secure additional investments. Relations with other partner Institutions will be governed by subcontracts. General subcontract language will be developed by the PMU in consultation with the BMGF Program Officer. Subcontracts will be negotiated between Cornell and its partner institutions in compliance with the grant agreement. Accounts will be established at Cornell for each Objective at each institution in order to ensure the equitable funding of multiple Objectives according to approved allocations. Annual task orders (one per Objective for each participating partner institution) will

330


specify deliverables (based on milestones/outputs) and budgets. Task orders will form the basis for programmatic coordination and oversight. Quarterly reconciliation of cooperating partner account invoices will be required. Timeliness of invoicing and performance against task orders will be part of Cornell’s performance evaluation for each partner institution. Protocols for requests to alter milestones or budget alignment will be established. In addition to annual reporting, performance will be monitored on a continuing basis by the Directors. Failure to perform to task orders requirements (e.g., not meet a milestone specified in the task order or not conform to budget) may, at the discretion of project management, preclude or modify invoicing against the task order, subject to negotiation between project management and the institutional PI (designated in the sub-contract). Disputes will be resolved by the PMU leadership, while being as consultative as possible with the concerned party. We will also remain in close contact with the BMGF Program Officer through monthly conference calls and joint site visits.

The PMU, in cooperation with BMGF and our partnering institutions, will continue with the development and implementation of the Global Access Strategy initiated in Phase I, ensuring that the outputs from this project are made effectively and widely available to farmers and consumers in developing countries. Prior to signing of subcontracts with partnering institutions, we will agree on global access with each partnering institution. The language of the subcontracts will define, and provide a basis for enforcement of, global access. The PMU will also exercise particular sensitivity to gender issues. The Advocacy activities of Objective 22 will be led by the Project Director, in coordination with the Associate Directors. They will determine the employment of funds, and drive the Advocacy agenda.

External guidance will be provided to the PMU through an External Project Advisory Committee (EPAC). Members are expected to carry forward from Phase I with the addition of a gender specialist, and, in any case, will be mutually acceptable to BMGF and Cornell and will serve for the duration of the project. The EPAC will convene at least annually and will serve in an advisory capacity to BMGF and Cornell. The EPAC will convene in connection with the Annual Project Meeting involving all participating scientists.

Justification for Proposed Work Efficient, transparent project management is key to the success of the DRRW project. The Activities proposed by the PMU will ensure efficient, transparent project management, as well as set the stage for a sustainable community of wheat rust researchers with the capacity and wherewithal to collaborate and innovate together well into the future.

II. Logframe Table

See next page.

331


Objective 28: Project management, communication, and coordination



28.a. Project management.

28.a.1. Financial/ contractual manage-ment.

Subcontracts executed, task orders issued, invoices paid, and ad hoc financial issues addressed. (Feb 2011, recurring annually)





Cornell

28.a.2.

Reporting to BMGF.

Reports from subcontractors submitted; compiled report from Cornell successfully submitted. (Sep and Oct 2011, recurring annually)

Regular communications with BMGF to give program officer good sense of day-to-day progress, challenges, and opportunities. (Dec 2010, recurring annually)


Ten Years The livelihoods of millions of wheat farmers and poor consumers worldwide have been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat

Cornell

332




varieties.


28.a.3.

Program-matic manage-ment.

Milestone monitoring system developed and maintained. (Sep 2009, recurring annually)

Project-wide metrics for impact monitored. (ongoing with annual update delivered to BMGF following September reporting period each year)

Collaborating scientists/institutions visited periodically by DRRW Management. (Feb 2011, recurring annually)

Regular interaction between DRRW Management and Team Leaders and key stakeholders is ongoing. (Feb 2011, recurring annually)

Annual DRRW project meeting held (may be in conjunction with BGRI annual meeting, or may be a separate affair) (Jun 2011, recurring annually)

Ad hoc objective-specific workshops supported. (Jun 2011, recurring annually)





Cornell

333




28.a.4. External Program Advisory Committee (EPAC).

EPAC provides regular input to DRRW and BMGF on project progress and travels as necessary to review DRRW progress. (Jun 2011, recurring annually)




Cornell

28.a.5.

Internal IT. Equipment and IT support provided to assist project administration and internal management and communication. (Jan 2011, recurring annually)

Five years DRRW Project has been successfully implemented and administered.

Ten years The livelihoods of millions of wheat farmers and poor consumers worldwide have been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat varieties.

Cornell

334





28.a.6.

Supplies. Internal administrative and project management supplies acquired and services rendered. (Jan 2011, recurring annually)



Fifteen years The livelihoods of millions of wheat farmers and poor consumers worldwide have been secured and enhanced due to the development and widespread distribution of new, high-yielding rust resistant wheat varieties.

Cornell

335




28.b. Communi-cations.

28.b.1. Perform communi-cations activities supporting project coordina-tion/man-agement.

Brochures, Power Point presentations, and posters to describe DRRW project developed and distributed to key audiences. (Feb 2011, recurring annually and ongoing)

Information about project progress regularly shared with DRRW collaborating scientists. (quarterly updates, as described in Objective 22) (Mar, Jun, Sep, Dec 2011, recurring annually)





Cornell

28.b.2.

Maintain comprehen-sive ‘wheat rust’ web presence.

Wheat Rust Knowledge Bank contains scientific information related to the wheat rusts requested by and provided by the rust community, and is a sustainable, well-trafficked online resource for scientists, policymakers, donors, and the public. (Jan 2011, recurring annually)

Virtual Communities for scientific discussion established and maintained. (Jan 2011, recurring annually)

DRRW project website developed and



Web resources have been developed to serve the wheat rust community and help ensure its sustainability.

Cornell

336




maintained with frequently updated information relevant to scientists, policy-makers, donors, the media, and the public. (Jan 2011, recurring annually)





337




28.c. Global access and impact.

28.c.1. Manage global access.

Annual update developed on DRRW innovations. (Nov 2011, recurring annually)


Global Access Strategy has been fully implemented and all DRRW innovations are delivered to the target users.





Cornell

338




28.d. Gender Opportunity Enhancement

28.d.1. Foster activities that enhance gender parity in wheat breeding and training.

Objective-specific gender activities implemented. (Jun 2012)

Gender and diversity issues in DRRW project regularly monitored. (Oct 2011, recurring annually)

Opportunities to enhance gender parity are realized and enhanced through contingency gender funds. (Jun 2011, recurring annually)


Gender equity has been improved as a result of the DRRW project efforts in this arena.





Cornell

339




28.e. Special Initiatives

28.e.1. Stem Rust Isolate Sequencing Initiative


SSR markers are shared between special initiative partners (Dec 2011)

Puccinia graminis (Pgt) isolates fingerprints are resolved and data are shared (Dec 2012 and ongoing)

Puccinia graminis (Pgt) isolates genomic sequences are resolved and data are shared (Jan 2015 )

Five Years Stem Rust Isolate Sequencing Initiative has been planned and initiated

BGRI community is sharing Pgt genomic resources and data

BGRI community-generated Pgt genetic data are archived and publicly available

Ten Years BGRI community-generated Pgt genetic data are archived and publicly available

The origin and evolutionary pathway of Ug99 is resolved

Fifteen Years The “next Ug99” epidemic is averted due to knowledge of pathogen and its evolutionary patterns.

Cornell

28.e.2. Gene Deployment Initiative


Four post docs are hired (August 2011)

2 x three major gene stacks are developed (non-transgenic)

Major gene stacks are integrated into CIMMYT germplasm

Five Years CIMMYT wheat germplasm contains at least 3 stacked major genes in an APR background

Ten Years National Programs adopt and adapt CIMMYT’s germplasm that contains 3 stacked genes in an APR background.

Farmers adopt this germplasm as made available by the National Programs.

Fifteen Years Globally, no wheat germplasm is released

Cornell

340



Component 28.a. Project Management Activity 28.a.1. Financial/Contractual Management

Managing subcontracts is key to the success of the DRRW project. Subcontractors receive an initial subcontract for the scope of the project. When approved, the Cornell Financial Administrator then uses an annual Task Order system to indicate to subcontractors their activities and the process by which they will be reimbursed. Subcontractors may receive an advance to support the initiation of work, and invoices are submitted to Cornell upon completion of tasks and expenditures of funds so that subcontractors are reimbursed. Cornell Financial Administrators also prepare financial report templates for subcontractors and compile the full Cornell financial report for submission to BMGF. Other financial management issues may arise in the course of a large project like this one, and those will addressed by the Cornell Financial Administrator and her staff.

Outputs • Subcontracts will be executed, task orders issued, invoices paid, and ad hoc financial

issues addressed. Activity 28.a.2. Reporting to BMGF

This activity concerns the development of templates for technical and financial reporting by the project subcontractors, the collection of reports from the DRRW subcontractors, and the compilation of those reports into the Cornell DRRW annual report to the Bill & Melinda Gates Foundation. This activity also includes the regular communication with the BMGF program officer responsible for the DRRW project, Katherine Kahn, to consult on project progress and any changes that might be necessary.

Outputs • Reports from subcontractors will be submitted; compiled report from Cornell will be

submitted. • Regular communications will be maintained with BMGF to give program officer good

sense of day-to-day progress, challenges, and opportunities. Activity 28.a.3. Programmatic management

Innovative mechanisms for efficient management of this large project are critical. This activity therefore includes the development of an online “milestone monitoring system” by the DRRW Website Administrator and IT Specialists for use by DRRW Management and subcontractors for tracking milestone progress in each Objective. In addition to this tool, DRRW Management needs to interact regularly, both face-to-face and virtually, with the project team leaders, and the team leaders and project collaborators need opportunities and support to interact regularly with each other as well. If opportunities or needs arise for Objective-specific meetings, this activity includes funds to support such gatherings, either face-to-face or virtually.

Monitoring project-wide metrics for impact is another key element to the success of the DRRW project. Project-wide metrics have been elaborated as below, and will be monitored by the PMU

341


continually throughout the year, with an update delivered to BMGF at the time of the annual project report.

Project metrics for impact Breeding:

— Tons of seed for rust-resistant wheat candidate varieties available for planting (specific targets) (or alternatively you can change tons to ha planted- up to you Hans)

— Number of women participating in project-sponsored farmer field days in Ethiopia and India

— Proof-of-concept for whether genomic selection improves efficiency of wheat breeding for rust resistance

Pre-breeding: — Number of plant genes identified as sources of resistance to TTKSK (Ug99) variants

— Number of identified resistance genes in the wheat breeders’ tool box — Number of optimized markers providing robust diagnostics for resistant germplasm

— Number of national focal points regularly contributing surveillance data to FAO — Number of rust disease samples race-typed in a timely manner by international

laboratories — Number of diagnostic markers shared among rust pathologists

— Co-funding raised by partners engaged in the Borlaug Global Rust Initiative (BGRI) — Number of self-funded participants in the annual BGRI meeting

— Number of rice mutants screened for loss-of-resistance to wheat rusts to reach a go/no-go decision on whether to pursue rice non-host immunity strategies

— Number of lines screened in international screening nurseries in Kenya and Ethiopia — Number of seasons at international screening nurseries that yield reliable data,

differentiating resistant and susceptible cultivars — Number and geographical distribution of national breeding programs screening cereal

germplasm in the East African rust nurseries. — Number of Ethiopian and Kenyan wheat breeders and pathologists who participate in

international training and apply skills learned to their own research programs Outputs

• Milestone monitoring system will be developed and maintained. • Project-wide metrics for impact will be monitored.

• Collaborating scientists/institutions will be visited periodically by DRRW management. • Regular interaction will be maintained between DRRW Management and Team Leaders

and key stakeholders.

342


• Annual DRRW project meetings will be held (may be in conjunction with BGRI annual meeting, described in Objective 22, or may be a separate gathering).

• Ad hoc Objective-specific workshops will be supported. Activity 28.a.4. External Program Advisory Committee

External guidance will be provided to the Cornell DRRW Management Unit through an External Project Advisory Committee (EPAC). Members will be mutually acceptable to BMGF and Cornell and will serve for the 5-year duration of the project. The EPAC will convene at least annually and will serve in an advisory capacity to BMGF and Cornell. In Phase II, we will add an EPAC member that will serve specifically to advise on the project’s gender activities. This activity will be supported by the Assistant Director as well as the Administrative Assistants.

Outputs • Regular input will be provided by EPAC to DRRW and BMGF on project progress (will

include travel as necessary to review DRRW progress). Activity 28.a.5. Internal IT

This activity involves the purchasing, setup, and management of IT-related services and goods in support of the daily operations of the project. The IT Specialist will support the purchase and maintenance of computers, smart phones, and other equipment, as well as facilitate in-house and online meetings for the PMU.

Outputs • Equipment and IT support will be provided to assist project administration and internal

management and communication. Activity 28.a.6. Administrative Support and Supplies

This activity involves general administrative duties, including meeting coordination and travel management, and the procurement of office supplies and services essential for project coordination and productivity. Outputs

• Internal administrative and project management supplies will be acquired and services rendered.

