Statistics for the AustralianGrains Industry

Technical Report Series

Progress Report 2011-2012 forSAGI-2 project

Brian CullisProfessor of Biometry

School of Mathematics and Applied StatisticsFaculty of Informatics

University of Wollongong andMathematics Informatics and Statistics, CSIRO

email:bcullis@uow.edu.au

August 23, 2012

Contents

1 Achievements 1

1.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1.1.1 ILT Division . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1.1.2 RCP Division . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

1.1.3 SDI Division . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1.2 Milestones . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1.2.1 Milestone 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1.2.2 Milestone 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

1.2.3 Milestone 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.2.4 Milestone 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

1.2.5 Milestone 5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

1.2.6 Milestone 6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

1.2.7 Milestone 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

1.2.8 Milestone 8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

1.2.9 Milestone 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

1.2.10 Milestone 10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

1.2.11 Milestone 11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

1.2.12 Milestone 12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

1.2.13 Milestone 13 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

1.2.14 Milestone 14 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

2 Planned Research 17

2.1 ILT Division . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

2.2 RCP Division . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

2.3 SDI Division . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Bibliography 19

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1.1 Overview

1.1.1 ILT Division

In the 2011 season, a total of 716 trials comprising both NVT and breeders late stagetrials, were analysed by SAGI-2 biometricians. Means and weights from the single siteanalyses were uploaded into Katmandoo and the data files were ready for all crops forMET analyses by the agreed date of January 19, 2012. Fourteen MET analyses wereundertaken in total using agreed protocol.

Numerous reruns of the single site and MET analyses were required due to naming in-consistencies in some trials, which were only identified post-analysis. There was also alengthy delay to the wheat MET due to questions raised by some of the breeding com-panies. These concerns were addressed in detail through further analyses of the dataand meticulous reporting of the results, particular in relation to the comparisons of threevarieties. This required a comprehensive report to be tabled and discussed, authored byBrian Cullis and Alison Smith. All MET results were endorsed by crop champions andreturned to ACAS by February 8 for uploading onto the NVT website.

All quality data for 2005 to 2011 has been loaded into the Katmandoo database, withvariance component MET analysis completed for three wheat quality traits and canolaoil. A report was submitted to GRDC on future opportunities and recommendations forNVT quality analyses in April.

The key achievement for this milestone was SAGI-2’s involvement with the “Science ofSelection” workshop series conducted at Adelaide, Horsham and Wagga Wagga in August2011. These workshops were a huge success with Alison Smith preparing much of theoriginal material and Alison Smith and Alison Kelly presenting and refining the materialbased on feedback and anticipated audience technical background and knowledge. Thisexercise has led to improvments to the planned delivery of the new NVT-MET analysis andinformation system SAGI-2 are developing in conjunction with ACAS. We look forwardto our continued involvement in this work and in similar meetings.

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1.1.2 RCP Division

The mmontap website migration project has been completed. This project involved a sig-nificant contribution from Phil Testa, Senior Project Manager, IT Portfolio, InformationTechnology Services (ITS), The University of Wollongong (UOW), who worked with BevGogel and Damian Collins. An ITS-hosted mmontap virtual server is in place which issecure and regularly backed up. The ITS server has been fully configured and tested andall material from the original site has been loaded. There was minimal disruption of usersof the web-site throughout the migration. The same domain name has been retained (iewww.mmontap.org).

In July 2011 Professor Fred van Eeuwijk, Professor in Applied Statistics, Biometris, Wa-geningen University, the Netherlands, visited Australia to attend the Australian AppliedStatistics Conference (AASC) and present three QTL workshops. The first workshopwas a pre-conference activity and was held on July 11. Approximately 25 people at-tended the workshop comprising mainly conference delegates. Professor van Eeuwijk alsopresented an invited talk at the meeting. This meeting was sponsored by GRDC. Theconference web-site and workshop details are http://aasc2011.science.qld.gov.au/

pre-conference/default.htm.

The second QTL workshop was held at the University of Adelaide (UA), Waite Campus,on July 18-19. It was organised locally by Bev Gogel and was very well attended. Theattendance limit of 48 participants was achieved, with 35 from the UA, 9 from the ACPFGand the remainder either private or commercial.

