The Integrated Breeding Platform: Progress and Perspectives

1. The Integrated Breeding Platform:Progress and Perspectives Graham McLaren IBP Annual Meeting 1st-3rd June 2011 Wageningen, Netherlands

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 will offer 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. Breeding Services • Strategies to implement Integrated Breeding (IB) in developing countries • Identification and engagement of genotyping service laboratories to support IB • Conversion of marker technologies for breeders to flexible SNP platforms • Facilitate access to high quality and timely genotyping services through the service laboratories

5. Support Services - data management and curation: 1. Training in Informatics and Data Management • Sorghum CI Data Management Workshop, • 2010 May 11-13, Eldoret, Kenya • Informatics Workshop for IBP Data Managers, • 2010 May 31- June 4, Zaragosa, Spain • Cassava CI Data Management Workshop, • 2010 July 19 – 21, Accra, Ghana • Tropical Legumes 1 Data Management Workshop, • 2010 August 25-27, Madrid, Spain • Wheat CI-India Data Management Workshop, • 2010 September 13-16,New Delhi, India • Wheat CI-China Data Management Workshop, • 2010 October 25-28, Beijing, China • West Africa Use Cases Data Management Worskhop, • 2011 February 7-11, IITA, Nigeria

6. Support Services - data management and curation: 2. Data Management Resources Developed • Trait Ontologies, Trait Dictionaries and Trial Templates have been developed for: • Maize - http://ibp.generationcp.org/confluence/display/MBP /Maize • Wheat - http://ibp.generationcp.org/confluence/display/MBP/Wheat • Rice - http://ibp.generationcp.org/confluence/display/MBP/Rice • Sorghum - http://ibp.generationcp.org/confluence/display/MBP/Improved+Sorghum • Cassava- http://ibp.generationcp.org/confluence/pages/viewpage.action?pageId=20449469 • Cowpea - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Cowpeas) • Chickpea - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Chickpeas) • Common Bean - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Beans) • Groundnut - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Groundnuts)

7. Support Services - data management and curation: 3. Electronic Fieldbooks and Hand-held Devices • Chickpea – Pooran Gaur (Honeywell) • Groundnuts – Vincent Vadez (Honeywell) • Cowpea – Jeff Ehlers (HP iPAQ) • Cowpea - Ousmane Boukar (Honeywell) • Bean – Matthew Blair (Honeywell) • Cassava – Jorge Franco (HP iPAQ) • Cassava – Emmanuel Okogbenin (HP iPAQ) • Rice – Ibnou Deang (HP iPAQ) • Rice - Tianqing Zheng (HP iPAQ) • Wheat - Ang Li (HP iPAQ) • Wheat – TR Sharma (HP iPAQ) • Sorghum – Niaba Teme (HP iPAQ) • Sorghum – Ibrahima Sissoko (HP iPAQ)

8. Support Services - data management and curation: 4. Comments about the use of hand-held devises • It was easy, simple and straight forward. However, the difficulty faced by some is in synchronizing the handheld with the PC because of configuration option • The screen and keyboard are small and the battery life is short • It increases efficiency and minimize data error because it saves time entering the data and they are already recorded in a format in which it can be used • There is an issue about collection of data for multiple samples • It is being suggested to look into other mobile device like tablet PC

9. Support Services - data management and curation: 5. Publication of Crop Information • A generic Web query interface for Crop Information has been under continued development and is deployed for: • Rice – http://rice.generationcp.org/germplasm-dev/ • Wheat - http://iwis.cimmyt.org/ • Maize - http://imis.cimmyt.org/ • Cowpeas - http://ibp.generationcp.org/ivis/ • Central Crop Information Databases have been implemented for: • Cassava, Cowpea, Common Bean • Web access will be extended and consolidated in the IB Portal

