Strides in Building collaborations for cassava breeding

A member of CGIAR consortium www.iita.org

Strides in Building Collaborations for Cassava Breeding

SK Hahn, AGO Dixon and other members of the IITA Cassava Breeding FamilyIITA Crop Improvement Workshop, Ibadan Nigeria 8 September 2015

TMS-IBA121635TMS-IBA121634

including many other National,

International and Private

Partners with women, men, experienced

and new farmers in

Africa


Cassava in Africa


Future Potential for Cassava – The Rambo Crop?

From Rosenthal and Ort (2012)


Global Agricultural Trial Repository

1,410 agronomic variables measured are mapped to Crop Ontology

29,633 trials out of 34,329 described use the Crop Ontology trait names.

CO terms used for metadata and search

http://www.agtrials.org/

Cassava – 1654 trials uploaded with 1293 uploaded by CIAT and 361 by IITA with traits conforming to ontology


Cassava Source Sink (2015 – 2019)

Metabolic engineering of carbon pathways to enhance yield of root and tuber crops•Andreas Gisel lead •Physiology of root yield •Genotypes: TMEB419, TMEB693, IBA30572, IBA980581, IBA010040, IBA980002•Testing of transgenics in 2018-2019

Partners:FAUETHFIFBTIUniv. IllinoisIITA


Drought Tolerance in Cassava

Cassava drought tolerance experiment:– Two treatments; irrigated control and drought stressed– Two years; two sites in Kenya; Kibwezi and Kiboko– Five drought tolerant and five drought susceptible varieties

Findings:– 59% reduction in fresh root yield– Main mechanism driving drought tolerance is stomata that

respond slowly, do not close immediately when relative humidity drops, thereby allowing photosynthesis to continue with increased fresh root weight

– Leaf retention assists assimilate accumulation for a few weeks

– Selection for yield is a good proxy for drought toleranceOrek et al. (in preparation)


Cassava Markets in Nigeria

1 Source: Context Network analysis based on field research, farmer interviews, and published source analysis2 Garri: “CTA Presentation”, October 20143 Industrial and Other Processed Food: “Sahel Rapid Appraisal of Nigerian Markets for Cassava”, August 2013

Nigeria Market Share

(by Usage)1,2,3

52.4 Million MT Production (2011)

Boil and eat – fresh consumption

Garri

Other Food Products (fufu, lafun and others)

Industry


Processing into High Quality Cassava Peel (HQCP) Mashes

http://news.ilri.org/2015/07/09/from-food-waste-to-animal-feed-cassava-peels-potentially-big-business-for-nigerian-women/




Slides from Dr. Chareinsuk Rojanaridpiched, Thai Tapioca Development Institute

Example of Impact from Thailand


Three generations of improved Thai varieties increased starch content to 23% to 29%

Slides from Dr. Chareinsuk Rojanaridpiched, Thai Tapioca Development Institute


Agronomic practices for research and farming successfully implemented


IITA contributed 500 Anagyrus lopezi introduced from Benin to TTDI in Oct. 2009 for biocontrol of Phenacoccus manihoti. In Jan 2010 was first release to 600 ha. (tapiocathai.org)

IITA contribution to solve mealy bug threat to Thai Cassava Industry


IITA contribution to development of cassava genomic resources

Cassava ultra-high density map• 532.5 Mb (~770Mb) draft

genome in 12977 scaffolds• Composite cassava map from

10 populations used to anchor the fragments to 18 pseudo-chromosomes

• Resulted in v5.1 reference genome!

• IITA contributed 9/10 of the populations

10 Populations; 22,403 SNPs

International Cassava Genetic Map Consortium,

Genes|Genomes|Genetics 5:133–144.


Log

of o

dds

ratio

Rabbi et al. (2014) Crop Science 54

QTLs underlying key traits (TMS961089A x TMEB117)


Major locus underlying carotenoid accumulation in cassava roots

Rabbi et al. Crop Science vol. 54:


Multiple sequence alignment featuring C/T and A/C SNP polymorphism


6128 clones genotyped and phenotypedWest Africa, East Africa~90K SNPs

GWAS supports narrow genetic base for major gene resistance to CMD

CMD2 Locus

(Wolfe et al. unpublished)


Molecular markers for CBSD tolerance in three mapping populations

Above LOD 3 is significant1,000x more likely to be linked than independent assortment

5

Chromosome scale for a 20 MB chromosome

Var1, Site 1, Year 1 (LOD 3.92; 8.2%)Var1, Site 1, Year 2 (LOD 3.92; 8.2%)Var1, Site 2, Year 1 (LOD 5.07; 11.6%)