Component 28.b. Communications

Activity 28.b.1. Perform communications activities supporting project coordination/management

Frequent and transparent communications among DRRW project collaborators will be paramount to the success of the project. Materials that describe the project and publicize its successes to the public and communicate intra-project announcements/information will be developed and distributed, including brochures, posters, electronic newsletters, web content, and other communications resources. Materials in support of advocacy goals will be developed, in particular to support efforts to reach out to media and to policymakers.

343


Outputs • Brochures, Power Point presentations, and posters to describe the DRRW project will be

developed and distributed to key audiences. • Information about project progress will be regularly shared with DRRW collaborating

scientists. Activity 28.b.2. Maintain comprehensive “wheat rust” web presence that includes knowledge sharing. This activity is critical to project management, as one of the main refrains in the rust community and from the DRRW project scientists is the lack of information online about what is happening in wheat rust research, who is doing what, and how scientists can access resources and learn from their far-flung colleagues. This activity will ensure that the most up-to-date and relevant information of interest to the wheat rust community will be accessible to that community. The DRRW web presence will serve the role of gathering, storing, and/or linking to all of this information in one place so that community members will be able to access it with minimal effort. This activity will be concerned not only with existing information but will consider each member of the wheat rust community as a potential source of information and support the sharing of knowledge among community members. The DRRW web resources will include an online Wheat Rust Knowledge Bank, online spaces for community collaboration, and the DRRW Project site hosted at Cornell University. Experts will be recruited periodically to review and vet all content for scientific quality and merit in specific sections pertaining to their expertise, and an annual content assessment of all of the web resources will be administered to determine that the needs of the audiences are being met. As this resource will be designed to be, “by the rust community and for the rust community,” user feedback will be very important to us, and will be actively solicited.

Virtual communities that provide scientists with a secure, password-protected online space for exchanging documents or sharing ideas is another resource that rust researchers have requested. The DRRW Website Administrator will advertise the availability of this resource and support the establishment of these communities.

The DRRW Project website is another important resource for information specific to the DRRW project. The DRRW Website Administrator will also be responsible for updating its design and content. Outputs

• The Wheat Rust Knowledge Bank will contain scientific information related to the wheat rusts requested by and provided by the rust community, and will be a sustainable, well-trafficked online resource for scientists, policymakers, donors, and the public.

• Virtual communities for scientific discussion will be established and maintained.

• DRRW project website will be developed and maintained with frequently updated information on the project relevant to scientists, policymakers, donors, the media, and the public.

344


Component 28.c. Global Access Activity 28.c.1. Manage Global Access

The BMGF requires a Global Access Strategy that will enable: • The knowledge gained during the project to be promptly and broadly disseminated to the

scientific community, subject to a limited delay to seek intellectual property protection if such protection would best facilitate the achievement of the project’s objectives, and

• The intended product(s) to be made accessible (with respect to cost, quantity and applicability) to the people most in need within the developing countries of the world.

The BMGF does not have a specific format or template for the Global Access Strategy, but it has elaborated key components, the nature and scope of which depend on the particular facts underlying each project (e.g., whether collaborators are involved, the stage of product development and nature of the underlying technologies and related intellectual property). These components specify that (Bill & Melinda Gates Foundation Key Components of a Global Access Strategy, 2008):

1) Background technologies and their owners must be identified and strategies for gaining access to them must be elaborated;

2) Project inventions must be described and strategies to secure, manage and allocate intellectual property rights associated with them must be identified;

3) A plan for reporting intellectual property events to project collaborators and to the foundation must be elaborated;

4) A plan for making the results of project research available to the scientific community and public must be articulated;

5) Key personnel and governing bodies that are charged with identifying intellectual property events and collecting information that could impact the ability to achieve the Global Access objectives must be described;

6) Anticipated post-project development, commercialization and sustainability strategies must be identified, as well as hurdles that might have to be addressed in order to ensure the Global Access objectives can be met;

7) Commitments made in the Global Access Strategy must be specifically identified; and 8) Any intention to market products resulting from the project in developed countries should

be elaborated, and how those activities may be leveraged to help create a sustainable solution for developing countries should be addressed.

The DRRW has made strides in the development of its Global Access Strategy. All Subcontractors have submitted official commitments to the BMGF Global Access language and have provided a first, draft accounting of the background technologies that are being employed in the DRRW project. In Phase II, the Global Access Strategy will be developed further, with the assistance of DRRW legal counsel and in close collaboration with the BMGF legal team.

345


Outputs • Annual update will be developed on the innovations or products created by the DRRW

project. Component 28.d. Gender Opportunity Enhancement

Activity 28.d.1. Foster the execution of activities that enhance gender parity in the field of wheat breeding and training.

Reflective of the value we place on global equity, the DRRW Project Management Unit is committed to developing and implementing a gender mainstreaming strategy. As with the research and plant breeding components of the DRRW project, we will engage the most appropriate experts (in this case, in gender research/action) in the development and implementation of our strategy while also engaging DRRW Team Leaders in the process. Importantly, gender mainstreaming extends beyond the question of empowering women; rather, it considers whole households and communities of wheat farmers and consumers holistically. Based on consultations with gender experts, we believe that the most effective way to mainstream gender within the project is to establish a gender component with defined activities and budget lines within the scientific areas of each scientific objective (breeding, surveillance, etc.) We would like to ensure that we take advantage of and complement the efforts of others in this arena, particularly those of our developing country partners. As a first step, we engaged with the BMGF gender specialist, Haven Ley, and Objective Leaders to create a gender strategy that is contained within the Activities of specific Objectives (22, 25, and 28). In Objective 28, we propose to manage these gender initiatives while remaining vigilant of other ways to enhance ad hoc opportunities that will contribute to gender parity. The annual technical report will monitor progress related to the gender strategy activities, ensuring Objective-specific and project-wide accountability of this component.

Outputs • A gender mainstreaming strategy will be implemented managed, and monitored.

• Objective-specific gender activities will be implemented. • Gender issues in DRRW project will be managed and monitored regularly.

• Opportunities to enhance gender parity will be realized and enhanced through contingency gender funds.

Component 28.e Special Initiatives

Activity 28.e.1. Stem Rust Sequencing Initiative Two special initiatives are proposed to be developed in conjunction with the BMGF Program Officer if the grant is funded. The first special initiative, “Stem Rust Sequencing Initiative,” aims to fund the collection and sequencing of a global population of Puccinia graminis (Pgt) isolates. By understanding the epidemiology and population structure of Pgt, we can better understand from what circumstances Ug99 evolved and what the next Ug99 might evolve to look like in the future. Laboratories for this initiative will be identified in January of 2011.

346


Activity 28.e.2. Gene Deployment Initiative

The second special initiative, the “Gene Deployment Initiative,” will fund four extraordinarily talented post-docs in four high profile, productive labs to identify and stack sets of three or more major genes that are otherwise not released as single genes. This strategy will be central to the responsible deployment of major genes and will ensure the longevity of materials developed and released by the project.

IV. Management Plan

In Phase I, the PMU at Cornell has adopted an “Action Team” framework to manage the project and organize individual staff work plans. This approach fosters internal coordination, transparency and group-wide communication. In Phase II, we expect to feature the Objective Team Leaders, individually and as a group, as the primary locus and conduit for programmatic coordination under Cornell's overall leadership. Regular meetings of the group, as needed but not less than monthly, will be held with participation facilitated electronically as needed, regardless of the Object Leaders location. Internally, as in Phase I, two types of Action Teams will be utilized: ad hoc teams will come together to coordinate a specific time-bound task, and permanent teams will be in place to work on project-wide and long-term tasks. The current Action Teams and a recent example of an ad hoc action team are:

• Advocacy: Active Resource Mobilization

• Annual Meetings • Annual Reports

• Communications • East Africa Infrastructure & Operations

• Gap Analysis • Gender

• Phase II Planning • Knowledge Bank

• February 2009 Ethiopia meeting (and example of an ad hoc Action Team) Action Teams are composed of several members of the PMU and are led by a “point person” who coordinates each team and provides progress updates. The point person is ultimately accountable for completion of the specific team work-plan. One or more members of the senior management engage with each Action Team, and a lead role is assigned to one manager per Action Team.

The teams are categorized based on related skills, tools, and other criteria. Members of the management unit are assigned to the teams and a “management lead” and point person are

347


designated. Action Teams hold regular team-specific meetings and the point persons for each team report on progress at general staff-wide meetings.

The nature of the action team framework allows for changes in project priorities over time, while still maintaining accountability and explicit direction towards the PMU goals. The Action Team structure has facilitated effective project management in the first phase of the DRRW project and promises to be a valuable organizational framework during the second phase.

V. Potential Risks and Unintended Consequences • Civil unrest in host countries of partner institutions restricts communication/coordination. • Sub-contractor show reluctance/inability to adequately track and report encumbering

background technologies, or project-funded value-added technologies • Coordination within the project or between the project and other actors is inefficient due

to insufficient commitment to transparency and inclusiveness. • Male-dominated science community shows resistance to gender equity measures.

• DRRW/BGRI web presence falls short of expectations because of inherent resistance to web collaborative environment or other factors.


Aarhus University http://www.au.dk/en

Aarhus University,Flakkebjerg, Denmark is home to the Yellow Rust Global Reference Center, led by stripe rust pathologist, Dr. Mogens Hovmoller and is best equipped to serve as a Global Reference Center for all three rusts,including stem rust. The establishment of a Global Reference Laboratory at Aarhus University will build on the existing Global Reference Centre for yellow rust, which was established in December 2008 via a Memorandum of Understanding between CIMMYT, ICARDA and Aarhus University (recommended by Nobel Peace Laureate, Dr. Norman Borlaug).

Agriculture and Agri-Food Canada (AAFC) http://www.agr.gc.ca/index_e.php

Agriculture and Agri-Food Canada (AAFC) provides information, research and technology, and policies and programs to achieve security of the food system, health of the environment and innovation for growth for Canada. AAFC, along with its portfolio partners, reports to Parliament and Canadians through the Minister of Agriculture and Agri-Food and Minister for the Canadian Wheat Board. The Rust Laboratory at Winnipeg (formerly the Dominion Lab) has been engaged in rust research since the early 1900s, and has coordinated national rust pathogenicity surveys,

348


which are currently conducted by Dr Tom Fetch, who has played a central role in understanding the current distribution and nature of the “Ug99 lineage.”

Australia’s Commonwealth Scientific and Industrial Research Organization (CSIRO)

http://www.fao.org/ag/AGP/agpc/doc/field/Wheat/asia/Turkey/inst_crifc.htm CSIRO is tackling the main wheat diseases in Australia by working to better understand pathogen biology, epidemiology, disease resistance and function, and innovative gene technology. Dr. Evans Lagudah is the Sub Program Leader of Plant Resistance Genes and leads a team investigating plant disease resistance genes to help improve cereal crops. Dr Evans Lagudah’s research activities are based on the integration of molecular genetics and conventional breeding of biotic and abiotic stresses, and grain quality attributes for cereal improvement. A major focus of his current activity is on slow-rusting disease resistance aimed at achieving durable resistance in wheat as part of the Plant Resistance Genes team - a team with a research spectrum including basic studies on flax-flax rust interaction, activation tagging of cereal genes, cloning of wheat disease resistance genes, genomic analysis of targeted disease resistance traits, and the identification and utilization of molecular markers for resistance breeding. Dr. Lagudah has availability of a cobalt source for generating gamma irradiation. He successfully demonstrated the use of gamma irradiation in generating overlapping set of interstitial deletion and point mutations and eventual cloning of the Lr34/Yr18 adult plant resistance. Well-established knowledge base and genetic resources on the diploid D genome, Ae tauschii, are also strategic advantages. The CSIRO group currently has a $1million/year-five year project funded from the Grains Research and Development Corporation. CSIRO is also in the process of finalizing a new $250,000 per year project for four years ($1million) in collaboration with the University of Sydney through the Australian Centre for International Agricultural Research-ACIAR in conjunction with partners from the Indian Council for Agricultural Research (ICAR) on Ug99 rust research.

Ethiopian Institute for Agricultural Research (EIAR) http://www.eiar.gov.et/

EIAR is the National Agricultural Research System (NARS) of Ethiopia with regional centers including Debre-Zeit Agricultural Research Center (with a strong focus on durum improvement), Kulumsa Agricultural Research Center (focusing on bread wheat improvement) and Ambo Plant Protection Research Center (focusing on plant pathology and plant protection). During Phase I of the DRRW project, facility upgrades have been planned or initiated at these stations, and will have reasonable capacity for screening international germplasm for rust resistance upon completion during Phase II. Dr. Bedada Girma, the national cereals research program coordinator (also coordinator for DRRW in Ethiopia), will be acting coordinator for the Ethiopia component. His team is comprised of doctorate-qualified scientists (Dr. Ayele Bedebo at Debra Zeit and Dr. Woldeab Getaneh at Ambo) at both research centers with good knowledge of breeding and pathology. Dr. Bedada is also coordinating another project funded by AGRA to develop and disseminate adapted wheat varieties with tolerance to wheat stem rust for the

349


moisture stress and marginal areas of Ethiopia to reduce hunger and poverty among smallholder Ethiopian farmers. Dr. Bedada is instrumental in linking the project with other regional projects and agencies. Dr. Ayele Bedebo is the wheat pathologist at EIAR and has extensive experience in nursery establishment, screening, and assessment of resistance to stem rust. The strategic location of his screening nursery at the Debre-Zeit location is critical to evaluate resistance in wild tetraploid accessions, mapping populations, and high breeding value lines.

