1 Integrated Breeding Platform (IBP) Configurable Workflow System Funding: Bill & Melinda Gates Foundation, UK Department for International Development, and European CommissionMartha Narro, iPlant CollaborativeJanuary 11, 2013Slides from Xavier Delannay and Graham McLaren, CGIAR
2 Integrated Breeding Platform IBP - a one-stop-shop where breeders can access:Databases (germplasm, pedigree, phenotypic, genotypic and environmental)A configurable workflow system (CWS)Logistics and data management toolsBreeding planning and management toolsAnalytical toolsBreeding decision support toolsHigh throughput breeding servicesSupport services to use these facilitiesScientific networkA single platform where breeders can access data, tools, services, support staff and a world-wide community of breeders.Most of this talk will focus on the configurable workflow system
3 Integrated Breeding Portal https://www.integratedbreeding.net/Developed as a collaboration between IBP and iPlantThe portal is still under active development, so expect some placeholders and changes.
4 IBP builds on existing tools already in use by IRRI and other CGIAR breeders Existing breeding management tools and related DBsICIS Database schema and query toolsIRIS Crop Information System and ToolsIWIS Genealogy Management & Int. Nursery SystemMaize Fieldbook and Maize Finder Query ToolICRIS Molecular Biology DatabaseNew Concepts: The IBP CWS willbe configurable for different crops and breeding strategies,be workflow driven – leading users through breeding workflows,have a new user-friendly interface, andwill be available as stand-alone and as a web-based system.Existing ICIS tools will continue to work with the CWS until all functionality is replicated and improved
5 Who should be interested in using the IB CWS? Starting late January 2013 the portal will be open broadly to all scientists working in plant science, for both the public and private sectorMore specifically:All CGIAR breeding programs and networksNARS partners wanting to enhance the effectiveness of their breeding programs by integrating molecular methodsSMEs working in developing countries without the capacity to build a breeding workflow system in house
6 Breeding schemes Project planning Population development Field trial managementStatistical analysisBreeding decisionThe integrated breeding platform will provide support for three molecular breeding schemes…
10 Inventory of existing functionality IB Database V1 IB Germplasm databaseGermplasm nomenclature, chronology, IP and passport dataPedigrees and breeding historyIB phenotypic database v1Available for use as central database or local databaseDatabases crop-specificGenotypic database (GDMS) for management of low to medium density genotyping data and MTA dataCentral database contains fingerprinting and MTA data for global useLocal database focuses on project-specific genotyping dataGermplasm and Phenotype Study BrowsersDatabases fully integrated into CWS workbenchAt a high level, four types of functionality will be in the integrated breeding platform.The first is the IB Database
11 Inventory of existing functionality Nursery and Trial Management Breeding Manager configured for different cropsIncludes crossing manager, nursery manager, pedigree recordingFocuses on breeding steps for population development and line selectionNursery advance and seed inventory trackingIB FieldbookFocuses on field trial management for germplasm evaluationTrait selection, field design, labels and sample tracking and data captureAndroid-based hand-held deviceOptimized for use with Samsung Galaxy tablet for field data collectionOther Android devices can be used if preferredBreeding manager and Field books fully integrated into CWS workbenchThe second type of functionality is tools for Nursery and Trial management.
12 Tools to be integrated into the CWS by the end of 2012 Inventory of existing functionality Analytical and breeding decision toolsStatistical tools available with the following options:Access to Genstat while complete suite of tools is being developedTemporary license to use cases while Breeding View is being developedBreeding View for user-friendly access to Genstat tools, focusing on main functionalities needed by breeders and molecular breedersR-based analytical suiteMost functionalities available now as standalone toolsTo be linked together soon in Java-based R-AP user interfaceDecision support tools:R-based selection indicesOptiMAS traces alleles by descent through breeding populationsAllows optimum recombination of lines with favorable alleles (MARS)MBDT - MABC management toolTools to be integrated into the CWS by the end of 2012The third and fourth types of functionality are analytical tools and breeding decision tools.
13 Launching the workbench will display a splash screen.
14 The Workbench Dashboard will be displayed after a successful login. The workbench dashboard lists a user’s projects with the most recently opened one highlighted.The Workbench Dashboard will be displayed after a successful login.The last opened project will be highlighted.
