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Integrated Breeding Platform (IBP) Configurable Workflow System Martha Narro, iPlant Collaborative January 11, 2013 Slides from Xavier Delannay and Graham.

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Presentation on theme: "Integrated Breeding Platform (IBP) Configurable Workflow System Martha Narro, iPlant Collaborative January 11, 2013 Slides from Xavier Delannay and Graham."— Presentation transcript:

1 Integrated Breeding Platform (IBP) Configurable Workflow System Martha Narro, iPlant Collaborative January 11, 2013 Slides 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 tools Breeding planning and management tools Analytical tools Breeding decision support tools High throughput breeding services Support services to use these facilities Scientific network

3 Integrated Breeding Portal https://www.integratedbreeding.net/

4 IBP builds on existing tools already in use by IRRI and other CGIAR breeders Existing breeding management tools and related DBs ICIS Database schema and query tools IRIS Crop Information System and Tools IWIS Genealogy Management & Int. Nursery System Maize Fieldbook and Maize Finder Query Tool ICRIS Molecular Biology Database New Concepts: The IBP CWS will be configurable for different crops and breeding strategies, be workflow driven – leading users through breeding workflows, have a new user-friendly interface, and will 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 sector More specifically: All CGIAR breeding programs and networks NARS partners wanting to enhance the effectiveness of their breeding programs by integrating molecular methods SMEs working in developing countries without the capacity to build a breeding workflow system in house

6 Breeding schemes Project planning Population development Field trial management Statistical analysis Breeding decision

7 Breeding with marker-assisted selection (MAS) Project planning Population development Field trial management Statistical analysis Breeding decision Genotyping

8 Marker-assisted backcrossing (MABC) Project planning Backcrossing Field trial management Statistical analysis Breeding decision Genotyping

9 Marker-assisted recurrent selection (MARS) Project planning Population development Field trial management Phenotypic analysis Final breeding decision Genotyping QTL analysis QTL selection Recombination cycle

10 Inventory of existing functionality IB Database V1 IB Germplasm database Germplasm nomenclature, chronology, IP and passport data Pedigrees and breeding history IB phenotypic database v1 Available for use as central database or local database Databases crop-specific Genotypic database (GDMS) for management of low to medium density genotyping data and MTA data Central database contains fingerprinting and MTA data for global use Local database focuses on project-specific genotyping data Germplasm and Phenotype Study Browsers Databases fully integrated into CWS workbench

11 Inventory of existing functionality Nursery and Trial Management Breeding Manager configured for different crops Includes crossing manager, nursery manager, pedigree recording Focuses on breeding steps for population development and line selection Nursery advance and seed inventory tracking IB Fieldbook Focuses on field trial management for germplasm evaluation Trait selection, field design, labels and sample tracking and data capture Android-based hand-held device Optimized for use with Samsung Galaxy tablet for field data collection Other Android devices can be used if preferred Breeding manager and Field books fully integrated into CWS workbench

12 Inventory of existing functionality Analytical and breeding decision tools Statistical tools available with the following options: Access to Genstat while complete suite of tools is being developed Temporary license to use cases while Breeding View is being developed Breeding View for user-friendly access to Genstat tools, focusing on main functionalities needed by breeders and molecular breeders R-based analytical suite Most functionalities available now as standalone tools To be linked together soon in Java-based R-AP user interface Decision support tools: R-based selection indices OptiMAS traces alleles by descent through breeding populations Allows optimum recombination of lines with favorable alleles (MARS) MBDT - MABC management tool Tools to be integrated into the CWS by the end of 2012

13 Launching the workbench will display a splash screen.

14 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

17 Query Tools At the outset of a breeding cycle users want to: browse all germplasm information review existing characterization and evaluation Project Planning

18 Breeding Management Query browsers Germplasm browser Study browser

19 Once the strategy and parental material have been identified, the breeder wants to: make crosses, develop populations, track pedigrees, track inventory, characterize lines Population Development Breeding Logistics

20 Breeding Management Crossing Manager

21 Breeding Management Nursery Manager

22 Breeding Management Pedigree recording

23 Breeding Management Inventory Manager

24 Field Testing Once populations are developed, the breeder wants to: select traits, make lists of germplasm, generate designs, produce fieldbooks, collect data, check and store data. Manage Field Trials

25 Breeding Management Trait Dictionaries Measurement Variate Trait property Reporting units or scale Measurement method

26 Breeding Management Trait Selector

27 Breeding Management Germplasm List Manager

28 Breeding Management IBP Fieldbook

29 Breeding Management Bar Code labels

30 Breeding Management Tablet Devices Fieldroid

31 Genotyping To use molecular technologies, the breeder wants to: select population, select markers, genotype population, check and store genotyping data. Genotyping

32 IBP marker services The new marker services concept based on high- throughput SNP genotyping was operational in 2011 Decision to focus on a single SNP genotyping provider (KBioscience, UK) SNP conversion to KBioscience platform almost complete GCP funds the conversion of 1,000-2,000 SNPs for each crop of interest Assays available to customers after that (between 8-10 cents/dp) First set of genotypes fingerprinted as part of conversion process SSR genotyping support still being provided by current labs as needed BecA ICRISAT

33 Availability of SNP markers at GCP for genotyping (as of August 27, 2012) CropsPartnersNo. of SNPsStatus Maize Converted by CIMMYT in early Available for genotyping Cowpea University of California Riverside - Jeff Ehlers1122Available for genotyping ChickpeasICRISAT - Rajeev Varshney2068Available for genotyping PigeonpeasICRISAT - Rajeev Varshney1616Available for genotyping RiceIRRI - Michael Thomson et al.2015Available for genotyping Cassava IITA - Morag Ferguson, P. Rabinowicz1740Available for genotyping sorghum EMBRAPA - Jurandir Magalhaes, CIRAD-Jean-Francois Rami1503Available for genotyping common bean USDA - Perry Cregan, CIAT – Stephen Beebe1497Available for genotyping Wheat CIMMYT - Susane Dreisigacker 2428Available for genotyping Soybean USDA - Perry Cregan; IITA - Melaku Gedil1082Available for genotyping GroundnutICRISAT - Rajeev Varshney91Available for genotyping

34 Genotyping Data Management

35 Once the data is collected, the breeder wants to: do single site analysis, combined analysis, Identify marker-trait associations (MTAs), Store results back to GDMS Analysis Pipeline The Analysis Pipeline

36 Analytical tools – Breeding View Single site analysis workflow QTL analysis workflow Configurable steps

37 Finally, the breeder wants to: select lines, predict effect of next crosses, promote lines for evaluation and release Decision Support Decision Support

38 Breeding Decision support – Marker implementation OptiMAS Developed at INRA, Le Moulon Implementation of markers in a MARS breeding scheme Identify and track favorable alleles through cycles of recombination and selection Molecular Breeding Decision Tool (MBDT) Developed by team at ICRISAT Implementation of markers in a MABC context

39 Release Milestones A first prototype of the CWS was demonstrated to users in Beijing in June 2012 Broad opening of IBP Portal by January 2013, with CWS (Configurable Workflow System) downloadable as single integrated application

40 Thanks!


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