Food and Agriculture Organization (FAO) of the United Nations

http://www.fao.org/agriculture/crops/core-themes/theme/pests/wrdgp/en/ The FAO has in place a fully operational trans-boundary pest monitoring and early warning system for Desert Locusts. FAO has been managing this system continuously since 1978 and the proposed work in the DRRW project of establishing a Rust Monitoring System will leverage the vast experience obtained in establishing the Desert Locust Monitoring system. Dr. Dave Hodson has over 11 years of experience implementing and managing a wide range of GIS projects related to agriculture in developing countries. For the last six years he managed the GIS laboratory at the International Maize and Wheat Improvement Center (CIMMYT) in Mexico. Dr. Hodson has worked on the application of GIS to the threat posed by the “Ug99” lineage of stem rust since 2005, and in this capacity was responsible for much of the currently available information relating to movements and distribution of the Ug99 lineage. FAO has a range of other projects focused on cereal rust diseases that include funding from IFAD (US$1.5 million), USAID (US$1 million), IAEA (US$1 million), Spain (US$551,100) and Italy (US$180,000). The unique position and comparative advantage of FAO to engage at a high level with national ministries concerned with agriculture is being used to ensure that official nominations and agreements are place for effective data and information flows between national and international agencies (and vice versa). The engagement of a neutral UN agency is considered to be the most effective way to ensure that barriers relating to the free flow of information are removed so an effective and sustainable monitoring network can be created.

Directorate of Wheat Research, Indian Council of Agricultural Research http://www.icar.org.in/dwr/dwrmain.htm

The All India Coordinated Wheat Improvement Project (AICWIP) established in 1965 by ICAR was elevated to level of Directorate of Wheat Research (DWR) in 1978. In 1990 DWR was delinked from IARI and shifted to the present location at Karnal, at a distance of 130 KM. North of New Delhi. The mission of the DWR is to enhance the productivity and profitability of wheat and barley on ecologically sustainable basis. The mandate of the DWR is to: 1) Evolve, organize, coordinate and monitor multi-location research for developing and identifying superior high yielding varieties tolerant to biotic and abiotic stresses under varied agro-climatic zones; 2) Collect, evaluate, catalogue, maintain and share working collections with a focus on identifying suitable donors for different stresses and quality attributes; 3) Develop appropriate crop production procedures and technology for wheat based cropping systems to optimize resource utilization in a sustainable manner; 4) Monitor the rust pathogen dynamics and develop technology to mitigate crop losses due to pests; 5) Establish

350


national and international linkages for strengthening wheat and barley improvement program; 6) Provide off-season nursery facility for rapid generation advancement and seed multiplication; 7) Serve as a core facility for proper data analysis and information management; and 8) Coordinate and organize breeder seed production and technology transfer activities.

Institute for Cereal Crops Improvement, Tel Aviv University

http://www.tau.ac.il/lifesci/units/ICCI/ The missions of the ICCI are focused at cereal crops and aim accordingly to conserve the natural biodiversity of cereal crops wild relatives threatened by land development and diminishing natural habitats; to evaluate the breeding value of these wild relatives and; to transfer genes of interest into modern crops. These activities are of invaluable importance for successful crop cultivation. An example for this is a gene for resistance to crown rust of oats found by us in wild oats in Israel and was transferred to cultivated oats in the U.S. that resulted in a 25-30% yield increase and higher grain protein content. Another example are genes for barley powdery mildew found by us in wild barley in Israel that are currently included in barley breeding programs in southern Germany. The research at the ICCI is further extended to the study of different aspects of pathogens of cereals and especially rust fungi. These obligate parasites co-evolved with their hosts over time. Consequently, cereal biodiversity of resistance genes is reflected in biodiversity of the virulence of the fungus. Tel Aviv University has wide experience in cytogenetic manipulations in general and in transferring genes from wild cereals, including Ae. sharonensis to wheat. The Institute for Cereal Crops Improvement (ICCI) at TAU holds a large collection of wild cereals, most of which were collected in Israel, including Aegilops spp. and Triticum dicoccoides. Dr. Jacob Manisterski is a highly skilled pathologist with 40 years of proven experience with cereal rusts. He isolates and maintains Israeli rust races and wild wheat accessions in The Harold and Adele Lieberman Germplasm Bank. He has authored many papers dealing with different aspects of rust fungi.

International Center for Agricultural Research in the Dry Areas (ICARDA)

http://www.icarda.org Established in 1977, the International Center for Agricultural Research in the Dry Areas (ICARDA) is one of the 15 centers strategically located all over the world and supported by the Consultative Group on International Agricultural Research (CGIAR). With its main research station and offices based in Aleppo, Syria, ICARDA works through a network of partnerships with national, regional and international institutions, universities, non-governmental organizations and ministries in the developing world; and with advanced research institutes in industrialized countries.

Miloudi Nachit, ICARDA durum breeding/germplasm enhancement program, is in a strategic position to systematically introgress variation discovered in wild tetraploids of wheat. A highly efficient breeding effort is the most sensible route for large-scale population development using wild relatives in the primary gene pool. Drs. Kumarse Nazari and Francis Ogbonnaya of ICARDA will work on selection of donor lines, population screening, and mapping population development will enhance germplasm outputs.

351


International Maize and Wheat Improvement Center (CIMMYT)

http://www.cimmyt.org CIMMYT is an internationally funded, nonprofit scientific research and training organization headquartered in Mexico global mandate for bread and durum wheat improvement for the developing world.. Drawing on strong science and effective partnerships, CIMMYT researchers create, share, and use knowledge and technology to increase food security, improve the productivity and profitability of farming systems and sustain natural resources. CIMMYT acts as a catalyst and leader in a global wheat innovation network that serves the poor in the developing world. It has regional offices both in Kenya (Nairobi) and Ethiopia (Addis). A key component of CIMMYT’s network is a well-established international nurseries system in which promising new wheat lines are distributed for evaluation all around the world. In addition to this, training of scientists from the National Agricultural Research Systems from developing countries and collaborative projects provide strong mechanisms for transfer of new knowledge and technology. CIMMYT has the appropriately skilled research scientists, breeders, technical staff, management and leadership capabilities to successfully implement this project.

Dr. Sridhar Bhavani, the CIMMYT scientist based in Kenya, was trained by Robert Park and Ravi Singh and has worked in the Cereal Rust Laboratory at the University of Sydney as well as CIMMYT HQ for the duration of the DRRW Phase I project, respectively. He has strong expertise in area of cereal rust genetics, breeding for resistance and molecular tools. He benefits from the strategic location of CIMMYT East-Africa offices and the networks developed by these offices in coordinating the regional and global activities. Dr. David Bonnett is responsible for many of the wheat pre-breeding activities at CIMMYT. He has a strong track record in development of germplasm carrying novel traits in adapted backgrounds. He emphasizes use of DNA markers in germplasm development and is recognized internationally for development and implementation of marker-assisted selection strategies. Many germplasm lines he has produced have been used by wheat breeders in Australia and at CIMMYT; some are undergoing evaluation for direct release as varieties and several are under consideration for release in Australia. Dr. Bonnett will oversee development of the germplasm delivery strategy and its implementation. Dr. Susanne Dreisigacker is the leader of CIMMYT’s wheat molecular marker group. She is responsible for marker development and screening in CIMMYT’s Global Wheat Program. She has extensive experience in diversity analysis, marker development and marker-assisted breeding, and a strong publication record in this area. Dr. Dreisigacker will oversee marker screening activities including refinement of protocols for high throughput screening and multiplexing where appropriate. Dr. Ravi Singh is the world leader in development/identification of APR for rust diseases in wheat. He has been involved in discovery and mapping of several genes and cloning of Lr34/Yr18. Resistance to Ug99 and its derivatives is an important target in all of CIMMYTs wheat breeding activities and Dr. Singh has been responsible for rapidly selecting resistance in elite backgrounds and fast-tracking release and increase of seed of resistant varieties in key environments under threat from Ug99. Dr. Hans Braun is the Director of the Global Wheat Program of CIMMYT. He will handle the management issues on behalf of CIMMYT. The other CIMMYT scientists involved will be Dr. Yann Manes (leading CIMMYT rain-fed wheat breeding program), Dr. Karim Ammar (leading CIMMYT durum wheat program) and Dr. Monica Mezzalama (leading CIMMYT seed inspection and distribution unit).

352


Kansas State University

http://www.k-state.edu/wgrc/ The internationally-recognized Wheat Genetic and Genomic Resources Center (WGGRC) is located at Kansas State University, in the heart of the Great Plains of the United States, one of the greatest wheat-growing regions in the world. Germplasm and the scientific method of breeding provide the foundation for bountiful wheat harvests. The WGGRC has three main missions to assure future advances in wheat breeding: 1) collect, conserve, and utilize germplasm in crop improvement for sustainable production by broadening the crop genetic base; 2) create and promote the free exchange of materials, technology, and new knowledge in genetics and biotechnology among the world's public and private organizations; and 3) sponsor graduate and postgraduate students and visiting scientists for academic training and advanced research in the WGGRC laboratories. The WGGRC maintains a gene bank, along with evaluation and passport data, on 2,500 wheat species accessions. In addition, the WGGRC houses 2,200 cytogenetic stocks, the genetic treasures produced by a lifetime of work by wheat scientists. The WGGRC has established a national and international network to conduct and coordinate genetic studies in wheat. Genes for host-plant resistance to viral, bacterial, fungal, and insect pests and abiotic stresses are identified, transferred to agronomically useful breeding lines, and deployed. The genetic bases of physiological, quality, and yield traits are studied. Chromosome and genetic maps of wheat and other Triticeae genera are developed. Biotechnological research emphasizes diagnostic assays, gene cloning, and plant transformation. State-of-the-art laboratories, greenhouses, and field plot facilities are available for teaching and research. Dr. Bernd Friebe (Research Professor at Kansas State University) is internationally recognized for his expertise in wheat cytogenetics, and has a career commitment to chromosome engineering of agronomically important traits. Dr. Friebe works with Bikram Gill in the Wheat Genetic and Genomic Resources Center. Drs. Friebe, Gill, and Mike Pumphrey (formerly at USDA-KSU, now at Washington State University) have a seamless relationship that has already produced translocations harboring several new broadly effective stem rust resistance genes, as well as several other genes of agronomic importance on small alien translocations.

Kenya Agricultural Research Institute (KARI) http://www.kari.org/

KARI, established as a semi-autonomous government institution, has a national mandate of implementing national, regional and global agricultural projects. Over the last 25 years, KARI has developed a strong physical resource base with support from the Kenyan government and a number of multilateral and bilateral donors. KARI has 21 research centers and 14 sub-centers across Kenya. The KARI-Njoro’s research focus is on crop improvement with a strong wheat breeding component. KARI-Njoro displayed good leadership and cooperation during the first phase of the project. The KARI staff has national expertise to support desired areas of the proposed objectives. Peter Njau is the principal plant breeder for KARI, and also holds the title of Deputy Director. He will be the acting coordinator for the Kenya component of this Objective. Peter has more than 15 years experience in plant breeding and has updated his skills

353


under Phase I of DRRW. Peter is currently obtaining his in-service Ph.D. in Plant Breeding in Switzerland, and has contributed significantly to this project in Phase I. His team includes principal pathologist Ruth Wanyera who has more than 20 years of experience in plant pathology and rust epidemiology.