The third and final QTL workshop was held at the University of Western Australia (UWA)in Perth on July 21-22. The workshop presented a flexible mapping approach for quan-titiative trait loci (QTL) and an introduction to the simulation of breeding strategies.It received support from UWA and CSIRO and was run at the International Centre forPlant Breeding Education and Research. The presenters were Fred van Eeuwijk, MarcosMalosetti, Assistant Professor in Applied Statistics, Biometris, Wageningen University,the Netherlands and Scott Chapman, Senior Scientist Crop Physiology and Simulation atCSIRO, Brisbane.

Preliminary research has been undertaken with Professor Robin Thompson. This workwas initiated after the AASC conference at Port Douglas in July 2011. At this meetingProfessor Thompson outlined an approach that can be easily implemented into ASRemland has the major advantage of significantly reducing the computational burden as thenumber of markers m, becomes large relative to the number of lines p. The approach hasbeen tested using a large data-set in wheat, comprising over 4,000 markers and approx-imately 400 lines. The standard approach took over 8 minutes per iteration comparedto the new approach which took 6 seconds per iteration. The memory required for thealternate approach relative to the standard approach was minimal with the implicationthat fitting more complex models to larger data-sets will be possible.

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This work will be completed by Colleen Hunt as a part of her PhD, in which severaldata-sets require genomic selection.

1.1.3 SDI Division

Experimental designs for plant improvement studies are often selected on an informalbasis, with due consideration to desirable properties such as replication, blocking, orthog-onality or connectedness. In practice, adjustments are sometimes made to experimentalprocedures if an off the shelf design does not quite fit the intended application. Opti-mal design allows flexible combinations of the design specification parameters for specialcases, and prespecified residual or treatment correlation structures. The software packageod is a freely available package which is currently under development and is availableas a β-version on request from David Butler. So far it’s use is mainly within the SAGI-2 project team as it is rapidly replacing sf DiGGeR as the design tool of choice. Thepackage allows for sensible specification of the linear mixed model using syntax similarto ASReml-R with user-friendly arguments and associated methods which allow generaldesign problems to be solved and operated on. Some designs which have been generatedrecently using od include glasshouse and ELISA slide designs for the LMA classificationnurseries, field trial designs for the prime hard project and complex multi-phase millingand baking designs involving the use of partial composites for the MAGIC population.

1.2 Milestones

1.2.1 Milestone 1

Description

Develop and implement a standard operating proceedure (SOP) for SAGI-2 support ofgrains industry research, development and extension projects. The SOP will involve aninitial assessment of the statistical requirements of each project, followed by the develop-ment and implementation of an appropriate action plan. The plan will encompass bothwithin-project capacity building and/or support from SAGI-2 biometricians. The effec-tiveness of the plan and client satisfaction will be monitored through annual follow-updiscussions with each project primary investigator.

Achievements

A SOP for provision of statistical support of grains industry research, development andextension is hereafter defined to be a document which presents detailed and written in-structions to achieve uniformity of the performance of members of the SAGI-2 project.The management team has put together a draft of the SOP for the SAGI project as awhole, as well as specific SOPs for each of the three divisions. Much of the draft SOPshave been based on the protocols and procedures that have been embedded within thework ethic of the SAGI project and carried forward to the SAGI-2 project. Some of thekey elements of this include:

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• Assessment of the nature of work to be done. This includes both significance,amount and technical content.

• Ensure that all preliminary meetings are minuted and SAGI-2 staff report back tothe relevant divisional leader with recommendations, timelines and an estimate ofresources required for completion of the work.

• Obtain agreement between client and SAGI-2 as to the nature and extent of thecollaboration with SAGI-2.

• Ensure that a minimum of two SAGI-2 staff are present at the design phase of theproject.

• Provide client with a full schedule of deliverables and timelines (and cost if appli-cable).

• Review SAGI-2’s knowledge and experience in the area and align available staff withproject if possible.

• Undertake project work with scheduled review points that align with either produc-tion of key outputs or payments.

• Production of outputs underpinned by a refereed SAGI-2 series report.

