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