United States Department of Agriculture-Agricultural Research Service

http://www.ars.usda.gov/main/site_main.htm?modecode=36-40-05-00 The USDA-ARS Cereal Disease Lab has a long-term commitment to leaf and stem rust epidemiology, population genetics, resistance screening and genetic characterization. The mission of the Cereal Disease Laboratory is to reduce losses in wheat, oat, and barley to major diseases including leaf rust, stem rust, and Fusarium head blight. This mission is accomplished through research on the biology of the pathogens that cause these diseases and on methods to enhance disease resistance in small grains. Program objectives are to: 1) identify genes used by plants in defense against pathogens and determine their cellular and biochemical mechanisms of action; 2) elucidate molecular aspects of the expression of virulence in rust fungi; 3) identify and utilize rust resistance factors to protect small grain crops against existing and future pathogenic races in rust populations; 4) analyze population genetics of cereal rust fungi and devise strategies to enhance durability of resistance against diverse rust populations; 5) identify and characterize resistance in wheat and barley to Fusarium head blight and determine impacts of partial resistance on pathogen populations in crop residue; and 6) identify genetic factors for pathogenicity in Fusarium and explore ways to block their activity and minimize pathogen attack in small grains. CDL has been involved in stem rust research, including nation-wide race analysis of the stem rust pathogen, since the early 1900s. Dr. Yue Jin provides global leadership on stem rust resistance phenotyping, gene discovery and postulation, and genetics. Dr. Jin currently leads the national race surveys, has many years experience in working with cereal rust pathogens, and has been involved in race typing samples of stem rust from eastern Africa and beyond for the past five years. Along with Dr. Fetch (see above), he has produced most of the information available on the virulence spectrum of the Ug99 lineage, including verification of two mutational derivatives carrying virulence for Sr24 and Sr36. In Phase II, Matthew Rouse is also included as a project partner. Dr. Rouse was trained, through his doctoral work, by Yue Jin. His work under Yue Jin contributed greatly to the success of the Phase I project. Now running his own lab at the CDL, Dr. Rouse will be a key collaborator in the pre-breeding work of Phase II. The CDL has recently been targeted to receive “Ug99 resistance breeding” funds via a recent government appropriation. While the language concerning the use of funds specifically designates enhancement of US readiness for the threat of Ug99 introduction, their overall efforts will be strengthened by this increase and retain global perspectives. From the same funding increase, USDA-ARS Regional Genotyping Laboratories and geneticists in Aberdeen, Idaho; Pullman, WA; and Raleigh, NC are increasing molecular mapping research and germplasm development focused on resistance to Ug99. Dr. Jin has strong collaborative relationships with these programs and will continue to coordinate activities to minimize redundancy and maximize output.

354


Steven Xu, USDA-ARS, Fargo, ND has unique expertise and capacity required for robust chromosome engineering, population development, genetic mapping, and trait introgression. His program is well-funded by the USDA-ARS, the United States Wheat and Barley Scab Initiative and other competitive grants. Dr. Xu is a highly productive wheat geneticist, efficiently integrating diverse aspects of trait discovery and improvement, and leveraging considerable resources and collaborations at both North Dakota State University and the USDA-ARS Cereal Crops Research Center.

University of Adelaide http://www.agwine.adelaide.edu.au/plant/pbg/cc/

The Cereal Cytogenetics laboratory at the University of Adelaide, Australia, has succeeded in producing many new candidate lines with shortened alien chromosome segments carrying stem rust resistance genes SrR, Sr26, Sr32, Sr37, Sr39, Sr40, SrTt3, Sr2S#1, Sr2S#3, Sr2S#4 and Sr2S#5 from Imperial rye, Thinopyrum ponticum, Triticum speltoides and T. timopheevii. Lines with SrR, Sr26, Sr32, Sr2S#1 and Sr39 genes have already been sent to all major wheat breeding programs around Australia and wheat lines with genes Sr40, SrTt3, Sr2S#3 and Sr2S#4 will soon be available. Dr. Ian Dundas has extensive connections to other Australian programs through the Australian Cereal Rust Control Program, including CSIRO and University of Sydney Plant Breeding Institute.

University of California-Davis http://maswheat.ucdavis.edu/

Jorge Dubcovsky is a world leader in map-based cloning in wheat. His lab has cloned four wheat genes that regulate vernalization and frost tolerance (Yan et al. 2003, 2004, 2006; Knox et al. 2008) and two QTLs for high grain protein content (Uauy et al. 2006) and APR resistance genes for stripe rust resistance (Fu et al. 2009). Dr. Dubcovsky has provided leadership during the last eight years for the implementation of MAS in public wheat breeding programs in the US (IFAFS and CAP programs) and developed the MAS wheat site that summarizes and distributes MAS in wheat. This web portal will be used to distribute the information generated by this project. Dr. Dubcovsky’s lab has developed four gene pyramids of seedling and APR resistance genes for stripe rust that will be useful to develop germplasm combining multiple stripe rust and stem rust resistance genes. Dr. Dubcovsky has recently established an active collaboration with the Ethiopian wheat breeding program and initiated MAS backcrossing projects in tetraploid and hexaploid wheat. The postdoc in charge of this activity at Dr. Dubcovsky’s laboratory (Zewdie Abate) was a member of the Ethiopian Wheat National program, which enormously facilitates the communication between these two groups. Dr. Zewdie Abate is interested in continuing work on the Phase II of this project.

355


University of Free State (South Africa) http://www.uovs.ac.za/

Zak Pretorius, University of Free State, South Africa, has 30 years experience in wheat rusts. His program is uniquely engaged in refining greenhouse tests on adult plant stem rust response. He has successfully applied for rust research funding from FRD/NRF and the Wheat Board/Winter Cereals Trust in South Africa, and recently the BBSRC in the UK. His expertise and available collection of stem rust races provide critical capacity for both seedling and adult plant phenotyping.

University of Minnesota

http://plpa.cfans.umn.edu/ The Department of Plant Pathology has 28 graduate faculty, many of them have national and international reputations for outstanding research and teaching. It also has support staff and numerous visiting and postdoctoral scientists. About half of the graduate students are U.S. citizens and half are international. The Department of Plant Pathology has a strong research and teaching emphasis in genetically-controlled disease resistance, molecular genetics and genomics, control of diseases caused by biotic pathogens (fungi, viruses, nematodes and bacteria), wood deterioration, and in the physiology and molecular biology of plant-microbe interactions. Research areas include: 1) genetics of disease resistance at the molecular, cellular, and whole plant levels; 2) plant disease management; 3) microbial ecology; 4) biological control; 5) population genetics; 6) plant virology; and 7) air pollution and global climate change. Dr. Brian Steffenson is a world-class cereal geneticist/pathologist with an active program focused on Ug99. The BL-3 screening facility available for Ug99 is an invaluable asset for both seedling and future APR screening. Dr. Steffenson’s long-term collaboration with Eitan Millet and others at Tel Aviv University will enhance coordination of activities. Dr. Jim Anderson (Professor, University of Minnesota) has been working in the areas of wheat breeding and genetics for 20 years. He has contributed to the development of 14 released wheat cultivars. His major research effort is the genetic investigations of complexly inherited traits including grain quality and disease resistance. Recent research has focused on Fusarium head blight, leaf and stem rust resistance and incorporating resistance into new cultivars using marker-assisted selection. Recent publications include those describing diagnostic DNA markers for stem rust resistance genes Sr6, Sr9a, and Sr36, the high molecular weight glutenins, a QTL validation strategy, and marker-assisted selection strategies. His close proximity to Drs. Brian Steffenson and Yue Jin facilitates frequent communication and collaboration on project activities.

University of Sydney http://www.agric.usyd.edu.au/plant_breeding_institute/index.shtml

Founded in 1850, USyd has an international reputation for outstanding teaching and research excellence. It has a fundamental moral commitment to intellectual discovery and development, responsible social commentary and the promotion of cultural and economic well being. The

356


University complies with the financial reporting requirements of agencies that contract it to undertake research projects. It has a robust accounting system that is used for all externally funded research programs. USyd has been engaged in teaching, research and development in cereal rust genetics on a continuous basis for over 80 years. This work was initiated by Professor Waterhouse in the early 1900s, continued with Professor Watson at the University’s Plant Breeding Institute (PBI) at Castle Hill (now at Cobbitty), then Professor McIntosh, and currently is being led by Professor Park. The PBI has since the early 1970s hosted the National Cereal Rust Laboratory, under a program currently known as the Australian Cereal Rust Control Program (ACRCP). The ACRCP includes cereal rust research and breeding activities at CSIRO Plant industry in Canberra, The University of Adelaide, and CIMMYT Mexico, all funded by the Australian Grains Research and Development Corporation (GRDC), an investment that in 2008 ran at about AUD$3.2 million. The National Cereal Rust Laboratory at PBI provides leadership to the overall ACRCP, undertakes cereal rust research, provides breeding support to all industry stakeholders (including cereal breeders, pathologists, advisors and growers), and is committed to providing high quality training to Australian and foreign scientists in cereal rust genetics. The project leader, Prof Park, has 25 years experience in working with cereal rust diseases, 21 years of which have involved project supervision and management. For the past 8 years he has been the Director of Rust Research at PBI, and has managed large externally funded projects. In his role as Director of this program, Prof Park has managerial and financial responsibility, which includes reporting against contracted milestones and management of budgets. He has 24 years experience in rust resistance genetics and has published 70 research papers in international peer-reviewed journals, several book chapters, and a book on rust research.

Dr. Harbans Bariana (Geneticist/Pre-breeder) and Dr. Urmil Bansal (Molecular Geneticist) are also located at PBI.

Of A$1.4 m per annum funding of the Australian Cereal Rust Control Program, a significant proportion is spent on pathology, genetics, germplasm development and marker development aspects of stem rust research. An Australian Centre for International Agricultural Research (ACIAR) funded project with India (Trethowan and Bariana) deals with implementation of markers linked with stem rust resistance genes in two Indian wheat breeding programs. An Australia India Strategic Research Fund project attracts A$310,477 from Australia (Bariana) and about INR 2.2 m from the Indian government (Gupta). This project started in July 2008 and will finish in 2011 and is focused on molecular mapping of adult plant stem rust resistance in wheat.

Washington State University

http://css.wsu.edu/ Mike Pumphrey (previously USDA-ARS at Kansas State University in Phase I) has an active program with heavy emphasis on germplasm enhancement focused on rust resistance. Dr. Pumphrey is now the Spring Wheat Breeder at Washington State University in Pullman, WA. Dr. Pumphrey has a unique combination of experience in molecular cytogenetics, wide-crossing, genetic mapping and map-based cloning, wheat germplasm enhancement and breeding, and cereal rust pathology. The Pumphrey program at WSU has outstanding infrastructure, including year-round air conditioned greenhouse facilities, extensive seed preparation and handling space and equipment, and a state-of-the-art laboratory. The USDA-ARS Regional Genotyping lab in

357


Pullman accelerates molecular marker screening. Four full-time technicians (and ~7 undergraduate students) are supported by a combination of state government and Wheat Grain Commission funds and these staff will assist in routine plant growth and handling. Washington State University and affiliated USDA-ARS research groups in Pullman have been working on stripe rust genetics, breeding and pathology for over 100 years. Dr. Xianming Chen's (a close USDA-ARS collaborator at WSU) expertise in rust genetics and pathology are recognized worldwide, and he is the principal stripe rust pathologist in the United States. Over a dozen additional wheat breeders, geneticists, and pathologists are active collaborators at WSU.

358


$

References Cited

Key Components of a Global Access Strategy. 2008. Bill & Melinda Gates Foundation.

359

Appendix D: Milestones / Durable Rust Resistance in Wheat Phase II

Appendix D: Milestones

360

DRRW Phase II Proposal Activity OutputsObjective 21: Improved testing, multiplication and adoption of replacement varieties

Component: 21.a. Trans-national coordination.Activity: 21.a.1. Explore, and establish as necessary, the development of an international committee toevaluate, coordinate, and recommend improvements and investments in seed systems. Representationfrom the following would be anticipated: Selected NARS, CG centers, FAO, Private sector, Donor agencies,and Legal/Regulatory policy.

Activity Output Target DateResponsible

Institution-UnitDetermine the need for developing a seed systems and policycommittee, to be established under the umbrella of the BorlaugGlobal Rust Initiative, which does not duplicate other internationalefforts.

Jun 2011 Cornell - IP

Develop consensus objectives, establish goals and associatedbudgets.

Dec 2011 Cornell - IP

Investments in equipment and training which lead to improvement in the precision of performance trails, providing greater discriminationamong a cohort of entries and focusing seed multiplication resourceson developing the most promising varieties.


Development of efficient regulatory systems which do not impedebreeding progress, but do enhance the speed with which improvedvarieties and new technologies are able to enter the marketplace.

Jun 2011(RecursAnnually)

Cornell - IP

Encourage regulations and policies which enable the development of private sector investments.


Cornell - IP

Component: 21.b. Kenya.

361Appendix D: Milestones / Durable Rust Resistance in Wheat Phase II

DRRW Phase II Proposal Activity OutputsActivity: 21.b.1. Improve the capability of KARI and KEPHIS to generate reliable data with improvedaccuracy from replicated trials (KARI) and National Performance Trials (KEPHIS).


Institution-UnitKARI plants International Wheat Information System (IWIS) designedAdvanced Yield Trials (AYT) at 8 locations (up from 3 in 2008). Eachlocation has single site, and multi-year analyses conducted in time toinform selection decisions prior to planting of the next season. >75%of data sets enable statistically significant discrimination between thetop yielding line and the mean of all lines.

Dec 2010(RecursAnnually)

KARI - Njoro

KEPHIS plants 5-8 additional locations (or at least 2 sites perlocation) of the NPT for yield and agronomic evaluation, and incollaboration with KARI, evaluates NPT entries in the KARI Njorostem rust screening nursery.


KARI - Njoro

Activity: 21.b.2. Identify and implement collaborative strategies enabling pre-release purification/multipli-cation and availability of KEPHIS endorsed Breeder Seed of KARI candidate lines at the time of approvalfor Official Release.


