Graham McLaren GCP21-II, Kampala, Uganda 19 June 2012

1. Graham McLaren GCP21-II, Kampala, Uganda 19 June 2012

2. Vision The IBP will provide a one-stop-shop where breeders can access: • high-throughput breeding services, • logistics and data management tools, • an intuitive analysis pipeline, • breeding decision support tools, • support to use these facilities and • breeding communities of practice in order to deploy molecular breeding technology for sustainability and development.

3. What the IBP offers Access to Breeding Services: • well characterised and useful genetic resources • quality, economic high throughput genotyping • sophisticated phenotype and metabolite analyses Support services for: • planning and comparing breeding strategies • data management and curation and quality control • analysis and decision support • use of markers and molecular breeding techniques • phenotyping sites and protocols • use and protection of intellectual property Access to Informatics Tools and Resources: • for breeding logistics and data management • analysis and decision support for molecular breeding • accumulated public crop information of certified quality Capacity and Community Development: • support for communities of practice by crop or discipline • facilitation of germplasm exchange

4. The Integrated Breeding Portal • Convenient and flexible access to • Crop information • Crop breeding tools and services • Capacity building resources and opportunities • Community interaction • Relevant news and events Fred Okono

5. The IB Portal A One-stop Shop for Integrated Plant Breeding

6. Crop Information • Downloadable crop databases • Online crop database query interface • Trait dictionaries • Molecular markers • Other information

8. Informatics Tools for Crop Breeding • Project planning tools • Germplasm management tools • Field trial management tools • Genotypic data management tools • Data analysis tools • Breeding decision support tools • Supplementary toolbox

10. Breeding and Support Services • Breeding plan development • Genotyping & Marker • Phenotyping • Trait & Metabolite • Data Curation &Information Management • Design & Analysis • Genetic Resources • IP & Policy

12. Capacity building opportunities • Molecular breeding • Genebank management • Data analysis • Data & Information Management • Tool use – tutorials and manuals • Intellectual property and policy • eLearning System

14. Communities • Blogs • Forums • Live chat • Collaborative work • Community specific information • Bibliographic information

16. News and Events • IBP Update • Online news pages • Online events calendar and information pages • Social media – Facebook and Twitter

18. The Integrated Breeding Platform: Breeding Services Xavier Delannay and Chunlin He

19. AvailableSNP Markers for Genotyping • http://ibp.generationcp.org/confluence/display/MBP/Activity+3.1.2

20. Next steps • The GCP is planning to fingerprint 200-300 breeding lines with all available SNPs for each crop • Lines to be chosen in collaboration with CG centers and NARS breeders • The data will be uploaded on the IBP fingerprinting database to facilitate the integration of molecular breeding in the CG and NARS breeding programs

21. The Integrated Breeding Platform: Data Management and Informatics Services Arllet Portugal

22. Support Services - data management and curation: 1. Training in Informatics and Data Management • Eight training courses for different crop groups in 2010/11 2. Data Management Resources Developed • Trait Ontologies, Trait Dictionaries and Trial Templates have been developed for eight crops 3. Electronic Fieldbooks and Hand-held Devices • User cases trained on use of the FieldBook and Fieldlog and Hand-held devices distributed 4. Publication of Crop Information

23. Support Services - analysis and decision support. Fred van Eeuwijk and Marcos Malosetti, WUR: Training courses in Analysis and Decision Support Data Analysis Workshop, 7-11 June 2010,Zaragoza, Spain Simulation Workshop Jan 21-23 2011, CIMMYT Mexico Existing training material on the use of the GenStat analytical pipeline was updated to incorporate new developments released in the latest version of GenStat In parallel, a set of tutorials similar to those for GenStat were developed for the analytical facilities in R including Single and multiple site analysis GxE analysis QTL analysis QTLxE analysis and the use of Phenotypic and Molecular Indices.

24. The Integrated Breeding Platform: Tools for Breeding Logistics, Data Management, Analysis and Decision Support Graham McLaren

25. The IBP Configurable Workflow System Breeding Activities Project Planning Data Analysis Molecular Analysis Germplasm Evaluation Breeding Decisions Germplasm Management Open Project Specify objectives Identify team Data resources Define strategy Selected lines Recombines Recombination plans Parental selection Crossing Population development Experimental Design Fieldbook production Data collection Data loading Marker selection Fingerprinting Genotyping Data loading Quality Assurance Trait analysis Genetic Analysis QTL Analysis Index Analysis Analytical Pipeline Field Trial Management System Breeding Project Planning Breeding Management System Genotypic Data Management System Decision Support System MB design tool, Cross prediction and Strategic simulation Trial field book and environment characterization system Statistical analysis applications and selection indices MABC MAS MARS GWS Breeding nursery and pedigree record management Lab book, quality assurance and diversity analysis Breeding Applications Development of a Configurable Workflow System to support Integrated Breeding

26. The MARS Breeding Workflow

27. Field Trial Management System The IB FieldBook wizard takes you through eight steps required to construct a Trial Fieldbook by merging together a Trial Template, a Germplasm List and a Field Design

28. Decision Support Tools • MB Design Tool (MBDT) • MBDT available for planning MB experiment with data inputs from local files. • MAS decision tool • Marker aided selection processing facilities based on major known genes added to MBDT • MARS decision tool • OptiMAS – a tool for tracking and assembling favorable alleles at QTL through bi- and multi-allelic breeding populations.

29. The Integrated Breeding Platform: Communities NdeyeNdackDiop

30. 14 use cases selected as first phase users of IBP

31. Communities of Practice (CoP) • Use Breeding support through IBP to: • Bring together breeders and crop scientists • Share of knowledge • Initiate of MAS programmes in developing countries • Training on MAS • Training on Data management

32. Existing COPs • Rice in the Mekong region • Cassava in Africa • Data managers • Chickpea • Cowpea and Soybean Future plans • Bean • Maize • Sorghum • Rice in Africa • Rice in Asia