1.2.2 Milestone 2

Description

• Provide timely design and analysis for near-to-market research and extension projects(VSAP trials, herbicide/fungicide trials, NVT trials, GRDC-supported farming sys-tem/agronomy trials and disease resistance/tolerance trials).

• Provision of refereed reports and appropriate plain-english summaries to projectleaders and the broader grains industry upon completion of project activities.

• Attendance at key industry/technical meetings to support activities (wheat breedersassembly, barley technical symposium, ARAB conference, WQA and at least 1 PBAmeeting and 3 GRDC updates per annum).

Achievements

Design and analysis activities In the 2011 season, a total of 716 trials were anal-ysed by SAGI-2 biometricians, comprising both NVT and breeders late stage trials.Means and weights from the single site analyses were uploaded into Katmandoo,

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with the data files ready for all crops for MET analyses by the agreed date ofJanuary 19, 2012. Fourteen MET analyses in total were undertaken using agreedprotocol.

Numerous reruns of the single site and MET analyses were required due to naminginconsistencies in some trials, which were only identified post-analysis. Also, therewas a lengthy delay to the wheat MET due to questions raised by some of the breed-ing companies. These concerns were addressed in detail through further analyses ofthe data and meticulous reporting of the results, and in particular, the comparisonof three varieties. This required a comprehensive report to be tabled and discussed,authored by Brian Cullis and Alison Smith. All MET results were endorsed by cropchampions and returned to ACAS by February 8 for uploading onto the website.

All quality data for 2005 to 2011 has been loaded into the Katmandoo database,with variance component MET analysis completed for three wheat quality traitsand canola oil. A report was submitted to GRDC on future opportunities andrecommendations for NVT quality analyses in April.

A list of project activities is as follows:

• 2012 Canola Blackleg analysis. Chris Lisle - CL

• Linkages with Grower Solution groups: Agritech NSW - Analysis of crownrot inoculum trials and NGA, Toowoomba - Advice on statistical design andanalysis. Susan Fletcher - SF

• National Frost trials 2008-2011, DEEDI. SF

• Crown Rot phenotyping, DEEDI. SF

• Barley disease screening, DEEDI. SF

• Barley grain defects, DEEDI. SF

• Root architecture in wheat, QAAFI. Alison Kelly - AK

• National Lupin Breeding for Southern Australia. Katia Stefanova - KS

• Molecular Diagnostics Group (Nematodes), SARDI. Bev Gogel - BG

• Fababean Breeding program, Pulse breeding Australia. BG

• Vetch Breeding, SARDI. BG

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• New Variety Agronomy, SARDI. BG

Reports A list of SAGI-2 series reports which are completed and reviewed is as follows:

1. 2008-2010 A3H/A4H wheat MET for 2011 season (BG)

2. MET analysis of the 2010 S4 hard wheat data (BG)

3. MET analyses: Intergrain wheat 2011 (BG)

4. Design of 2011 Pratylenchus bioassay tests for NVT (BG)

5. Analysis of resistance and tolerance of cereal varieties to Pratylenchus andCCN: 2010 trials (BG)

6. Analysis of 2011 Pratylenchus bioassay tests for NVT (BG)

7. Analysis of tolerance of cereal varieties to Pratylenchus and CCN: 2011 trials(BG)

8. The effect on soil acidity through Managing Acid Soils Through Efficient Ro-tations (MASTER) Part I - unlimed section (CL)

9. Oat stage4 grain MET (CL)

10. Blackleg report for CAA (CL)

11. The effect on soil acidity through Managing Acid Soils Through Efficient Ro-tations (MASTER) Part II - Limed section (CL)

12. Gladius×Drysdale map construction (Paul Eckermann)

13. Wheat time of sowing 1998-2010 (CL)

14. How to handbook: Analysing NVT single site trials (CL)

15. Agritech NSW - Analysis of CR inoculum trials (SF)

16. Analysis of the National Frost Program data 2008-2011: For the final reporton frost resistance and testing methodology (SF)

17. Statistical approaches for the NVT MET analysis: faba beans 2011 (SF)

Meetings SAGI-2 staff members have attended and presented an invited session at each

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of the following meetings. The sessions covered interpretation of NVT trial resultsand current developments in statistical methodology, with the aim of informing bothindustry representatives and researchers at a level appropriate to their understand-ing.