Institution-UnitKARI and KEPHIS seek agreement on modalities and logistics bywhich the following anticipatory steps can occur concurrently withdescriptor development, DUS assessment, and final stage of NationalPerformance Trials: First round of ear-row purification, Ear-rowderived plot grow-out/purification, and Follow-on bulking of BreederSeed.

Apr 2011 KARI - Njoro

Dedicated and irrigation-enabled land (two hectares) available forear-row purification of candidate varieties at KARI-Njoro.

Apr 2011 KARI - Njoro

One or more hectares of seed production concurrent with NPT ofeach KARI line in 2nd year of NPT; the harvest of which KEPHISendorses as eligible to be considered Breeder Seed, contingent onKEPHIS inspection; enabling availability of three tons of putativeBreeder Seed of each candidate after 2nd year NPT; (contingent onagreement of first output for this activity).


KARI - Njoro


DRRW Phase II Proposal Activity OutputsActivity: 21.b.3. Identify and implement streamlined approaches to Breeder Seed production subsequent toinitial production.


Institution-UnitThe current three stage ear-row, ear-row derived plot, and follow-onbulk method is employed less often without loss of purity of BreederSeed lots.

Nov 2012(RecursAnnually)

KARI - Njoro

Activity: 21.b.4. Promote awareness of new Ug99 resistant varieties and/or lines that are candidates forrelease as varieties.


Institution-Unit4-8 Field Days jointly planned and executed by Ministry of Agriculture(MoA), KARI, Cereal Growers Association (CGA), and the KenyaSeed Company (KSC).

Aug 2011(RecursAnnually)

KARI - Njoro

Activity: 21.b.5. Maximize efficiencies and effectiveness of Certified wheat seed supply chain from Pre-Basic Seed to farm and industry/consumer use.


Institution-UnitKey representatives of milling/processing, growers (CGA+), MoA Extension, KSC, KEPHIS, and KARI jointly visit key AYT and NPT sites; and actively engage in communication on current and futurewheat varieties.


KARI - Njoro

Annual production of Breeder Seed by KARI matches KSC needs. Nov 2011(RecursAnnually)

KARI - Njoro

Certified Seed production by KSC of stem rust resistant andotherwise improved lines meets producer and consumer demands.


KARI - Njoro


DRRW Phase II Proposal Activity OutputsMutual awareness of milling, flour, and processing properties ofwheat grain (including characteristics of new varieties) enhancedthrough a workshop involving flour millers, KARI and other keystakeholders.

Mar 2011 KARI - Njoro

Component: 21.c. Ethiopia.Activity: 21.c.1. Increase capacity, stability, and quality of Breeder and Pre-Basic Seed production.


Institution-UnitOff-season irrigation capacity is created or enhanced for Breeder andPre-Basic Seed production at Kulumsa, Debre-Zeit, Melkassa, andWerer.

Dec 2011 EIAR

Planting and harvest methods and equipment are upgraded to reducelabor costs and ensure timely completion of field work.

Dec 2011 EIAR

Seed processing equipment is upgraded at key Centers. Apr 2012 EIAR

Seed quality laboratories are upgraded, equipped, and staffed at keyCenters.

Apr 2012 EIAR

Key staff responsible for seed quality testing, equipmentmaintenance, field management and post-harvest seed handling areprovided in-service training.

Sep 2012 EIAR


DRRW Phase II Proposal Activity OutputsObjective 22: Increased levels of global investments and coordination in stemrust research and development

Component: 22.a.BGRIActivity: 22.a.1. Act as an effective Secretariat to the BGRI, enabling communication and providing supportfor the activities of this body.


Institution-UnitBGRI members and stakeholder communities receive quarterlyupdates on rust research and news (information drawn from otherrelevant activities, media reports, etc).


Cornell - IP

BGRI Executive Committee (ExCo) and other key membersproactively engaged in advocacy and fundraising.

Feb 2011(RecursAnnually)

Cornell - IP

Annual BGRI technical workshop held; regular ongoing communications arranged among ExCo members.


Cornell - IP

Strategic investments outside the purview of the BGRI have beenmade, and have, as a result, enabled leveraged advocacy.

Sep 2011(RecursAnnually)

Cornell - IP

Activity: 22.a.2. Foster Professional Development of Women Wheat Breeders through the BGRI.


Institution-UnitA Gender Equity luncheon is held at Annual BGRI TechnicalWorkshop, sensitizing the BGRI participants to gender issues inagricultural development.


Cornell - IP

BGRI establishes the annual Jeanie Borlaug Women in Triticum(WIT) award.


Cornell - IP


DRRW Phase II Proposal Activity OutputsThree WIT award recipients are chosen annually. Sep 2010

(RecursAnnually)

Cornell - IP

The Women in Triticum Mentor Award is established by the BGRI. Jun 2010(RecursAnnually)

Cornell - IP

One Women in Triticum Mentor Award is granted annually. Jan 2011(RecursAnnually)

Cornell - IP

Component: 22.b. Media activities for reaching key audiences.Activity: 22.b.1. Promote media coverage of the rust problem and need for sustained support for rustresearch through key message development, press releases, media training, and media monitoring.


Institution-UnitClear and concise messages developed with input from the stem rustresearch community.


Cornell - IP

Advocacy and communications strategy operates in real-time viaongoing strategic discussion regarding advocacy and media.


Cornell - IP

Press release developed in collaboration with Project managers(topics based on review of presentations, peer-reviewed papers,white papers to determine news value and in light of advocacyobjectives) translated into relevant languages (Arabic, French,Farsi...), and stories published in key outlets in target countries.

May 2011(RecursAnnually)

Cornell - IP

Desk side meetings with journalists arranged for key spokespeople,organized around four trips a year (these meetings will take placeduring trips made as part of meeting other objectives).


Cornell - IP


DRRW Phase II Proposal Activity OutputsElectronic and hard copy report compiled for each media outreacheffort, with a summary of the coverage and original clippings for keydonors and policy makers, and DRRW internal files.


Cornell - IP

Press release developed in collaboration with Project managers(topics based on review of presentations, peer-reviewed papers,white papers to determine news value and in light of advocacyobjectives) translated into relevant languages (Arabic, French,Farsi...), and stories published in key outlets in target countries.


Cornell - IP

Component: 22.c. Targeted Fundraising.Activity: 22.c.1. Visits to donor nation embassies in nations vulnerable to stem rust.


Institution-UnitFunds obtained from donor nation officials to support local researchand other activities aimed at combating stem rust.


Cornell - IP

Component: 22.d. Advocacy activities for reaching keyaudiences.Activity: 22.d.1. Promote awareness and action by policy makers and donors to address stem problem in acoordinated way and to support stem rust research and wheat improvement.


Institution-UnitFive high-level meetings arranged between critical players andrelevant government officials.

Sep 2013 Cornell - IP

Results of media outreach packaged and disseminated to promotefurther awareness.

Oct 2011(RecursAnnually)

Cornell - IP


DRRW Phase II Proposal Activity OutputsPrint and electronic materials available in relevant languages tosupport advocates in their outreach efforts.


Cornell - IP

Activity: 22.d.2. Conduct annual gap analysis to identify shortfalls in funding and opportunities forinvestment in rust research and wheat improvement, and disseminate results.


Institution-UnitGap analysis report finalized and approved (reviewed for newsvalue--as described under media activities).


Cornell - IP

Component: 22.e. Web-based activities in support ofadvocacy, fundraising and collaboration.Activity: 22.e.1. Maintain and augment a catalogue of wheat improvement and rust research projects andassociated information.


Institution-UnitAdvocacy Resource maintained and in use to support Advocacyactivities.


Cornell - IP

Activity: 22.e.2. Maintain content of BGRI website.


Institution-UnitBGRI website is redesigned and plan in place for daily maintenance,with input/interaction from rust community; content reviewed regularlyfor news value.


Cornell - IP

BGRI website will be viewed as a major source of wheat rustknowledge.



DRRW Phase II Proposal Activity OutputsObjective 23: Stem rust populations tracked and monitored

Component: 23.a. Global Cereal Rust Monitoring System(GCRMS).Activity: 23.a.1. Maintain and enhance the functional information platform and core databases for trackingand monitoring stem rust populations.


Institution-UnitCore data bases populated with quality controlled rust survey datafrom at least 10 countries per year.


UN-FAO

Automated / semi-automated data import tools and routines. Sep 2012 UN-FAO

Customized analytical tools developed. Sep 2013 UN-FAO

Activity: 23.a.2. Spatial data platform.


Institution-UnitThe Wheat Atlas internet-based data hub populated, with NARs datainputs and validation.

Jun 2012 CIMMYT - Mexico

Activity: 23.a.3. Deliver timely and accurate information on stem rust populations via an expandedGCRMS.


Institution-UnitA range of targeted information updates for stem rust available on aregular basis (i.e. web situation updates, bulletins, race frequencysummaries, trap nursery summaries).


UN-FAO


DRRW Phase II Proposal Activity OutputsActivity: 23.a.4. Leverage establishment of a Global Rust Reference Center (GRRC) by supporting raceanalysis and training.


Institution-UnitGRRC is established with significant investments from Denmark. Sep 2013 U Aarhus

National Program Pathologists from at-risk countries are trained inpathotype (race) analysis.


U Aarhus

Component: 23.b. Surveillance.Activity: 23.b.1. Trap plot network support.


Institution-UnitPure and adequate seed of genotypes used in trap plots maintainedand stored.


ICARDA

Seed distributed to all countries participating in trap plots nurseries. Sep 2012(RecursAnnually)

ICARDA

Activity: 23.b.2. Expand and enhance national capacity to undertake rust surveillance.


Institution-UnitNational survey teams established and contributing annually tonational and global cereal rust monitoring systems in at least 10countries.


ICARDA

Technical backstopping provided to national focal points and/orsurvey teams in at least 10 countries per year.


ICARDA


DRRW Phase II Proposal Activity OutputsStem rust surveillance in regions of strategic importance but notcovered by core activities.


ICARDA

Component: 23.c. Pathogen characterization.Activity: 23.c.1. Stem rust race analysis backstopping –ARIs.


Institution-UnitSelected key stem rust samples or isolates are race typed by ARIs. Sep 2011

(RecursAnnually)

AAFCUSDA - ARS

Activity: 23.c.2. Stem rust race analysis in country.


Institution-UnitPure and adequate seed of genotypes used as differentialsmaintained, stored and distributed.


ICARDAU of Sydney

National rust laboratories in at least 5 countries equipped toundertake race analysis (Quick sets and/or full race analysis) .


ICARDAU of Sydney

Activity: 23.c.3. Targeted surveillance of barberry for stem rust.


Institution-UnitPreliminary surveys of barberry conducted in Kenya (Jin), Uzbekistanand Turkey (Park) have established the existence of aecial infectionsby a form of the stem rust pathogen Puccinia graminis.

Nov 2011 USDA - ARS

Preliminary surveys of barberry conducted in Kenya (Jin), Uzbekistanand Turkey (Park) have established the existence of aecial infectionsby a form of the stem rust pathogen Puccinia graminis.

Nov 2012 USDA - ARS


DRRW Phase II Proposal Activity OutputsPreliminary surveys of barberry conducted in Kenya (Jin), Uzbekistanand Turkey (Park) have established the existence of aecial infectionsby a form of the stem rust pathogen Puccinia graminis.

Nov 2013 USDA - ARS

Activity: 23.c.4. Stem rust fingerprinting.


Institution-UnitInternational consensus on a core panel of informative SSR markersfor fingerprinting stem rust isolates.


U of Sydney

Selected key stem rust isolates fingerprinted with SSR markers. Sep 2011(RecursAnnually)

U of Sydney

Activity: 23.c.5. Stem rust molecular diagnostics.


Institution-UnitUp to 20 key stem rust isolates sequenced to a depth of about 20X. Sep 2011

(RecursAnnually)

USDA - ARS

Component: 23.d. Host characterization.Activity: 23.d.1. Host R gene determination.


Institution-UnitR gene determinations in global wheat germplasm, at least 50cultivars per year.


ICARDAU of Sydney

On request, marker genotyping for key R genes of host tissue fromstem rusted crops.


U of Sydney


DRRW Phase II Proposal Activity OutputsInformation on R genes present in cultivars incorporated into WheatAtlas.


CIMMYT - Mexico

Activity: 23.d.2. Genetic stock development.


Institution-UnitUp to 35 catalogued stem rust resistance backcrossed into acommon genetic background.


U of Sydney

Component: 23.e. Coordination.Activity: 23.e.1. Objective 23.


Institution-UnitObjective 23 outputs harmonized. Sep 2011

(RecursAnnually)

U of Sydney

Intra and inter-objective (DRRW) harmonization. Feb 2011(RecursAnnually)

U of Sydney


DRRW Phase II Proposal Activity OutputsObjective 24: World-class stem rust response phenotyping facilities in EastAfrica

Component: 24.a. Kenya Phenotyping.Activity: 24.a.1. Common wheat stem rust phenotyping of breeding germplasm and research materials inthe field screening nursery at Njoro Kenya (KARI).


