GRM 2011: The Integrated Breeding Platform tools and services


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GRM 2011: The Integrated Breeding Platform tools and services

  1. 1. The Integrated BreedingPlatform: OverviewGraham McLarenGCP-GRM21st September 2011Hyderabad
  2. 2. VisionThe IBP will provide a one-stop-shopwhere 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 practicein order to deploy molecular breedingtechnology for sustainability anddevelopment.
  3. 3. Integrated Breeding PlatformBreedingServicesSupportServicesServicesConfigurable Breeding Workflow SystemCyber InfrastructureCustomFormattedDataFilesLocalDatabaseWeb ServiceData SourceHighPerformanceComputerInformationSystemPortalSoapLabMOBY, GDPC,BioCase/TAPIRData Sources
  4. 4. The IB PortalA One-stop Shop for Integrated Plant Breeding
  5. 5. Tools and Services
  6. 6. The Integrated BreedingPlatform: Breeding ServicesGraham McLarenGCP-GRM21st September 2011Hyderabad
  7. 7. IBP marker services In 2009, a new marker services concept was put in place thatuses established high-throughput genotyping servicesproviders to support the projected rapid growth of genotypingneeds Transition from low throughput, low capacity, public SSRgenotyping labs to high throughput, high capacity, commercialSNP genotyping services 6-10X reduction in genotyping costs Identification of breeder-friendly SNP platforms that can meet theflexible needs of MAB applications Ability to ship leaf samples from around the world (no local DNAextraction needed) Fast turnover to meet tight timelines for MAS and MABC projects Ability to integrate into the informatics tools of the IBP
  8. 8. IBP marker services Chunlin He is leading marker services: GSS consists of genotyping projects funded by the GCPto expose NARS researchers to molecular breeding andhelp get them started with MB Marker Services provides access to genotyping servicesto interested researchers to help in their MB projects The new marker services concept based on high-throughputSNP genotyping was implemented in 2010 Decision to focus on a single SNP genotyping provider(KBioscience, UK) SNP conversion to KBioscience platform almost complete SSR genotyping support still being provided by currentlabs as needed – ICRISAT, BecA and DNA Landmarks
  9. 9. Crops Partners # SNPs StatusMaize Converted by CIMMYT in early 2010 1250 Available for genotypingCowpeaUniversity of California Riverside - JeffEhlers 1122 Available for genotypingChickpeas ICRISAT - Rajeev Varshney 2005 Available for genotypingPigeonpeas ICRISAT - Rajeev Varshney 1616 Available for genotypingRice IRRI - Michael Thomson et al. 805Available for genotypingMore to be added soonCassava IITA - Morag Ferguson, P. Rabinowicz 1740 Available for genotypingSorghumEMBRAPA - Jurandir MagalhaesCIRAD - Jean-Francois Rami 1407 Available for genotypingCommon bean USDA – Perry Cregan; CIAT – S. Beebe 1577 Conversion in progressWheat CIMMYT – Susanne Dreisigacker 2000 Available by end of 2011Available SNP Markers for Genotyping
  10. 10. Next steps The GCP is planning to fingerprint 200-300 breedinglines with all available SNPs for each crop Lines to be chosen in collaboration with CG centersand NARS breeders The data will be uploaded on the IBP fingerprintingdatabase to facilitate the integration of molecularbreeding in the CG and NARS breeding programs
  11. 11. The Integrated BreedingPlatform: Data Managementand Informatics ServicesGraham McLarenGCP-GRM21st September 2011Hyderabad
  12. 12. Support Services - datamanagement and curation:1. Training in Informatics and Data Management• Eight training courses fordifferent crop groups in 2010/112. Data Management Resources Developed3. Electronic Fieldbooks and Hand-held Devices• Trait Ontologies, Trait Dictionaries and TrialTemplates have been developed for eight crops• User cases trained on use of the FieldBook andFieldlog and Hand-held devices distributed4. Publication of Crop Information
  13. 13. Support Services - analysis anddecision support:Training courses in Analysis and Decision SupportData Analysis Workshop, 7-11 June 2010,Zaragoza, SpainSimulation Workshop Jan 21-23 2011, CIMMYT MexicoExisting training material on the use of theGenStat analytical pipeline was updated toincorporate new developments released inthe latest version of GenStatIn parallel, a set of tutorials similar to thosefor GenStat were developed for theanalytical facilities in R including Singleand multiple site analysis GxE analysisQTL analysis QTLxE analysis and the useof Phenotypic and Molecular Indices.