Mb 2010 15Mb 5

Var2, Site 1, Year 1 (LOD 10.75; 25.8%)Var2, Site 1, Year 2 (LOD 6.06; 21.4%)

Var2, Site 2, Year 1 (LOD 3.91; 8.6%)Var2, Site 2, Year 2 (LOD 3.62; 8.4%)

Var3, Site 1, Year 1 (LOD 3.56; 10.6%)

Var3, Site 2, Year 2 (LOD 4.33; 12.2%)

Tolerant parents are related: Namikonga (Kaleso), NDL06/132 and Nachinyaya

(Ferguson and students, unpublished)


Resistance to cassava green mite


Germplasm management

GRC core(256+24)TMEB(831+59)

669 duplicates

501 unique


ADMIXTURE plots from ~4000 cassava accessions, including CIAT.

All samples (includes accessions with one or more clonal relationships were included in the analysis).

Below: Within individual inbreeding coefficient (F)


Tracking of improved varieties in Ghana using DNA fingerprinting

Individual ancestry estimated

Hierarchical clustering


Projection of identified clones on the Ghana map.


Farmer-elicited variety names often do not match specific genotypes

182 different names recorded for the entire sample collection and here only names that occurred > 9 times are represented.


Cassava Breeding Methods

1. Phenotypic Recurrent Selection – pedigree selection

2. Genomic selection3. Marker discovery leading to marker

assisted selection4. Hybrid breeding focused on development

of inbred lines and strategies for exploitation of heterosis

5. Polyploid Breeding


Progress in genomic-selection breeding at IITA

SeedlingsCross

Select Genotype

Predict Breeding

Value

Clonal

PYT

AYT

UYT

Dramatic reduction in cassava breeding cycle length from 5 to 1 year through genomic selection

Conventional phenotype-based selection (> 5 years)


Genomic selection:Prediction using many markers

Meuwissen et al. 2001: “It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants.”

GEBV = Genomic Expected Breeding Value = predicted quality as a parent


Annual Breeding Cycle


Popn. Trial Name

Locations # of plots Ubiaja Ibadan Ikenne MokwaLocal germplasm

Local Germplasm

[907plots, 1row, 5plants, unrep]

907

Genetic Gain

Genetic Gain [764plots, 1row, 10plants,unrep]


1528

Genomic Selection Cycle 0

GS.C0.PYT88(from genetic gain)

[88plots, 1row, 10plants, 2reps]



[88plots, 1row, 10plants, 2reps] 704


GS.C0.C1 Crossing Block

C0 = 86; C1 = 158 [244plots, 4rows, 20plants, unrep]

244

GS.C1 Expanded CET

[293plots, 4rows, 20plants, unrep]

[331plots, 4rows, 20plants, unrep]

[329plots, 4rows, 20plants, unrep] 953

GS.C1.CET (Ungenotyped)


GS.C1 Expanded CET (Ungenotyped)


GS.C1.AYT40 (Ungenotyped)

[40plots, 4rows, 20plants, 3reps]

120


GS.C2 Crossing Block


173

GS.C2.CET [381plots, 1row, 5plants, unrep]


[432plots, 1row, 5plants, unrep] 1260

GS.C2 Extra Selections


884

GS.C2 Rescued CET


151

GS.C2.CET (Ungenotyped)


195


Broad-sense Heritability estimates from different trial designs

Trial Traits

Carotenoids (calorimetric)

DM FYLD RTNO MCMDS Average (env)

PYT88_2013.2015 0.793 0.55 0.23 0.18 0.73 0.50

Genetic Gain_Historical NA 0.26 0.14 0.14 0.59 0.28

Genetic Gain_2013.2015 NA 0.57 0.25 0.27 0.56 0.41

GS.C1.CET_2013.2014 NA 0.47 0.44 0.33 0.86 0.52

GS.C1.Expanded.CET_2014.2015

0.730 0.68 0.75 0.64 0.67 0.69

GS.C1.CET_2013.2015 0.730 0.64 0.53 0.38 0.86 0.63

GS.C2.CET_2014.2015 0.943 0.64 0.71 0.61 0.93 0.77

GS.C1.C2.CET_2013.2015 0.721 0.44 0.47 0.43 0.82 0.58

Average (trait) 0.783 0.53 0.44 0.37 0.75 0.56


Population Improvement

after three cycles of GS-based

recombination


Principal Components Analysis using filtered SNPs


Global GCP cassava reference set

CIAT BreedersCIAT GenebankIITA GenebankIITA BreedersSEC Africa

Level-2 OTUSampleSize

GeneDiversity (He)