10. Support Services - analysis and decision support: 1. Training courses in Analysis and Decision Support Data Analysis Workshop, 7-11 June 2010,Zaragoza, Spain Simulation Workshop Jan 21-23 2011, CIMMYT Mexico

11. Informatics Tools and Services • Maintenance and support for existing • informatics tools Bug fixes and New Features

12. 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 2. Development of a Configurable Workflow System to support Integrated Breeding

13. The MARS Breeding Workflow

14. Functionalities and timeline for the Stand-alone Configurable Workflow System

15. Application 1: Configuration and Customization - The IB Workbench

16. Application 2: 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

17. Development stages of the IB Fieldbook I 12345 Documentation of the structure and functionality of the tool Graphical representation of the tool workflow annotated flow diagrams Development of corresponding algorithms to run the analysis Basic mock-up (MU) Stages 2&3 iteration (3–4weeks) Functional MU: α & β prototypes User interactions Coordination parameters for the user interface 6a 6b Integrated version in iPLant Cyber-infrastructure Stand-alone version (Java, C ++, etc)

18. Integrated Breeding Field Book 1. Functionalities design – Dec 2010 Reviewed in CIMMYT Jan 2011 and at San Diego Jan 2011 http://wiki.cimmyt.org/confluence/display/MBP/Objective%202.3%20IBFB

19. 2. Informatics Architecture – Dec 2010 Reviewed at San Diego Jan 2011

20. 3. Technical Design – Jan 2011

21. 4. User Interface Mockup – Jan 2011 Reviewed by breeders at CIMMYT

22. 5. Alpha Prototype – Feb 2011 Reviewed by data managers at IITA WS- Feb Distributed to IBP Use Cases – Mar Tested by Data Managers at ICRISAT WS - Mar Tested by breeders at TL1 - Apr

23. 6. Stand-alone Beta Version – May 2011 To be tested by breeders at IBP WS - May

24. Application 4: Genotyping Data Management System • Team established between ICRISAT and IRRI led by Trushar Shah • to convert the ICRIS web-based genotyping system to a stand-alone system • improve integration of the system with sample tracking and genealogy management components • developing data loading algorithms • load data for different use case crops • improve and expand the user query interface

25. Application 4: Analytical Pipeline Statistical Methodology • Experimental design • Generate basic designs with R connected to the Fieldbook • Phenotype analysis • Genetic variance analysis, single site and multi-site analysis available in GenStat and R • QTL analysis • QTL and QTLxE analysis tools with tutorials available in Genstat and R • Selection Indices • Phenotype Selection Indices available in R scripts

26. Application 5: 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.

28. Application 6: Simulation Tools • Stand-alone versions of simulation programs available for use with manuals and training material for: • inbred line development (QULine) • hybrid development and (QUHybred) • MARS schemes (QUMARS)

30. Communication Communication strategy drafted, incorporating feedback from launch meeting + input from Communications and Marketing Advisor on SiMAC (Nancy White) Branding the project: name and logo Name change from Molecular Breeding Platform to Integrated Breeding Platform, following recommendations from participants at launch meeting in Feb 2010 Name choice a consultative process between GCP MT, UC and SiMAC, with MT presenting 3 choices to UC and SiMAC Logo colours and art direction representative of water, farming, people, productivity and integration

31. Public awareness (PA) Press releases and feature stories written and circulated widely Brochure, bookmarks and posters to present IBP to a non-technical audience Website: alpha version • Going forward • Phase I (early years): continue focus on supporting the development of the platform, and dissemination (new products, user testimonies, etc) • Phase II: communications to support building membership, usage and support for IBP

32. Capacity Building and Community Development • Fledgling IB Portal • Training courses in marker technology, data management, statistical analysis, simulation, phenotyping and farm management • Communities of practice established: • Rice biotechnology (since 2005) • Cassava research and breeding (since) • Breeding Informatics (since 2010) • Chickpea Integrated Breeding (since 2011) • Cowpea Integrated Breeding (since 2011)