Institution-UnitMain season nurseries planned, seed imported and planted, andresulting material phenotyped.


KARI - NjoroCIMMYT - Kenya

Main season data recorded, data and/or seed returned tocollaborators and shared where appropriate and as governed by the Germplasm Acquisition Agreement (GAA).



Off-season nurseries planned, seed imported and planted, andresulting material phenotyped.

Apr 2012(RecursAnnually)


Off-season data recorded, data and/or seed returned to collaboratorsand shared where appropriate and as governed by the GAA.



Activity: 24.a.2. Seedling and adult plant phenotyping of bread wheat in greenhouse and tunnel house insupport of gene mapping and novelty studies (joint with Objective 26) at Njoro Kenya (KARI).


Institution-UnitGreenhouse and tunnel house screening planned and seed imported. Feb 2011

(RecursAnnually)


Greenhouse and tunnel house screening planned and materialscreened.




DRRW Phase II Proposal Activity OutputsAccurate seedling (greenhouse) and adult reaction (tunnel house)phenotype data generated and returned to collaborators and sharedwhere appropriate.



Activity: 24.a.3. Confirmation and initial characterization of resistance in bread wheat germ-plasm at Njoro,Kenya (KARI) for varieties under release consideration in at-risk countries.


Institution-UnitField resistance of candidate or released varieties is re-evaluated ingreenhouse for seedling reaction.



Field resistance of candidate or released varieties is re-evaluated intunnel house for adult response.



Field resistance of candidate or released varieties is re-evaluated ingreenhouse for seedling reaction and tunnel house for adult responseto confirm resistance and initiate resistance gene postulation work.



DNA of confirmed resistances shared with Objective 26 to enablemarker based determination of genetic basis of resistance.



Activity: 24.a.4. Collection, characterization, and maintenance of stem rust cultures, and monitoring of fieldraces of stem rust in the screening nursery (KARI-Njoro).


Institution-UnitRelevant cultures purified and maintained. Feb 2011

(RecursAnnually)


Effective epiphytotics of stem rust on screening materials maintainedin field and tunnel house.




DRRW Phase II Proposal Activity OutputsPredominant virulent pathotypes in the screening nurseries areserially collected throughout the season and race typed to aidinterpretation and validation of phenotypic data recorded during eachscreening cycle. Frequency and predominance of pathotypesrecorded and reported to collaborators.


KARI - Njoro

Predominant virulent pathotypes in the screening nurseries areserially collected throughout the season and race typed to aidinterpretation and validation of phenotypic data recorded during eachscreening cycle. Frequency and predominance of pathotypes recorded and reported to collaborators.






Activity: 24.a.5. National pathogen surveillance and race analysis in Kenya.


Institution-UnitRust surveys during wheat growing seasons conducted and samplescollected (methods conforming to Objective 23.



Race analysis conducted at KARI-Njoro/AAFC on collected samplesand virulence patterns of races in Kenya determined.



Activity: 24.a.6. Establishment of a Seed Health unit, including standard protocols to be implemented forseed exchange in complementation with national regulatory authorities.


Institution-UnitSeed health unit operational. Apr 2011 KARI - Njoro

CIMMYT - Kenya

Seed health management protocols established and communicated. Jun 2011 KARI - NjoroCIMMYT - Kenya


DRRW Phase II Proposal Activity OutputsStaff trained in seed health. Aug 2011 KARI - Njoro

CIMMYT - Kenya

Seed health quarantine protocols implemented, includingenforcement.



Activity: 24.a.7.In-service learning/training opportunities for KARI and national skill development.


Institution-UnitScientists trained in the area of cereal rust genetics, racesurveillance, and race analysis, screening and rust pathologytechniques by visiting scientists and by CIMMYT IFP.



Three staff trained (one per year) at CIMMYT (2011-2013) in the areaof field management, screening, data collection, data management,and methodologies related to rust resistance evaluation, selectionand breeding. KARI scientists attend and participate in internationalconferences.



One national Post-graduate student trained per year in area of plantpathology, breeding and genetics.

Jul 2011(RecursAnnually)


Activity: 24.a.8. Strategic investments to enhance the precision and capacity to generate reliable andaccurate stem rust phenotypic data.


Institution-UnitFifteen hectares of land and excellent research facilities are available for national and international rust screening activities.

Oct 2011 KARI - NjoroCIMMYT - Kenya


DRRW Phase II Proposal Activity OutputsGreenhouse capable of high throughput rust resistance seedlingassays becomes available.

Jun 2011 KARI - NjoroCIMMYT - Kenya

Tunnel house capable of generating reliable and repeatablephenotypic data is available and seed health unit operational.

Apr 2011 KARI - NjoroCIMMYT - Kenya

Component: 24.b. Ethiopia Phenotyping.Activity: 24.b.1. Durum wheat stem rust phenotyping of breeding germplasm and research materials in thefield screening nursery at Debre-Zeit, Ethiopia (EIAR).


Institution-UnitMain season nurseries planned, seed imported and planted, andresulting material phenotyped.


EIARCIMMYT - Kenya

Main season data recorded, data and/or seed returned tocollaborators and shared where appropriate and as governed by theGermplasm Acquisition Agreement (GAA).


EIARCIMMYT - Kenya

Off season nurseries planned, seed imported and planted, andresulting material phenotyped.


EIARCIMMYT - Kenya

Off-season data recorded, data and/or seed returned to collaboratorsand shared where appropriate and as governed by the GAA.


EIARCIMMYT - Kenya


DRRW Phase II Proposal Activity OutputsActivity: 24.b.2. Seedling and adult plant phenotyping of durum wheat in greenhouse and tunnel house insupport of gene mapping and novelty studies (joint with Objective 26) at Debre-Zeit, Ethiopia (EIAR).


Institution-UnitGreenhouse and tunnel house screening planned and seed imported. Feb 2011

(RecursAnnually)

EIARCIMMYT - Kenya

Material screened. Oct 2011(RecursAnnually)

EIARCIMMYT - Kenya

Accurate seedling (greenhouse) and adult reaction (tunnel house)phenotype data generated and returned to collaborators and sharedwhere appropriate.


EIARCIMMYT - Kenya

Activity: 24.b.3. Confirmation and initial characterization of resistance in durum wheat germ-plasm atDebre-Zeit, Ethiopia (EIAR) for varieties under release consideration in at-risk countries.


Institution-UnitField resistance of candidate or released varieties is re-evaluated ingreenhouse for seedling reaction.


EIARCIMMYT - Kenya

Field resistance of candidate or released varieties is re-evaluated intunnel house for adult response.


EIARCIMMYT - Kenya

Field resistance of candidate or released varieties is re-evaluated ingreenhouse for seedling reaction and tunnel house for adult responseto confirm resistance and initiate resistance gene postulation work.


EIARCIMMYT - Kenya


DRRW Phase II Proposal Activity OutputsDNA of confirmed resistances shared with Objective 26 to enablemarker based determination of genetic basis of resistance.


EIARCIMMYT - Kenya

Activity: 24.b.4. Collection, characterization and maintenance of stem rust cultures and monitoring of fieldraces in the screening nursery (EIAR Debre-Zeit and Ambo).


Institution-UnitRelevant cultures purified and maintained. Feb 2011

(RecursAnnually)

EIARCIMMYT - Kenya


Mar 2011(RecursAnnually)

EIARCIMMYT - Kenya

Predominant virulent pathotypes in the screening nurseries field areserially collected throughout the season and race typed to aidinterpretation and validation of phenotypic data recorded during eachscreening cycle. Frequency and predominance of pathotypesrecorded and reported to collaborators.


EIARCIMMYT - Kenya

Predominant virulent pathotypes in the screening nurseries field areserially collected throughout the season and race typed to aidinterpretation and validation of phenotypic data recorded during eachscreening cycle. Frequency and predominance of pathotypesrecorded and reported to collaborators.


EIARCIMMYT - Kenya

Activity: 24.b.5. National pathogen surveillance and race analysis in Ethiopia. (EIAR-Ambo)


Institution-UnitRust surveys during wheat growing seasons are conducted andsamples collected (methods conforming to Objective 23).


EIARCIMMYT - Kenya

Race analysis conducted by EIAR-Ambo on collected samples andvirulence patterns of races in Ethiopia determined.


EIARCIMMYT - Kenya


DRRW Phase II Proposal Activity OutputsActivity: 24.b.6. Characterize the nature and distribution of the stem rust population in Ethiopia’sdurum/tetraploid wheat crop through surveys and established trap nurseries. (EIAR-Ambo)


Institution-UnitRust samples systematically collected from farmer fields and trapnurseries of durum wheat.


EIARCIMMYT - Kenya

Distribution of stem rust virulences and races determined. Jun 2011(RecursAnnually)

EIARCIMMYT - Kenya

Activity: 24.b.7. Establishment of a Seed health unit, including standard protocols to be implemented forseed exchange in complementation with national regulatory authorities.


Institution-UnitSeed health unit operational and complementing role of nationalquarantine authorities.

Apr 2011 EIARCIMMYT - Kenya

Seed health management protocols established and communicatedin consultation with national quarantine authorities.

Jun 2011 EIARCIMMYT - Kenya

Staff trained in seed health issues and protocols. Aug 2011 EIARCIMMYT - Kenya

Seed health quarantine protocols implemented, includingenforcement.


EIARCIMMYT - Kenya


DRRW Phase II Proposal Activity OutputsActivity: 24.b.8.In-service learning/training opportunities for EIAR and national skill development.


Institution-UnitThree scientists trained (one per year, 2011-2013) at internationalcereal rust labs in the area of cereal rust genetics, race surveillance,race analysis, screening and rust pathology techniques.

Jul 2011(RecursAnnually)

EIARCIMMYT - Kenya

Three staff trained (one per year, 2011-2013) at CIMMYT in the areaof field management, screening, data collection and methodologiesrelated to rust resistance evaluation, selection and breeding.


EIARCIMMYT - Kenya

EIAR scientists attend and participate in international conferences,2011-2013.


EIARCIMMYT - Kenya

National technical staff trained by two local training events relevant tofield and greenhouse rust screening.


EIARCIMMYT - Kenya

Activity: 24.b.9. Strategic investments to enhance the precision and capacity to generate reliable andaccurate stem rust phenotypic data.


Institution-UnitSeven hectares of land and excellent research facilities are availablefor national and international rust screening activities.

Oct 2010 EIARCIMMYT - Kenya

Greenhouse capable of high throughput rust resistance seedlingassays becomes available.

Jun 2010 EIARCIMMYT - Kenya


DRRW Phase II Proposal Activity OutputsTunnel house capable of generating reliable and repeatablephenotypic data is available.

Apr 2011 EIARCIMMYT - Kenya

Seed health unit is operational. Apr 2011 EIARCIMMYT - Kenya


DRRW Phase II Proposal Activity OutputsObjective 25: Durably resistant, high yielding wheat varieties

Component: 25.a. Bread wheat.Activity: 25.a.1. Spring bread wheat varieties with resistance to TTKSK and other stem rust variants forirrigated and higher production environments of Africa, Middle East, West, Central and South Asia.


Institution-UnitBetween 30–50 high yielding, rust resistant potential replacementvarieties tested annually in replicated yield trials in various countriesat more than 50 field sites.


CIMMYT - Mexico

Between 100–150 additional high yielding, multiple rust resistant linesdistributed annually for evaluation and selection as small plots atmore than 100 sites worldwide.


CIMMYT - Mexico

About 10 new multiple rust resistant varieties with >5% higher yieldpotential than current cultivars released officially in various countries.

Dec 2014 CIMMYT - Mexico

Application of appropriate breeding methodology and use ofgermplasm with durable resistance promoted for NARS breedingprograms.


CIMMYT - Mexico

Strong partnerships built for the fast release and promotion of newstem rust resistant cultivars.

Feb 2013 CIMMYT - Mexico

Activity: 25.a.2. Spring bread wheat varieties with resistance to TTKSK and other stem rust variants fordrought-stressed and low production environments of Africa, Middle East, West, Central and South Asia.


Institution-Unit15–20 lines sent every year to NARS coming from rainfedinternational trials and screening nurseries with good yield potential,tolerance to drought and resistance to yellow rust, leaf rust and Ug99stem rust.


CIMMYT - Mexico


DRRW Phase II Proposal Activity OutputsAt least 50 lines sent to NARS with good yield potential, tolerance todrought, resistance to yellow rust, leaf rust and Ug99 stem rust.


CIMMYT - Mexico

3–4 stem rust resistant varieties selected for release by NARS. Dec 2014 CIMMYT - Mexico

Component: 25.b. Africa and South Asia.Activity: 25.b.1. Durum wheat varieties for Ethiopia, South Asia, and North Africa with resistance to TTKSKand other rust races.


Institution-UnitApproximately 50 high yielding, stem rust resistant durum linesdistributed worldwide in CIMMYT screening nurseries.