15 The Create New Project form allows the user to set the target Crop of the project. The crop is then used to determine the central database for the project.Users can set the Project Members, Methods and Locations used in the project.
16 A breeding workflow I’ll go through an example workflow for Marker assisted recurrent selection (MARS)
17 Query Tools At the outset of a breeding cycle users want to: browse all germplasm informationreview existing characterization and evaluationProjectPlanning
18 Breeding Management Query browsers Study browserGermplasm browser
19 Breeding LogisticsOnce the strategy and parental material have been identified, the breeder wants to:make crosses,develop populations,track pedigrees,track inventory,characterize linesPopulationDevelopment
28 Breeding Management IBP Fieldbook The fieldbook manager has a “create Trial” wizard thatWalks users through the steps for creating a field trial.
29 Breeding Management Bar Code labels There’s a tool to help users manage the barcode labels.
30 Breeding Management Tablet Devices FieldroidKey fieldbook tools are implemented on mobile devices that are easy to use in the field.Android tablets
31 Genotyping To use molecular technologies, the breeder wants to: select population,select markers,genotype population,check and store genotyping data.When it’s time to genotype the plants, the IBP workbench provides tools to support…Genotyping
32 IBP marker servicesThe new marker services concept based on high-throughput SNP genotyping was operational in 2011Decision to focus on a single SNP genotyping provider (KBioscience, UK)SNP conversion to KBioscience platform almost completeGCP funds the conversion of 1,000-2,000 SNPs for each crop of interestAssays available to customers after that (between 8-10 cents/dp)First set of genotypes fingerprinted as part of conversion processSSR genotyping support still being provided by current labs as neededBecAICRISATIBP decided to use the KBioscience platform for SNP genotyping.Good set of genotypes fingerprinted as part of conversion process, good basis to build on to understand germplasm relationships and provide foundation for wide MB use
33 Converted by CIMMYT in early 2010 1250 Available for genotyping Cowpea Availability of SNP markers at GCP for genotyping (as of August 27, 2012)CropsPartnersNo. of SNPsStatusMaizeConverted by CIMMYT in early 20101250Available for genotypingCowpeaUniversity of California Riverside - Jeff Ehlers1122ChickpeasICRISAT - Rajeev Varshney2068Pigeonpeas1616RiceIRRI - Michael Thomson et al.2015CassavaIITA - Morag Ferguson, P. Rabinowicz1740sorghumEMBRAPA - Jurandir Magalhaes, CIRAD-Jean-Francois Rami1503common beanUSDA - Perry Cregan, CIAT – Stephen Beebe1497WheatCIMMYT - Susane Dreisigacker2428SoybeanUSDA - Perry Cregan; IITA - Melaku Gedil1082Groundnut91This is a list summarizing the SNP markers available for genotyping through GCP.
34 Genotyping Data Management This shows views of the tools available for managing genotyping.
35 The Analysis PipelineOnce the data is collected, the breeder wants to:do single site analysis,combined analysis,Identify marker-trait associations (MTAs),Store results back to GDMSAnalysisPipelineCWS will offer two optionsBreeding ViewR-APNon-integrated tools will be offeredE.g., IciMappingAvailable through the IBP portalhttps://www.integratedbreeding.net/
36 Analytical tools – Breeding View Single site analysis workflowBreeding viewTool for conducting field and QTL analysesBased on GenstatConfigurable stepsQTL analysis workflow
37 Decision Support Finally, the breeder wants to: select lines, predict effect of next crosses,promote lines for evaluation and releaseDecisionSupportLastly, there are decision support tools.
38 Breeding Decision support – Marker implementation OptiMASDeveloped at INRA, Le MoulonImplementation of markers in a MARS breeding schemeIdentify and track favorable alleles through cycles of recombination and selectionMolecular Breeding Decision Tool (MBDT)Developed by team at ICRISATImplementation of markers in a MABC contextBased on OptiMAS and MBDT
39 Release MilestonesA first prototype of the CWS was demonstrated to users in Beijing in June 2012Broad opening of IBP Portal by January 2013, with CWS (Configurable Workflow System) downloadable as single integrated applicationI hope that gives you with an idea of the tools the IBP CWS workbench providesAnd how they are organized based on a breeder’s workflow.Release milestonesA prototype of the CWS was demo’d six months ago.The public release of the IBP portal with the CWS is scheduled for the end of this month.