1. Crown Rot project meeting, November 2011 (SF and AK)

2. Pulse Breeding Australia project meeting, October 2011 (Gabriela Borgognone- GB)

3. Canola Breeders meeting, February 2012 (AK)

4. Wheat Breeders meeting, March 2012 (BC, CL, AK)

5. GRDC Northern panel, December 2011 (GB)

6. GRDC Western panel, January 2012 (AK)

7. NVT advisory committee - West, April 2012 (AK)

8. GRDC updates, “Creating a level playing field for on-farm trials”, Dubbo andGoondiwindi, March 2012 (AK)

9. Wheat breeders assembly, Perth, August 2011 (Alison Smith - AS:oral)

10. ARAB, Wagga Wagga, August, 2011 (AS:oral)

11. Australasian Applied Statistics Conference, Cairns, 2011 (BC:(oral, workshop),PE:oral, SF:oral, BG:oral, AS:oral, DB:workshop, Arthur Gilmour - AG)

12. Biometrics, Kiama, 2011 (SF:oral, PE, BC-(workshop,invited/oral), AS, DB:(oral,workshop) AG:oral, AK:oral, KS:oral, BG:oral)

1.2.3 Milestone 3

Description

Develop and deliver in-region statistical training modules for near-to-market researchers,advisors and grower groups. A minimum of 3×1day and 6×2day workshops to be deliveredper year in each of three GRDC regions and distributed across key stakeholder groups,including Regional Cropping Solution Groups (RCSG), farming systems groups, NVTusers, PBA and organisations performing critical near-to-market functions (eg. pilotbrewing). Coordination of in-region training activities will be made by interaction throughRCSG coordinators and GRDC regional Grower Services Managers.

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Achievements

The key achievement for this milestone was SAGI-2’s involvement with the “Science ofSelection” workshop series conducted at Adelaide, Horsham and Wagga Wagga in August2011. These workshops were a huge success with Alison Smith preparing much of theoriginal material and Alison Smith and Alison Kelly presenting and refining the materialbased on feedback and expected audience technical background and knowledge. Thisexercise has led to improvments to the planned delivery of the new NVT-MET analysis andinformation system SAGI-2 are developing in conjunction with ACAS. We look forwardto our continued involvement in this work and in similar meetings.

Progress on preparation and delivery of training materials has been limited due to thedelay in finalising a contract for SAGI-2. One FTE has not yet been appointed and therole of this position is specifically NVT and training. Chris Lisle only commenced atCharles Sturt University (CSU) in January, creating a further shortfall in delivery of ILT.Furthermore, the external consultancies undertaken by Bev Gogel and DEEDI staff havetaken resources from ILT at the expense of developing training material. The milestoneof delivering all training courses in this financial year will not be met.

However, there have been some successes with the limited staff available and some achieve-ments incluide:

• Contact has been made with Elders to scope the training needs of their Agronomygroup.

• Presentation of information sessions has been widespread, and this phase has pavedthe way for further project linkages and networks for delivery of training. For ex-ample, talks with the private agronomy company linking the three northern groups:northern grower alliance, Emerald farming systems group in DEEDI and GOA, hasresulted in a plan for SAGI-2 training at their next meeting.

1.2.4 Milestone 4

Description

• Co-ordinate a revision of the statistical methods and statistical reasoning coursesoffered at Charles Sturt University (CSU) and offer these courses to a wider audience(linked to UW00004).

• Provision of support at the University of WA (UWA) to advise higher degree stu-dents in Agriculture and present Applied Statistics workshops to them.

• Provision of support for Dr O Kravchuk at the University of Adelaide (UA) to en-able development of Applied Statistics training workshops for Agricultural scientists(linked to UW00004). Utilise UOW, CSU, UWA and UA service course material to

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foster collaboration with other universities in the provision of undergraduate andpostgraduate statistics and biometry courses.

