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

2. Vision The IBP will provide a one-stop-shop where breeders can access: high-throughput breeding services, high-throughput breeding services, logistics and data management tools, logistics and data management tools, an intuitive analysis pipeline, an intuitive analysis pipeline, breeding decision support tools, breeding decision support tools, support to use these facilities and support to use these facilities and breeding communities of practice 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 : Trait Ontologies, Trait Dictionaries and Trial Templates have been developed for: Maize - http://ibp.generationcp.org/confluence/display/MBP /Maize http://ibp.generationcp.org/confluence/display/MBP /Maize Wheat - http://ibp.generationcp.org/confluence/display/MBP/Wheat http://ibp.generationcp.org/confluence/display/MBP/Wheat Rice - http://ibp.generationcp.org/confluence/display/MBP/Ricehttp://ibp.generationcp.org/confluence/display/MBP/Rice Sorghum - http://ibp.generationcp.org/confluence/display/MBP/Improved+Sorghum http://ibp.generationcp.org/confluence/display/MBP/Improved+Sorghum Cassava- http://ibp.generationcp.org/confluence/pages/viewpage.action?pageId=20449469 http://ibp.generationcp.org/confluence/pages/viewpage.action?pageId=20449469 Cowpea - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Cowpeas) http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Cowpeas) Chickpea - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Chickpeas) http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Chickpeas) Common Bean - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Beans) http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Beans) Groundnut - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Groundnuts) http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Groundnuts) 2. Data Management Resources Developed

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: 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 4. Comments about the use of hand-held devises

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/http://rice.generationcp.org/germplasm-dev/ Wheat - http://iwis.cimmyt.org/http://iwis.cimmyt.org/ Maize - http://imis.cimmyt.org/http://imis.cimmyt.org/ Cowpeas - http://ibp.generationcp.org/ivis/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 1.Maintenance and support for existing informatics tools Bug fixes and New Features

12. The IBP Configurable Workflow System Breeding Activities Parental selection Crossing Population development Germplasm Management Open Project Specify objectives Identify team Data resources Define strategy Project Planning Experimental Design Fieldbook production Data collection Data loading Germplasm Evaluation Marker selection Fingerprinting Genotyping Data loading Molecular Analysis Quality Assurance Trait analysis Genetic Analysis QTL Analysis Index Analysis Data Analysis Selected lines Recombines Recombination plans Breeding Decisions MB design tool, Cross prediction and Strategic simulation Breeding Project Planning Breeding nursery and pedigree record management Breeding Management System Trial field book and environment characterization system Field Trial Management System Genotypic Data Management System Statistical analysis applications and selection indices Analytical Pipeline MABC MAS MARS GWS Decision Support System Breeding Applications Lab book, quality assurance and diversity analysis 2. Development of a Configurable Workflow System to support Integrated Breeding to support Integrated Breeding

13. The MARS Breeding Workflow

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

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

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

17. 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

18. Eight Steps to follow to create a Fieldbook

19. Users can sort and scroll the this table as well as save it or export it for use in hand-held data gathering devices. These steps produce a Measurements Table Bar-coded labels can also be prepared for printing.

20. Development stages of the IB Fieldbook I I 1234512345 6a6b Basic mock-up (MU) Stages 2&3 iteration (3–4weeks) Functional MU: α & β prototypes Stand-alone version (Java, C ++, etc) Coordination parameters for the user interface 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 Integrated version in iPLant Cyber-infrastructure User interactions

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

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

23. 3. Technical Design – Jan 2011

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

25. 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

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

27. 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

28. 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

29. 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.

31. 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)

33. Communication Communication strategy drafted, incorporating feedback from launch meeting + input from Communications and Marketing Advisor on SiMAC (Nancy White) Communication strategy drafted, incorporating feedback from launch meeting + input from Communications and Marketing Advisor on SiMAC (Nancy White) Branding the project: name and logo 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 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 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 Logo colours and art direction representative of water, farming, people, productivity and integration

34. Public awareness (PA) 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 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

35. 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)