CIAT breeders 121 0.3465

CIAT genebank 91 0.3433

IITA breeders 102 0.3190

IITA genebank 101 0.3375

SEC Africa 123 0.3410

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Ghana, Sierra Leonne, Togo

Muzege, Bwana Mrefu, Nyaraboke…

“Cassava Potato”, Kigoma

1125 SNPs


Doubled Haploid Project (2010 – 2017)

Objectives•Development of doubled haploid technology•Partially inbred genetic stocks – IITA role

Partners:CIATNaCRRIIITAConsultants


Cassava Doubled Haploid Project

IITA Contribution – Development of Parially Inbred Genetic Stocks

Seedling nursery (SN)4,741 inbred plants from 199

families

Clonal evaluation (CE)Ubiaja, Ibadan, Ikenne: ~500

Preliminary yield trial (PYT)256

New Seeds2013-2014 – 27,1892014-2015 – 20,013


Genetic Stock Groups

1 agronomic traits Drought tolerance2 High dry matter3 Early Bulking4 breeders traits Selected CASTOR progenies5 Polyploids6 High flowering7 Male sterile source

8 disease/pest resistance White root CBSD resistance/tolerance9 CMD resistance

10 CGM resistance11 Hairy apical leaves (CGM biocontrol)12 Multiple pest resistance, yield and dry matter13 Genetic root necrosis14 Yellow root CBSD Population15 geographic location CIAT lines16 East African lines17 morphological traits Deep red color18 quality High HCN potential19 High carotenoids20 Poundability 21 Post harvest physiological deterioration22 High protein23 Yellow/white roots


Challenge 1: Improve Starch Yield

• Break the dry matter content barrier to reliably produce starch of 23 to 29%.

• TMEB419 is the standard for high starch production in Nigeria and many countries with starch yield near 23%. Few have exceptionally high starch yield.

• Seasonal time of harvest is a key constraint to starch yield with best starch production in the dry season– Few year round harvest datasets to document

this


Root weight vs Dry matter content

Ibadan Ikenne


High Starch Genotypes in Advanced TestingHigh Starch set A – 7 locations, 2 years


Partnership with FMARD and NRCRIHigh Starch set B, 7 locations, 2 years


Challenge 2: Reaching needs of important beneficiaries

• Cassava breeding research must be gender responsive and address needs of all groups of farmers.

• Extension information reaches men easier than women

• 2015 Cassava Monitoring Study of 2500 households in Nigeria will be very helpful for guiding new strategies.


Gender Differentiated Cassava Preferences

• Nextgeneration Cassava Breeding Project• Results from a pilot study in the four communities in SW and SE

Nigeria• Focus group discussions and individual interviews were held with

women, men and youth (women and men separately)• Results were analyzed using qualitative methods• Questions included:

– Characteristics of Respondents– The varieties grown– Traits preferred (implications to the Breeding program)– Access to resources– Marketing and Processing– Decision making


Preferred Traits of Dangaria


Preferred Traits of IITA


Challenge 3: Meeting end user preferences

• Over 80% of cassava is consumed as food• While income can purchase nutrition security,

adoption of cassava varieties in many situations will depend on providing desired end user characteristics.

• Includes functional properties of cassava starches, leaf harvest, biofortification and time of harvest/in ground storage.

• Industrial traits will have specific target niches and will address specific markets. Do not assume one variety will meet all needs.


Challenge 4: Breeding methods need to be accessible to all breeders in Africa

• Improved phenotyping methods for key traits• Field designs and analysis methods to maximize

heritability and address GxE• Successfully implement databases and secure

and accurate data collection• Determine the appropriate roles of genomic and

phenotypic selections with efficient use of appropriate markers.


Cassavabase:A global open

access resource

All Data Available with Open Access with agreement to observe theToronto Protocol regarding use of unpublished data


195 Traits in Cassava Ontology

Agronomic 47Morphological 61Physiological 3Quality 33Stress 51

Total 195


Challenge 5 – addressing the challenge of dual resistance to CMD and CBSD

• Appropriate use of of different modes of resistance and tolerance

• Production and dissemination of clean planting materials

• Effective hybridization sites for international exchange of botanic seed

• Safe and efficient germplasm exchange of tissue culture clones


Effect of CMD on yield in TMEB117 and TMEB693


Planting material Tubers Starch Ethanol

Poor quality No managemen

tPoor yield

CropManagement Increase in yield Good quality

Quality planting material is fundamental to increase and sustain cassava productivity

Quality planting material to manage biotic threats

Invest in clean seed systems


Production & distribution of pest-free germplasm

Transfer to pots in isolated growth chamber. Disease monitoring

Screenhouse propagation of healthy plants in treated soil.

International distribution with Germplasm Health Statement, Phytosanitary Certificate, Material Transfer Agreement and Import Permit

Plants produced by meristem-tip culture; indexed, multiplication in vitro

Harvest material (stems, tubers, suckers) cleaned of soil/dirt, treated before despatch with fungicide or hot-water treatment.