Achievements

CSU There has been significant challenges meeting this milestone with the delay in ap-pointing the additional staff member at CSU, as a large component of the new ap-pointment’s role is based on the delivery of this milestone. Despite this, ProfessorKen Russell has made significant progress with revising some of the key statisti-cal modules offered to undergraduate students studying agriculture at CSU. A fullreport has been provided to the progress report for the companion GRDC fundedproject, UW0004. Copies of this report can be obtained on request.

UWA This activity is also linked to UW0004. A brief overview of activities thus far is:

• Modules on Experimental Design and ANOVA, Students Year 4, Unit SCIE4401,Faculty of Natural and Agricultural Sciences, UWA.

• Module on Linear Mixed Models, Students Year 4, Unit SCIE4402, Faculty ofNatural and Agricultural Sciences, UWA.

• “Spatial Variation and Statistical Analysis of Field Trials” at AusAID-sponsoredshort course (5-weeks) of Iraq Partnership Facility: Crop Improvement for Iraq,3 October 2011.

UA This activity is also linked to UW0004. Much focus has been centred on the prepara-tion and planning for the workshop on Statistical consulting linked to the AustralianStatistics Conference which was held in Adelaide in July 2012. A full report in thisworkshop has been included in the progress report for 2011/12 for the UW0004project. Copies of this report can be provided on request.

1.2.5 Milestone 5

Description

Upgrade and relocate the MMonTAP website to UOW. Implement a fully functionalweb-based report series to:

• Account for SAGI staff time allocation to research areas (to also be used for GRDCprogress reporting)

• Facilitate internal interaction between SAGI members

• Provide R,D & E clients with peer-reviewed reports relating to work conducted forthem

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Populate the web-site with training materials, software downloads, howto guides, courseand workshop materials, upcoming news and events and current research topics.

Achievements

The mmontap website migration project has been completed. This project involved a sig-nificant contribution from Phil Testa, Senior Project Manager, IT Portfolio, InformationTechnology Services (ITS), UOW, who worked with Bev Gogel and Damian Collins. AnITS-hosted MMontap virtual server is in place which is secure and regularly backed up.The ITS server has been fully configured and tested and all material from the originalsite has been loaded. There was minimal disruption of users of the web-site throughoutthe migration. The same domain name has been retained (ie www.mmontap.org).

1.2.6 Milestone 6

Description

Application of the SAGI-2 SOP (Milestone 1) to all GRDC strategic and/or appliedresearch projects and pre-breeding projects involving SAGI-2 collaboration. Ensure thatthe statistical components of each project are met in accordance with the project Outputand Milestone timelines. See attachment AA for assignment of SAGI-2 staff to GRDC R,D & E areas.

Achievements

A SOP for provision of statistical support to all GRDC strategic and/or applied researchprojects and pre-breeding projects has been defined to be a document which presentsdetailed and written instructions to achieve uniformity of the performance of a membersof the SAGI project. The management team has put together a draft of the SOP forthe SAGI project as a whole, as well as specific SOPs for each of the three divisions.Much of the draft SOPs have been based on the protocols and procedures that have beenembedded within the work ethic of the SAGI project and carried forward to the SAGI-2project. Some of the key elements of this include:

• Assessment of the nature of work to be done. This includes both significance,amount and technical content.

• Ensure that all preliminary meetings are minuted and SAGI-2 staff report back tothe relevant divisional leader with recommendations, timelines and an estimate ofresources required for completion of the work.

• Obtain agreement between client and SAGI-2 as to the nature and extent of thecollaboration with SAGI-2.

• Ensure that a minimum of two SAGI-2 staff are present at the design phase of the

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project.

• Provide client with a full schedule of deliverables and timelines (and cost if appli-cable).

• Review SAGI-2’s knowledge and experience in the area and align available staff withproject if possible.

• Undertake project work with scheduled review points that align with either produc-tion of key outputs or payments.

• Production of outputs underpinned by a refereed SAGI-2 series report.

1.2.7 Milestone 7

Description

Develop and deliver a minimum of 2×2 day specialist (researcher/breeder focussed) train-ing workshops per year covering QTL analysis, whole-genome selection methodologies,advanced software application and other areas based upon need (areas will be identifiedthrough Milestones 1, 2 and 6). Bi-annual presentation of specialist workshops involvingleading international collaborators to ensure locally applied methods are of an interna-tional standard. The frequency of topic coverage to be based on demand, release of newsoftware and implementation of new statistical methods.

