Graham McLarenGCP21-II, Kampala, Uganda19 June 2012

VisionThe 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 offersAccess 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

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

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

Crops Partners # SNPs StatusMaize Converted by CIMMYT in early 2010 1250 Available for genotyping

CowpeaUniversity of California Riverside - Jeff Ehlers 1122 Available for genotyping

Chickpeas ICRISAT - Rajeev Varshney 2005 Available for genotyping

Pigeonpeas ICRISAT - Rajeev Varshney 1616 Available for genotyping

Rice IRRI - Michael Thomson et al. 805Available for genotypingMore to be added soon

Cassava IITA - Morag Ferguson, P. Rabinowicz 1740 Available for genotyping

Sorghum EMBRAPA - Jurandir MagalhaesCIRAD - Jean-Francois Rami 1407 Available for genotyping

Common bean  USDA – Perry Cregan; CIAT – S. Beebe 1577 Conversion in progress

Wheat  CIMMYT – Susanne Dreisigacker 2000 Available by end of 2011

Available SNP Markers for Genotypinghttp://ibp.generationcp.org/confluence/display/MBP/Activity+3.1.2

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

3. Electronic Fieldbooks and Hand-held Devices

• Trait Ontologies, Trait Dictionaries and Trial Templates have been developed for eight crops

• 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. Fred van Eeuwijk and Marcos Malosetti, WUR:

Training courses in Analysis and Decision Support

Data Analysis Workshop, 7-11 June 2010,Zaragoza, SpainSimulation 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 Activities

Parental selectionCrossingPopulation development

GermplasmManagement

Open ProjectSpecify objectivesIdentify teamData resourcesDefine strategy

Project Planning

Experimental DesignFieldbook productionData collectionData loading

GermplasmEvaluation

Marker selectionFingerprintingGenotypingData loading

MolecularAnalysis

Quality AssuranceTrait analysisGenetic AnalysisQTL AnalysisIndex Analysis

DataAnalysis

Selected linesRecombinesRecombination plans

BreedingDecisions

MB design tool,Cross predictionand Strategic simulation

Breeding ProjectPlanning

Breeding nurseryand pedigreerecordmanagement

Breeding Management

System

Trial field bookand environment characterizationsystem

Field Trial Management

System

Genotypic DataManagement

System

Statistical analysisapplications andselection indices

AnalyticalPipeline

MABCMASMARSGWS

Decision Support System

Breeding Applications

Lab book,quality assuranceand diversityanalysis

Development of a Configurable Workflow System to support Integrated Breeding

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

Beans  S. Beebe Africa: Ethiopia, Kenya, Tanzania, MalawiCassava  E. Okogbenin AfricaChickpeas  P. Gaur Africa: Ethiopia, Kenya 

Asia: IndiaCowpeas  J. Ehlers Africa: Burkina Faso, Mozambique, SenegalMaize (DT Maize)  G. Atlin Africa: Angola, Ethiopia, Kenya, Malawi ,

Mozambique, Tanzania, Uganda, Zambia , Maize (AMDROUT) B. Vivek Asia: China, India. ThailandRice (STRASA) A. Kumar Sub-Saharan Africa 

South AsiaRice (Green Super Rice) Z. Li Africa and AsiaRice (RI) MN Ndjiondjop West Africa - Nigeria, Burkina Faso, MaliSorghum  J-F Rami Africa: Ethiopia, MaliWheat (RI, India) V. Prabhu IndiaWheat (RI, China) R. Jing ChinaWheat  (ACIAR) R. Trethowan Asia: IndiaWheat (rust) S. Dreisigacker Asia: China 

Africa: Ethiopia, Kenya

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

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