Challenge 6 – Set and reach our impact targets

• Set targets for each regions and design programs to reach those targets

• Work together as a team across regions avoiding unnecessary duplication of effort– Breeders meetings– Regional training workshops

• Position resources where they are needed• Expand regional trials beginning with 5CP in

East Africa and Harvest Plus in West Africa • Monitor results and adjust methods and targets


Regional Updates

• Set targets for each regions and design programs to reach those targets

• Work together as a team across regions avoiding unnecessary duplication of effort– Breeders meetings– Regional training workshops

• Position resources where they are needed• Expand regional trials beginning with 5CP in

East Africa and Harvest Plus in West Africa • Monitor results and adjust methods and targets


Suitability area for cassava in SADC

Source: (IITA GPS lab)


Participatory Variety Selection leading to variety release in Southern Africa

• Malawi: Mlora (83350), Phoso (LCN801), Sagonja CH92/082 ); Chiombola (TME 6); Kalawe (CH02/0066); Mpale (NDL90/34); and Chamandanda (01/1313)

• Mozambique: Colicanana, Nziva, Okhumelela, Orera and Eyope

• Zambia: Three varieties submitted for variety release to Seed Control and Certification Institute -SCCI)

• Biofortified clones introduced in evaluation in Malawi, Mozambique, Zambia and Swaziland.


Cassava Breeding Achievements in East Africa

• Tanzania: with ARI released 8 varieties for the coastal lowlands of Tanzania in the past 5 years.

• Uganda: with NARO two breeding lines submitted for release as the first varieties with dual resistance to CMD (especially, EACMV-UG) and tolerance to both CBSD and UCBSD for the mid-altitude areas of East Africa bordering Lake Victoria

• Dozens of highly promising breeding lines in advanced stages of evaluation

• Under 5CP facilitating exchange and cooperative testing of 25 elite clones among 5 NARS breeding programs: Malawi, Mozambique, Kenya, Tanzania and Uganda.

• Botanical seeds from CBSD tolerant parents sent to Burundi (6,000), Rwanda (6,000) and DR Congo (10,000) to initiate national selection programs for specific adaptation to their agro-ecologies.


Cassava Breeding Achievements in DR Congo

• With INERA released and registration of 21 improved varieties with harvest period from 12 to 20 months and root yield between 21 to 47 t/ha.

• New selection approach for cassava brown streak disease (CBSD) comprising evaluation of maturity time every 3 months and in ground storage to 24 MAP maintaining high starch yield

• Selection for new industrial traits including dietary fibre in leaves, amylose free starch for pasting industry and sugary cassava for ethanol

• In partnership with INERA and HarvestPlus new biofortified genotypes have been selected with total carotene content (TCC) up to 15µg/g fresh weight and more than the released check TMS-IBA01/1661 (9.5 µg/g)


Building National Programs in Sierra Leone and Liberia

• Introduce and characterize local and advanced germplasm using morphological, biochemical and biotechnology tools

• Generate improved and adapted populations with desired characteristics for different agro-ecologies targeting different end uses (farming systems, food, feed and industry) and markets

• Establish special backup populations• Conserve a core set of local cultivars and improved germplasm • Fast track on farm evaluation through participatory evaluation using

innovation platforms• Expedite farmer access to quality planting materials on sustainable

basis• Improve NARs capacity and facilities (human, financial,

infrastructure) for effective execution of germplasm development, deployment and communication


IITA Cassava Breeding Trials in Nigeria

TRIAL TYPE 2011/2012 2012/2013 2013/2014 2014/2015Seedling Nursery 3 4 3 4Clonal Evaluation 2 4 9 8Preliminary Yield Trials (PYT) 10 13 17 19Advanced Yield Trials (AYT) 32 45 22 15Uniform Yield Trials (UYT) 10 28 44 29Additional Trials: Genomic Selection Trials 1 10 18Student Trials 14Mapping populations/biotech 1 6 5 5Germplasm (local germplasm/genetic resources) 1 3 2 2

Genetic gain & Genetic stocks 2 3 4 6Overall Total 61 107 116 120

Current program is about 50% white root and 50% biofortified


• First large scale distribution of 1st Wave Vitamin A Cassava in Nigeria to about 700,000 farmers in 2015

• Release in Nigeria with NRCRI of IITA-TMS-IBA070593, IITA-TMS-IBA070539 and NR070220 with significantly higher beta carotene levels

Pro-Vitamin A Cassava


Regional Trials and Breeders Meeting – West Africa and DRC

Government & Nonprofit

Strides in Building collaborations for cassava breeding