Achievements

In July 2011 Professor Fred van Eeuwijk visited Australia to attend the Australian Ap-plied Statistics Conference (AASC) and present three QTL workshops. The first work-shop was a pre-conference activity and was held on July 11. Approximately 25 peopleattended the workshop comprising mainly conference delegates. Professor van Eeuwijkalso presented an invited talk at the meeting. This meeting was sponsored by GRDC.The conference web-site and workshop details are http://aasc2011.science.qld.gov.

au/pre-conference/default.htm.

The second QTL workshop was held at UA, Waite Campus, on July 18-19. It was or-ganised locally by Bev Gogel and was very well attended. The attendance limit of 48participants was achieved, with 35 from the UA, 9 from the ACPFG and the remaindereither private or commercial.

The third and final QTL workshop was held at the University of Western Australia (UWA)in Perth on July 21-22. The workshop presented a flexible mapping approach for quan-titiative trait loci (QTL) and an introduction to the simulation of breeding strategies.It received support from UWA and CSIRO and was run at the International Centre forPlant Breeding Education and Research. The presenters were Fred van Eeuwijk, Marcos

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Malosetti, Assistant Professor in Applied Statistics, Biometris, Wageningen University,the Netherlands and Scott Chapman, Senior Scientist Crop Physiology and Simulation atCSIRO, Brisbane.

The course was aimed at graduate students and professionals interested in a flexible QTLmapping approach in GenStat applicable to single traits in single environments as wellas to multiple traits and multiple environments, for standard bi-parental populations aswell as association panels and multi-parent populations. In addition, the simulation ofbreeding strategies provided an introduction to the QuGene software.

QTL mapping was introduced as an extension of mixed model analysis of single traits insingle trials. The calculation of these genetic covariates was explained for various typesof populations: inbreeders, outbreeders and association panels. After mixed model QTLanalysis for single traits in single trials, extensions were described for multiple trials andmultiple traits. Hands on QTL analyses utilized Windows menus in GenStat.

By the end of the course the participants were able to:

• Construct a genetic map from marker scores on different types of breeding popula-tions

• Perform a QTL analysis for a wide array of breeding populations, for single andmultiple environments, and for single and multiple traits

• Use various inference procedures for assessing QTL evidence

• Report QTL locations and effects

• Formulate and evaluate breeding strategies given QTL locations and effects.

There were 18 participants who attended the course, with most from UWA (9) andDAFWA (4). The feedback was vey positive with the average rating for all componentsof the course exceeding 4 (on a 5 point scale: 1 very bad to 5 very good).

1.2.8 Milestone 8

Description

Internal capacity and staff development.

• Completion of PhD studies by David Butler on optimal design

• Completion of PhD studies by Alison Kelly on use of factor analytic and othersingular variance models in plant breeding

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• Enrolment of Colleen Hunt in PhD studies on advanced statistical methods forhybrid breeding programs

• Engage Arthur Gilmour for ASReml development.

Achievements

David Butler was granted study for four days per week by DAFF to concentrate oncompleting his PhD. Since this time there has been significant progress made towardssubmission. The working title of the thesis is “On the Optimal Design of ExperimentsUnder the Linear Mixed Model”. Two additional papers are in preparation which add tothe three already published from the PhD making the thesis a very worthy award. Thesubmission date is the end of January 2013.

Alison Kelly has also made good progress towards completion of her PhD. This workingtitle is “Reduced rank variance models in a linear mixed model framework” and is plannedto be completed by December 2012.

Colleen Hunt has commenced her PhD studies and enrolled in November 2011 (part time)at the University of Queensland, School of Agriculture and Food Science. The workingtitle at the time of enrolment was “Statistical analysis of sorghum breeding trials withcomplex genetic components”. Her supervisors are David Jordan and Brian Cullis. Onepaper is under revision and another in preparation.

Arthur Gilmour has been employed as a Senior Research Fellow at UOW since 2010.His funding is secure as UOW and VSN International (the owners of the ASReml IP)have entered into a long-term research agreement in which UOW provides support forASReml.