  14. 14. The Integrated BreedingPlatform: Tools for BreedingLogistics, Data Management,Analysis and Decision SupportGraham McLarenGCP-GRM21st September 2011Hyderabad
  15. 15. The IBP Configurable Workflow SystemBreeding ActivitiesParental selectionCrossingPopulationdevelopmentGermplasmManagementOpen ProjectSpecify objectivesIdentify teamData resourcesDefine strategyProjectPlanningExperimental DesignFieldbook productionData collectionData loadingGermplasmEvaluationMarker selectionFingerprintingGenotypingData loadingMolecularAnalysisQuality AssuranceTrait analysisGenetic AnalysisQTL AnalysisIndex AnalysisDataAnalysisSelected linesRecombinesRecombinationplansBreedingDecisionsMB design tool,Cross predictionand StrategicsimulationBreeding ProjectPlanningBreeding nurseryand pedigreerecordmanagementBreedingManagementSystemTrial field bookand environmentcharacterizationsystemField TrialManagementSystemGenotypic DataManagementSystemStatistical analysisapplications andselection indicesAnalyticalPipelineMABCMASMARSGWSDecisionSupport SystemBreeding ApplicationsLab book,quality assuranceand diversityanalysisDevelopment of a Configurable Workflow Systemto support Integrated Breeding
  16. 16. The MARS Breeding Workflow
  17. 17. Tool and CWS Development123456a 6bBasic mock-up (MU) Stages 2&3 iteration (3–4weeks)Functional MU: α & β prototypesDownloadable CWS(Java, middleware)Documentation of the structure and functionality of the toolGraphical representation of the tool workflow annotated flow diagramsDevelopment of corresponding algorithms to run the analysisWeb-based CWSiPlant Cyber-infrastructureUser interactions6cStand-alone Tools(Java, C ++, etc, FlapJack)Coordination parameters for the user interfaceJune 2011 June 2012 June 2013
  18. 18. Stand-Alone CWS: BreedingLogistics and Data Management Workbench Admin & Configuration (CIMMYT) Database and Middleware (CIMMYT, ICRISAT) The Breeding Manager (CIMMYT) Genealogy manager (IRRI) Query Tools (IRRI) Field Trial Management System (CIMMYT) Environment Characterization System (GCP) Genotypic Data Management System (ICRISAT)+EFFICIO+EFFICIO+EFFICIO
  19. 19. Stand-Alone CWS: AnalyticalPipeline and Decision Support R-based Analytical Pipeline Menu Interface (IRRI) Data Management (IRRI) Phenotypic Data Analysis (WUR) Molecular Genetic Analysis (WUR) Selection Indices (CIMMYT) Decision Support System Breeding Decision Support (ICRISAT) MARS Application (INRA) Simulation Tools (UQ, CSIRO and CIMMYT)+ VSNiTo produceBreeding Viewan analyticalWorkflow forbreeding analysisbased onGenStatalgorithms
  20. 20. Application 2: Field Trial ManagementSystemThe IB FieldBook wizard takes you through eight stepsrequired to construct a Trial Fieldbook by merging togethera Trial Template, a Germplasm List and a Field Design
  21. 21. Application 4: Genotyping DataManagement System Team established between ICRISAT and IRRIled by Trushar Shah to convert the ICRIS web-based genotyping system toa stand-alone system improve integration of the system with sample trackingand genealogy management components developing data loading algorithms load data for different use case crops improve and expand the user query interface
  22. 22. Application 4: Analytical PipelineStatistical Methodology Experimental design Generate basic designs with R connected to theFieldbook Phenotype analysis Genetic variance analysis, single site and multi-siteanalysis available in GenStat and R QTL analysis QTL and QTLxE analysis tools with tutorials available inGenstat and R Selection Indices Phenotype Selection Indices available in R scripts
  23. 23. Application 5: Decision SupportTools MB Design Tool (MBDT) MBDT available for planning MB experiment withdata inputs from local files. MAS decision tool Marker aided selection processing facilitiesbased on major known genes added to MBDT MARS decision tool OptiMAS – a tool for tracking and assemblingfavorable alleles at QTL through bi- and multi-allelic breeding populations.
  24. 24. Application 6: Simulation Tools Stand-alone versions of simulationprograms available for use with manualsand training material for: inbred line development (QULine) hybrid development and (QUHybred) MARS schemes (QUMARS)
  25. 25. Application 6: Simulation Tools
  26. 26. The Integrated BreedingPlatform: CommunitiesGraham McLarenGCP-GRM21st September 2011Hyderabad
  27. 27. The IBP PartnershipUSERS TOOLS AND SERVICES PARTNERSGenetic Resource SupportServiceBreeding Logistics &Data ManagementMarker & TraitServicesAnalysisPipelineDecisionSupport ToolsTraining &Capacity DevelopmentAccumulated Crop Informationfor Predictive BreedingCGIAR Pre-Breeding& Breeding ProjectsCGIAR BreedingNetworksNARES BreedingProjectsSmall & MediumSized EnterprisesCGIAR Lead CropCenters:· Set breeding standards andprocedures· Help train external users· Curate and Host PublicCrop Information· Promote use and access tothe PlatformMolecularBreedingCommunitiesofPracticeUse Case Projects:· Specify requirements· Test tools and services· Ensure Relevance· Promote use of andaccess to the Platform
  28. 28. 14 use cases selected as first phase users of IBPBeans S. Beebe Africa: Ethiopia, Kenya, Tanzania, MalawiCassava E. Okogbenin AfricaChickpeas P. Gaur Africa: Ethiopia, KenyaAsia: 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 AfricaSouth 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: ChinaAfrica: Ethiopia, Kenya
  29. 29. 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
  30. 30. Existing COPs Rice in the Mekong region Cassava in Africa Data managers Chickpea Cowpea and SoybeanFuture plans Bean Maize Sorghum Rice in Africa Rice in Asia
  31. 31. Informatics Meetings – 23rd Discussion on workflow for ontology and traitdictionary curation Linking the on-line ontology and trait dictionariesto data management tools such as the IBFieldbook. Workplan development for the Ontology project. Tutorial of uploading data from local to centraldatabases. Progress and plans for analysis and decisionsupport tools for Integrated breeding