Mar 2012 CIMMYT - Mexico

20–30 stem rust resistant durum varieties with >5% higher yield thancurrent varieties distributed worldwide for yield/adaptation testing byNARS.

Mar 2014 CIMMYT - Mexico

2–3 stem rust resistant candidates varieties for release in Ethiopia. Dec 2014 CIMMYT - Mexico

Activity: 25.b.2. Kenya breeding.


Institution-UnitStrengthen research capacity in wheat improvement through closecollaboration with wheat scientists in Kenya.




DRRW Phase II Proposal Activity OutputsAssist the Kenyan Njoro ARI in building research infrastructure. Oct 2011

(RecursAnnually)


Liaise with multiple partners for germplasm and data exchange. Oct 2011(RecursAnnually)


Activity: 25.b.3. South Asia.


Institution-UnitStrengthen research capacity in wheat improvement through closecollaboration with wheat scientists in South Asia.

Jan 2011(RecursAnnually)

Cornell - IPSathguru

Assist South Asia (Afghanistan, Bangladesh, India and Nepal)national programs in identifying and promoting new improved wheatcultivars with genetic protection to rust and other pathogens,including cultivars for the newly opened irrigated areas.



Liaise with multiple partners for germplasm and data exchange. Jan 2011(RecursAnnually)


Component: 25.c. Whole Family Variety Selection.Activity: 25.c.1. Foster the engagement of the entire household in participatory variety selection through“Family variety selection” in India and Ethiopia.


Institution-UnitAll organizing partners from NGOs, national programs, and DRRWproject are convened to plan Whole Family Variety Selectionapproach and implementation. Realistic targets are agreed uponincluding: What data will be collected at Family Field Days isdetermined, A strong mission statement is drafted for this projectcomponent and MoUs are agreed upon.

Sep 2011 Cornell - IP


DRRW Phase II Proposal Activity OutputsWhole Family Variety Selection is implemented in two countries. Sep 2012 Cornell - IP

Results of Whole Family Variety Selection are shared with DRRWbreeders.


Cornell - IP

Component: 25.d. Strengthened national program capacity.Activity: 25.d.1. Foster a new generation of wheat pathologists and breeders in contempor-ary wheatimprove-ment with emphasis on durable adult plant resistance to stem rust.


Institution-UnitA cadre of young research technicians and scientists (40) trained,enabling uniform reporting of global wheat rust surveillance data andknowledge.

Aug 2013 CIMMYT - Mexico

Senior scientists (24-30) trained at CIMMYT and ICARDA on wheatpathology/breeding, particularly on the use of minor gene resistancein pathology research and variety development.

Oct 2014 CIMMYT - Mexico

IWIS3 (an ICIS application) implemented across all Objective 25DRRW partners, enabling better sharing of germplasm phenotypicdata and information, and deployment of molecular breeding platformtools to enable more robust application of marker assisted selection.



DRRW Phase II Proposal Activity OutputsObjective 26: High breeding value wheat lines with two or more marker-selectable stem rust resistant genes

Component: 26.a. Gene discovery, postulation, and phenotypicsupport of genetic mapping and germplasm development.Activity: 26.a.1. Seedling stem rust screening of wild relatives of cultivated wheats, introgression lines,mapping populations, and high breeding value lines.


Institution-UnitIdentification of Ug99 resistant Triticum/Aegilops spp., Haynaldiavillosa, Secale cereale (and derived triticales) accessions, andThinopyrum spp.-derived amphiploids with potentially new sources ofseedling resistance based on multipathotype analysis; 2000 entriestested per year.


USDA - ARSU of MN

Identification of Ug99 resistant rye (Secale cereale and derivedtriticales) accessions and introgression lines with new sources ofseedling resistance based on multipathotype analysis; 100 entriesper year.


U of MN

Identification of Ug99 resistant Sitopsis accessions (Ae. bicornis, Ae.longissima, Ae. sharonensis, and Ae. speltoides) and Ae. variabilis,Ae. kotschyi and Ae. geniculata with potentially new sources ofseedling resistance; 300 entries tested per year (12/2010, recurringannually) at TAU; up to 300 entries tested per year.


U of MN

Seedling phenotypic data for genetic mapping and selection ofintrogression lines and breeding parents; 500-1000 entries tested peryear at UMN (03/2011, recurring annually); 300 entries tested peryear (12/2010, recurring annually) at Free State; 500 entries testedper year at UMN.


U of MNU of Free State

Seedling Phenotyping of Mapping Populations; Pheotyping T.monococcum populations: Einkorn/ PI 272557

Mar 2012 U of MN

Activity: 26.a.2. Controlled APR screening of seedling-susceptible wild relatives, landraces, mappingpopulations, and high breeding value lines.


Institution-UnitUg99 resistant Triticeae accessions identified with potentially newsources of adult plant resistance, validation of adult-plant resistanceQTL, and confirmation of high-value breeding lines; 100 lines testedper year in greenhouse APR screens with 5 replicates (~500 data points).




DRRW Phase II Proposal Activity OutputsAdult-plant phenotypic data for QTL mapping. 300 lines tested peryear with 5 replicates (~1500 data points).



Adult-plant phenotypic data for QTL mapping, validation of adult-plantresistance QTL, and confirmation of high-value breeding lines. 200lines tested per year with 4 replicates in BL-3 facility. (~800 datapoints).

Mar 2011 U of MNU of Free State

Tetraploid wheat accessions with potentially new sources of APR;APR phenotypic data for genetic mapping, validation of APR QTL, and confirmation of high-value breeding lines in controlled screen-house.


EIAR

Methods for quantitative infection and measurement of APR aredetermined, standardized and communicated to the rust community.

Dec 2011 U of Free State

Component: 26.b. Population development and introgressionof new sources of resistance.Activity: 26.b.1. Introgression, population development, and/or allelism testing of primary gene poolsources of seedling and adult plant resistance.


Institution-UnitRecombinant inbred line populations developed for new sources ofseedling and APR resistance identified in Watkins collection wheatlandraces. At least two populations advanced two generations peryear.


U of Sydney

Five or more new doubled-haploid and/or recombinant inbredpopulations for mapping novel sources of resistance in tetraploidwheats. ~200 DH and/or 400 SSD progeny advanced twogenerations per year .


USDA - ARS


DRRW Phase II Proposal Activity OutputsActivity: 26.b.2. Introgression, population development, and/or allelism testing of intractable (secondary/tertiary gene pool) sources of seedling and adult plant resistance.


Institution-UnitNew amphiploid and chromosome addition stocks for Haynaldiavillosa and Aegilops spp.. Direct introgression lines and synthetichexaploids with potentially new sources of seedling and APRresistance from Ae. tauschii. Mapping/allelism testing populations forhigh-priority resistance sources. Five amphiploids, directintrogressions from ten Aegilops accessions, and eight


WSU

Allelism tests, amphiploids and chromosome addition lines forSitopsissection species. Six allelism/mapping populations andamphiploids with four Sitopsis accessions produced each year.


U of MN

Backcross introgression/mapping/allelism testing populations withUg99-resistant Ae. speltoides (4 accessions) and T. dicoccoides (8accessions) advanced two generations per year.


U of Adelaide

Activity: 26.b.3. Targeted molecular-cytogenetic manipulation of intractable sources of seedling and adultplant resistance.


Institution-UnitTranslocation stocks with minimal alien chromatin for four new Ug99-effective resistance genes from Th. intermedium, Ae. caudata, Th.ponticum, and Th. junceum.

Dec 2014 USDA - ARS

Translocation stocks with minimal alien chromatin for new Ae. sharonensis-derived stem rust resistance genes.

Dec 2013 U of MN

Translocation stocks with minimal alien chromatin for four Ug99-effective resistance genes from Ae. geniculata, Ae. searsii, Ae.speltoides, H. villosa (7/2011) and additional resistance genesidentified in via 26.b.2.

Dec 2014 WSUKSU


DRRW Phase II Proposal Activity OutputsTranslocation stocks with minimal alien chromatin for Ae. speltoidesand Th. ponticum derived resistance genes.

Dec 2014 U of Adelaide

Component: 26.c. Mapping, validation, and delivery of marker-selectable resistance genes.Activity: 26.c.1. Mapping rust resistance loci toward development of diagnostic markers for effective genes.


Institution-UnitHigh-resolution genetic maps of two or more Ug99-effective stem rust resistance loci. Robust DNA markers that are tightly linked or diagnostic for stem rust gene detection.

Dec 2014 Cornell - PBG

High-resolution genetic maps of two or more Ug99-effective stem rustresistance loci. Robust DNA markers that are tightly linked ordiagnostic for stem rust gene detection.

Dec 2014 U of MN


Dec 2014 UC Davis

Chromosomal location two or more new sources of stem rustresistance (Ug99-effective) through molecular mapping and andidentification of linked markers.

Dec 2014 U of Sydney


Dec 2014 CSIRO

Mapping populations suitable for APR mapping, phenotypic data, andframework genetic maps for three APR populations.



DRRW Phase II Proposal Activity OutputsHigh-resolution genetic maps of the Ug99-effective stem rustresistance loci in durum wheat. Robust DNA markers that are tightlylinked or diagnostic for stem rust gene detection.

Dec 2014 USDA - ARS

Activity: 26.c.2. Validation of effective APR genes conferring resistance to the Ug99 lineage.


Institution-UnitBackcross near-isogenic populations for APR loci in Kingbird, Juchi,and Kiritati. Heterogeneous inbred families suitable for near-isogenicline development.


Backcross-derived doubled haploid populations contrasting for APRloci in multiple genetic backgrounds.


Near-isogenic lines/populations for two or more APR loci in two ormore spring wheat backgrounds.


Near-isogenic lines/populations for two or more APR loci in two ormore spring wheat/durum backgrounds (12/2013) Study of epistaticinteractions among APR genes.

Dec 2013 U of MNUC Davis

Mutant populations for Kingbird and appropriate parent. Single QTLbackcross isolines from Parula.

Dec 2013 CSIRO

Backcross-derived isolines of two APR loci derived from wheatlandraces.

Dec 2013 U of Sydney


DRRW Phase II Proposal Activity OutputsNear-isogenic lines/populations for two or more APR loci in two ormore CWANA winter wheat backgrounds.

Dec 2013 Cornell - PBG

Study of epistatic interactions among APR genes. Dec 2014 CSIRO

Activity: 26.c.3. Parent building and delivery to breeding programs.


Institution-UnitHigh breeding value lines homozygous for two or more effectivemarker-selectable stem rust resistance genes distributed inInternational Stem Rust Screening Nursery. Twelve elite genotypesused as recurrent parents.


CIMMYT - Mexico

Optimized screening conditions for DNA markers linked to Ug99-effective resistance loci and marker-assisted pyramids in high-breeding value lines.


CIMMYT - Mexico

Component: 26.d. Collection, preservation and distribution ofgenetic resources and information.Activity: 26.d.1. Preservation and distribution of germplasm.


Institution-UnitGenetic stocks, amphiploids, mapping populations, resistancedonors, validation, and high-value breeding lines preserved anddistributed to international wheat breeding community. reservation: H.Bockelman/ NSGC Aberdeen, H. Tsujimoto/NBP Japan, B.S.Gill/WGGRC (in-kind collaborators); Additional distribution viaInternational Stem Rust Screening Nursery


CIMMYT - Mexico


DRRW Phase II Proposal Activity OutputsActivity: 26.d.2. Management of genetic information and resources.


Institution-UnitCentralized web-accessible information on effective sources of stemrust resistance, including donor germplasm, mapping information,useful DNA markers, detailed protocols, feedback tools, and availablehigh breeding value lines. Coordination of Obj. 26 germplasmdistribution and screening nursery entries. Strong internationalpartnerships.


UC Davis

Component: 26.e. Evaluation of Genomic Selection Models forBreeding for APR.Activity: 26.e.1. Recurrent selection scheme yielding lines with high levels of APR while empiricallyevaluating GS models for APR.


Institution-UnitInitiation of cycle one of recurrent selection scheme by crossing 10high performing parents in all possible combinations and intermatingthe F1s.

Jul 2012 Cornell - PBG

Selection of lines to be intermated in cycle two of recurrent selectionscheme using Genetic Estimated Breeding Values (GEBVs) calculated with GS models.

Oct 2012 Cornell - PBG

Selection of intermated cycle two lines using GEBVs calculated withGS models.

Apr 2013 Cornell - PBG

Phenotypic evaluation in Njoro, Kenya of selected cycle one andcycle two lines for APR, and empirical evaluation of GS models.

Apr 2014 Cornell - PBG


DRRW Phase II Proposal Activity OutputsActivity: 26.e.2. Genomic Selection: A Tool to Decrease Work-Life Conflict in Agricultural Research.


Institution-UnitUse data from CGIAR and private companies to look at effect ofmolecular advancements on time spent away from home.

Sep 2011 Cornell - PBG

Train female graduate student in GS while also testing hypothesisthat GS will reduce amount of time spent phenotyping in the field(Jessica Rutkoski).