1.2.9 Milestone 9

Description

Cluster based approach to NVT-MET will be developed and tested. Approach will beapplied to each of the NVT crops in collaboration with key stakeholders and breeders.New approach will be reviewed on an annual basis. Initiate a whole-industry approach tothe provision of information from these new methods.

Achievements

Some progress towards this milestone has been made. Brian Cullis presented an invitedtalk at the Biometrics by the Blowholes, Australasian Region of The International Biomet-ric Society Conference, Kiama, NSW which was held in December 2011. The underylingprinciples of implementing the new MET analysis have been resolved. An internal work-shop was conducted in May 2012 to inform those within SAGI-2 of progress and the

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outstanding tasks to be completed. Each biometrician is now undertaking a retrospectiveanalysis of each crop for each year to prepare for the next and final stage which dependson the development of an algorithm to groups trials with similar factor loadings withina year. Development of this algorithm is technically challenging and requires at leastsix weeks input from Brian Cullis. He intends to spend whatever time is needed for theremainder of 2012 to complete this work, given that we are committed to implementationof the new MET analysis for the upcoming NVT season.

1.2.10 Milestone 10

Description

Software conversion of GENSTAT procedures to R for

• Mixed model QTL mapping facilities: source code & documentation (includingworked examples) for a) diploid biparental populations single trait & single envi-ronment and for multiple traits and/or environments

• As above but for multi-cross populations, like, for example, nested association map-ping populations (star design populations), diallel populations, and for multi-parentpopulations and association panels

• As above plus including additional full or partial pedigree/kinship information ifavailable

Work closely with Wageningen group.

Achievements

There has been no progress towards this milestone for this report.

1.2.11 Milestone 11

Description

Review existing methods for genomic selection (GS) and develop new methods for GS withability to model non-genetic variation and GxE interaction. This work to be performedin collaboration with Professor Robin Thompson.

Achievements

Preliminary research has been undertaken with Professor Thompson. This work wasinitiated after the AASC conference at Port Douglas in July 2011. At this meetingProfessor Thompson outlined an approach which can be easily implemented into ASRemland has the significant advantage that the computational burden can be significantly

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reduced as the number of markers m, becomes large relative to the number of lines p.The approach has been tested using a large data-set in wheat which comprised over 4,000markers and around 400 lines. The standard approach took over 8 minutes per iterationcompared to the new approach which took just 6 seconds per iteration. The amountof memory required for the alternate approach was minimal implying that fitting morecomplex models to larger data-sets will be possible.

This work will be completed by Colleen Hunt as part of her PhD, where there are severaldata-sets in place that require GS.

1.2.12 Milestone 12

Description

New release of ASReml software, namely ASReml 4 in 2012. This release requiresimproved R documentation and UOW and VSN will work together on this. Agreementwith VSN in place to allow free access for academic use to open the way for ASReml tobe used as a teaching tool in new courses developed in this project. See other milestones.

Achievements

The new release of ASReml will occur in December at the AASC 2012 meeting to beheld at Queenstown. Bev Gogel has been contracted by VSN for 10% of her time for theperiod from July 2012 to December 2012 to help complete the documentation.

1.2.13 Milestone 13

Description

Collaboration with Professor Thompson and Dr. Hackett to continue extensions of tech-niques for identification of QTLs in complex experiments and genetic designs includingexperiments with multiple treatments.

Achievements

Another paper has been recently published which considers QTL×E or QTL×T, whereE and T are environments or traits respectively. This paper is joint work between BrianCullis and Ari Verbyla and extends the WGAIM approach. Further work will considerthe extension of the model described in the previous section to multi-environment ormulti-trait data-sets.

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1 Achievements

1.2.14 Milestone 14

Description

Contribute to a mid-term, independent technical and strategic GRDC review of the SAGI-2 program as directed by the relevant GRDC manager.

Achievements

NIL

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2 Planned Research

2.1 ILT Division

Many of the planned activities for the ILT division remain focussed on the existing list ofclients and activities. Staff of the division will remain active in attending and presentingat relevant meetings. Two examples include an oral presentation at the AustralasianWeeds Conference, Melbourne, 2012 and papers for the Soil-bourne diseases conference,Fremantle, 2012.

