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

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.

What the IBP offers Access to Breeding Services: Support services for: 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

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

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

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

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

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

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

Communities Blogs Forums Live chat Collaborative work Community specific information Bibliographic information

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

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

Available SNP Markers for Genotyping http://ibp.generationcp.org/confluence/display/MBP/Activity+3.1.2 Crops Partners # SNPs Status Maize Converted by CIMMYT in early 2010 1250 Available for genotyping Cowpea University of California Riverside - Jeff Ehlers 1122 Chickpeas ICRISAT - Rajeev Varshney 2005 Pigeonpeas 1616 Rice IRRI - Michael Thomson et al. 805 More to be added soon Cassava IITA - Morag Ferguson, P. Rabinowicz 1740 Sorghum EMBRAPA - Jurandir Magalhaes CIRAD - Jean-Francois Rami 1407 Common bean  USDA – Perry Cregan; CIAT – S. Beebe 1577 Conversion in progress Wheat  CIMMYT – Susanne Dreisigacker 2000 Available by end of 2011

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

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

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

Support Services - analysis and decision support 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.

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

The IBP Configurable Workflow System Breeding Applications Development of a Configurable Workflow System to support Integrated Breeding 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 Evaluation Marker selection Fingerprinting Genotyping Molecular Analysis Quality Assurance Trait analysis Genetic Analysis QTL Analysis Index Analysis Data Selected lines Recombines Recombination plans Breeding Decisions MB design tool, Cross prediction and Strategic simulation Breeding Project Breeding nursery and pedigree record management System Trial field book and environment characterization system Field Trial Genotypic Data Statistical analysis applications and selection indices Analytical Pipeline MABC MAS MARS GWS Decision Support System Breeding Applications Lab book, quality assurance and diversity analysis

The MARS Breeding Workflow

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

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.

The Integrated Breeding Platform: Communities Ndeye Ndack Diop

14 use cases selected as first phase users of IBP 30

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 Having in mind GCP sun set it is important for GCP to identify and implement way to make available GCP research products to a large number of scientists in the world. CoP has been identify as one way to get there but also as a user case of the IBP.

Existing COPs Future plans 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