Support publication of paper title “Genomic Selection: A New Tool toDecrease Work-Life Conflict in Agricultural Research.”


Component: 26.f. Molecular Genetics of Rust ResistanceActivity: 26.f.1. Molecular Genetics of Rust Resistance near the Sr9 locus; identification of markers,population development, phenotyping and marker validation


Institution-UnitIdentification of markers tightly linked to Sr9 allelles—DArT derivedmarkers and markers linked to Yr5

Mar 2012 USDA - ARS

Linkage testing between Sr9e and SrGabo 56. Mar 2013 USDA - ARS

Publication of genetics and mapping of stem rust resistnace in Gabo56/alelism with Sr9.

Mar 2014 USDA - ARS


DRRW Phase II Proposal Activity OutputsVIGS induced gene silencing of putative Yr5 homologs in wheat linespossessing Sr9 alleles.

Mar 2015 USDA - ARS

Molecular characterization of SrGabo56 / Yr5 homologs. Mar 2015 USDA - ARS


DRRW Phase II Proposal Activity OutputsObjective 27: Optimized wheat improvement system in Ethiopia

Component: 27.a. All.Activity: 27.a.1 Coordinate DRRW wheat breeding activities in Ethiopia for an integrated wheatimprovement program.


Institution-UnitAn integrated and evolving national wheat improvement program(breeding, plant protection, extension) that serves Ethiopia, Africa,and the world.


EIAR

Collaboration within the National program and between the Nationalprogram and International programs, Regional programs, and NGOsis coordinated: CIMMYT, ICARDA, DRRW (Cornell), AGRA, ARIs,GCP, USDA, Sasakawa Global 2000, and other NARS.


EIAR

Agro-ecologies and farming systems identified and confirmed asbreeding targets.

Apr 2011 EIAR

Wheat-based research centers (RARI’s) engaged in evaluation andselection.

Apr 2011 EIAR

Staffing positions identified and filled, with responsibilities outlined. May 2011 EIAR

Maintenance and repairs to equipment, purchase of budgetedequipment, with equipment being placed into service.


EIAR


DRRW Phase II Proposal Activity OutputsBreeding and replicated testing programs tailored to match resourcesand budgeted priorities.

May 2011 EIAR

Progress and direction of programs Monitored/Evaluated. Apr 2011(RecursAnnually)

EIAR

Progress and direction of programs Monitored/Evaluated. Sep 2011(RecursAnnually)

EIAR

Activity: 27.a.2. Bread wheat breeding.


Institution-UnitTwo cycles per year Kulumsa-based spring bread wheat breedingprogram is operating. Program outlined: Holeta (Septoria hot-spot),Bekoji/Meraro (Yellow rust), KARI-Njoro (shuttle SR screening),KU/DZ/Arsi Robe (stem rust).

Apr 2011 EIAR

Agronomic, pathologic and end-use quality objectives prioritized andlisted: Seed color, Volume weight, Industrial baking quality, other.

Apr 2011 EIAR

10,000 introductions from international nurseries evaluated andpromising lines selected for entry into Observation Nurseries atdesignated sub-centers.


EIAR

10,000 introductions from international nurseries evaluated and promising lines selected for entry into Observation Nurseries atdesignated sub-centers.


EIAR


DRRW Phase II Proposal Activity OutputsParent lines used in hybridization identified and 300 crosses outlined Jan 2011

(RecursAnnually)

EIAR

Parent lines used in hybridization identified and 300 crosses outlined. Aug 2011(RecursAnnually)

EIAR

F2 – F6 germplasm / generations evaluated at hotspot shuttlelocations over seasons for traits of interest.


EIAR



EIAR

Five sets of 200 promising lines evaluated in observation nurseries attwo to three locations.


EIAR

Five sets of 20 high yielding, rust resistant entries evaluated annuallyin replicated trials (NVT) at 4-6 locations for two years.


EIAR

Four sets of variety release verification trials (VVT) with at least onecandidate variety planted on-station and on-farm trials.


EIAR

An array of key breeding lines genotyped at CG centers. Mar 2011(RecursAnnually)

EIAR


DRRW Phase II Proposal Activity OutputsRelationships with NARS, CG, and Objective 26 scientistsstrengthened and cultivated.

Sep 2011 EIAR

Activity: 27.a.3. Durum wheat breeding.


Institution-UnitTwo cycles per year Debre-Zeit based durum wheat breedingprogram is operating. Program outlined.

Apr 2011 EIAR

Agronomic, pathologic and end-use quality objectives prioritized andlisted.

Apr 2011 EIAR

International durum wheat nurseries evaluated and promisingintroductions identified.


EIAR

International durum wheat nurseries evaluated and promisingintroductions identified.


EIAR

Parent lines used in hybridization identified and 150 crosses outlined. Jan 2011(RecursAnnually)

EIAR

Parent lines used in hybridization identified and 150 crosses outlined. Aug 2011(RecursAnnually)

EIAR


DRRW Phase II Proposal Activity OutputsF2 – F6 germplasm / generations evaluated at hotspot shuttlelocations over seasons for traits of interest.


EIAR



EIAR

Two sets of 200 promising lines evaluated in observation nurseries at2-3 locations.


EIAR

Two sets of 20 high yielding, rust resistant entries evaluated annuallyin replicated trials (NVT) at 4-6 locations for two years.


EIAR

Two sets of variety release verification trials (VVT) with at least onecandidate variety planted on-station and on-farm trials.


EIAR

Relationships with NARS, CG, and Objective 26 scientistsstrengthened and cultivated.

Sep 2011 EIAR

Activity: 27.a.4. Develop the human resource capacity for wheat research in Ethiopia.


Institution-UnitSkills of the EIAR technical staff and assistants are enhanced withshort-term training opportunities.


EIAR


DRRW Phase II Proposal Activity OutputsTraining opportunities for EIAR scientists, such as biotechnology,data management and interaction with ARI counterparts result inprogressive breeding programs. Exchange visits with ARIs and sisterinstitutions and long-term training at ARIs.

Apr 2011 EIAR

Enhanced skills and training in preventative maintenance and repairsto research equipment. Small engine repair and maintenance andpreventative maintenance of field and lab equipment.

Apr 2011 EIAR

Activity: 27.a.5. Acquire necessary equipment to modernize and improve efficiencies of EIAR bread wheatand durum wheat improvement programs.


Institution-UnitNecessary equipment has been acquired. Nov 2011 EIAR

Irrigation capacity is maximized to meet program requirements. Nov 2012 EIAR

Lab, greenhouse, cold room, and seed health facilities improved or constructed.

Nov 2012 EIAR

Essential field equipment has been acquired and / or receivednecessary repairs to achieve functional use.

Apr 2011 EIAR


DRRW Phase II Proposal Activity OutputsObjective 28: Project management, communications, and coordination

Component: 28.a. Project management.Activity: 28.a.1. Financial/contractual management.


Institution-UnitSubcontracts executed, task orders issued, invoices paid, and ad hocfinancial issues addressed.


Cornell - IP

Activity: 28.a.2. Reporting to BMGF.


Institution-UnitReports from subcontractors submitted; compiled report from Cornellsuccessfully submitted.


Cornell - IP

Regular communications with BMGF to give program officer goodsense of day-to-day progress, challenges, and opportunities.


Cornell - IP

Activity: 28.a.3. Programmatic management.


Institution-UnitMilestone monitoring system developed and maintained. Sep 2009

(RecursAnnually)

Cornell - IP

Collaborating scientists/institutions visited periodically by DRRWManagement.


Cornell - IP


DRRW Phase II Proposal Activity OutputsRegular interaction between DRRW Management and Team Leadersand key stakeholders is ongoing.


Cornell - IP

Annual DRRW project meeting held (may be in conjunction withBGRI annual meeting, or may be a separate affair).


Cornell - IP

Ad hoc objective-specific workshops supported. Jun 2011(RecursAnnually)

Cornell - IP

Project-wide metrics for impact monitored. (ongoing with annualupdate delivered to BMGF following September reporting period eachyear)


Cornell - IP

Activity: 28.a.4. External Program Advisory Committee (EPAC).


Institution-UnitEPAC provides regular input to DRRW and BMGF on projectprogress and travels as necessary to review DRRW progress.


Cornell - IP

Activity: 28.a.5. Internal IT.


Institution-UnitEquipment and IT support provided to assist project administrationand internal management and communication.


Cornell - IP


DRRW Phase II Proposal Activity OutputsActivity: 28.a.6. Supplies.


Institution-UnitInternal administrative and project management supplies acquiredand services rendered.


Cornell - IP

Component: 28.b. Communications.Activity: 28.b.1. Perform communications activities supporting project coordination/management.


Institution-UnitBrochures, Power Point presentations, and posters to describeDRRW project developed and distributed to key audiences.


Cornell - IP

Information about project progress regularly shared with DRRWcollaborating scientists. (Quarterly updates)


Cornell - IP

Activity: 28.b.2. Maintain comprehensive 'wheat rust' web presence.


Institution-UnitWheat Rust Knowledge Bank contains scientific information related tothe wheat rusts requested by and provided by the rust community,and is a sustainable, well-trafficked online resource for scientists,policymakers, donors, and the public.


Cornell - IP

Virtual Communities for scientific discussion established andmaintained.


Cornell - IP

DRRW project website developed and maintained with frequentlyupdated information relevant to scientists, policy-makers, donors, themedia, and the public.


Cornell - IP


DRRW Phase II Proposal Activity OutputsComponent: 28.c. Global access and impact.

Activity: 28.c.1. Manage global access.


Institution-UnitAnnual update developed on DRRW innovations. Nov 2011

(RecursAnnually)

Cornell - IP

Diligence on freedom-to-operate conducted. Feb 2011(RecursAnnually)

Cornell - IP

Annual review of project level workflows ensuring impact conducted. Nov 2011(RecursAnnually)

Cornell - IP

Component: 28.d. Gender opportunity enhancement.Activity: 28.d.1. Foster the execution of activities that enhance gender parity in the field of wheat breedingand training.


Institution-UnitObjective-specific gender activities implemented. Jun 2012

(RecursAnnually)

Cornell - IP

Gender and diversity issues in DRRW project regularly monitored. Oct 2011(RecursAnnually)

Cornell - IP


DRRW Phase II Proposal Activity OutputsOpportunities to enhance gender parity are realized and enhancedthrough contingency gender funds.


Cornell - IP

Component: 28.e. Special InitiativesActivity: 28.e.1. Stem Rust Isolate Sequencing Initiative


Institution-UnitConvening is held to plan special initiative work plan. Jan 2011 Cornell - IP

SSR markers are shared between special initiative partners. Dec 2011 Cornell - IP

Puccinia graminis (Pgt) isolates fingerprints are resolved and dataare shared.


Cornell - IP

Puccinia graminis (Pgt) isolates genomic sequences are resolvedand data are shared .

Jan 2015 Cornell - IP

Activity: 28.e.2. Gene Deployment Initiative


Institution-UnitConvening is held to plan special initiative work plan. Jan 2011 Cornell - IP


DRRW Phase II Proposal Activity OutputsFour post docs are hired. Aug 2011 Cornell - IP

2 x three major gene stacks are developed (non-transgenic) Dec 2015 Cornell - IP

Major gene stacks are integrated into CIMMYT germplasm. Dec 2015 Cornell - IP


Appendix E: Impact Metrics / Durable Rust Resistance in Wheat Phase II

Appendix E: Impact Metrics

Durable Rust Resistance In Wheat

Project-Wide Impact Metrics

Breeding and seed delivery — Tons of seed for rust-resistant wheat candidate varieties available for planting — Number of women participating in project-sponsored farmer field days in Ethiopia

and India — Proof-of-concept for whether genomic selection improves efficiency of wheat

breeding for rust resistance Pre-breeding — Number of plant genes identified as sources of resistance to TTKSK (Ug99) variants — Number of identified resistance genes in the wheat breeders’ tool box — Number of optimized markers providing robust diagnostics for resistant germplasm Surveillance — Number of national focal points regularly contributing surveillance data to FAO — Number of rust disease samples race-typed in a timely manner by international

laboratories — Number of diagnostic markers shared among rust pathologists Advocacy — Co-funding raised by partners engaged in the Borlaug Global Rust Initiative (BGRI) — Number of self-funded participants in the annual BGRI meeting East African screening facilities — Number of lines screened in international screening nurseries in Kenya and Ethiopia — Number of seasons at international screening nurseries that yield reliable data,

differentiating resistant and susceptible cultivars — Number and geographical distribution of national breeding programs screening cereal

germplasm in the East African rust nurseries. Human capacity — Number of Ethiopian and Kenyan wheat breeders and pathologists who participate in

international training and apply skills learned to their own research programs

409

Documents

Durable Rust Resistance in Wheat Phase IIwheatrust.cornell.edu/documents/DRRW_II_21Feb10 Final-sans.pdf · Project Name: Durable Rust Resistance in Wheat Organization Name: Cornell