The NVT quality data for 2005 to 2011 has been loaded into the Katmandoo database,with variance component MET analysis completed for three wheat quality traits andcanola oil. We plan to undertake a more comprehensive study to examine the feasibiltiyof undertaking a formal analysis of receival traits for wheat and barley and key qualitytraits in canola annually as is currently done for yield. Funds have been allocated for thispurpose for the next twelve months.

With the appointment of the new position at CSU there will be a concerted effort todeliver on the development and delivery of industry based training modules. Contact hasbeen made with Elders to scope the training needs of their Agronomy group and alongwith the preliminary discussions with private agronomy groups we area confident that wecan establish the linkages for our training package to deliver.

There has also been much activity with SAGI-2 staff working directly with private indus-try. Three significant contracts have been established and the work will continue over thenext year. These include the following:

• Intergrain - Bev Gogel undertook a five month contract with Intergrain to analysetrial data from their wheat and barley breeding programs. The 2011 trials werecombined in a multi-environment trial analysis with trials from previous years, usinga factor analytic model to produce cluster summaries of genotype by environmentinteraction and prediction of genotypic performance and stability. The agreementhas been renewed for 2012 and covers statistical design and analysis of wheat andbarley trials from the breeding programs.

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2 Planned Research

• Longreach - A contract with Longreach Plant Breeding has been negotiated withBertus Jacobs for statistical design and analysis of wheat breeding trials. Stage 1trials were analysed from the 2011 season. Design and analysis of stage 1 and 2 trialsis planned for the 2012 season. The agreement is that each year an additional stageof testing will be added to the statistical design and analysis provided by SAGI-2until the entire program is utilising best practice statistical methodologies.

• Pacific Seeds - A five month contract is currently underway providing statisticalsupport to canola, maize and sorghum programs in Pacific Seeds. The agreementcovers both the breeding and research groups and marketing and extension teams.At the end of the five month period, part of the work will be re-negotiated to staywith SAGI-2 and the majority of statistical support will be passed back to theirbiometrician who is currently on leave.

2.2 RCP Division

The focus of the RCP division remains to underpin GRDC’s near-to-market researchwith high quality statistical support. Significant progress has been made with the Frostresearch programme and a detailed report is in preparation which outlines an approachto the design and analysis of the frost benchmarking trials. This report also discussesoptions for improving the current protocol which are aimed at reducing the amount ofwithin plot variability which is the dominant source of variation in these data-sets.

Some other activities for the coming year include:

• The new MET analysis for the NVT yield data will be developed, published andimplemented this year.

• Attendance at the Australasian Applied Statistics Conference in December 2012 -invited papers from Brian Cullis and Julian Taylor, workshop presented by BrianCullis and Sue Welham, talks from other SAGI project staff. GRDC are majorsponsor.

• Release of ASReml 4 in December.

• Attendance at XVth meeting of the Eucarpia section - Biometrics in plant breedingto be held 5-7 September at Stuttgart Germany. Bev Gogel and Brian Cullis willpresent talks.

• Attendance at International Biometric Conference to be held from 27-31 August atKobe Japan - Brian Cullis will chair the inaugural planning meeting for the Inter-national Scientific Programme Committee for the next IBC to be held at Florence,Italy in 2014.

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2 Planned Research

• Visits to Rothamsted UK in September and October - Brian Cullis, Alison Smith,David Butler and Bev Gogel will work on a range of problems spanning the newMET analysis, the analysis of large MET data-sets with pedigree information, ge-nomic selection and the release of ASReml 4 and associated documentation. Workwith Professor van Eeuwijk will be undertaken on conversion of GENSTAT QTLroutines into R.

• New protocols for frost research to be implemented and published - Paul Eckermannwill lead this work.

• Submission of PhD theses for David Butler and Alison Kelly.

• Submission of papers describing the design of multi-phase experiments with partialcompositing.

2.3 SDI Division

The main acitivity will involve the release of ASReml 4 and commencement of work toconvert GENSTAT QTL facilities into R.

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