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Integrated Breeding Platform (IBP) Configurable Workflow System

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Presentation on theme: "Integrated Breeding Platform (IBP) Configurable Workflow System"— Presentation transcript:

1 Integrated Breeding Platform (IBP) Configurable Workflow System
Funding: Bill & Melinda Gates Foundation, UK Department for International Development, and European Commission 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 A 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 iPlant The 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 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 The integrated breeding platform will provide support for three molecular breeding schemes…

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 At 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 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 The 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 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 The 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 information review existing characterization and evaluation Project Planning

18 Breeding Management Query browsers
Study browser Germplasm browser

19 Breeding Logistics 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

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
The fieldbook manager has a “create Trial” wizard that Walks 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
Fieldroid Key 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 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 IBP 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) Crops Partners No. of SNPs Status Maize Converted by CIMMYT in early 2010 1250 Available for genotyping Cowpea University of California Riverside - Jeff Ehlers 1122 Chickpeas ICRISAT - Rajeev Varshney 2068 Pigeonpeas 1616 Rice IRRI - Michael Thomson et al. 2015 Cassava IITA - Morag Ferguson, P. Rabinowicz 1740 sorghum EMBRAPA - Jurandir Magalhaes, CIRAD-Jean-Francois Rami 1503 common bean USDA - Perry Cregan, CIAT – Stephen Beebe 1497 Wheat CIMMYT - Susane Dreisigacker 2428 Soybean USDA - Perry Cregan; IITA - Melaku Gedil 1082 Groundnut 91 This 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 Pipeline 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 CWS will offer two options Breeding View R-AP Non-integrated tools will be offered E.g., IciMapping Available through the IBP portal https://www.integratedbreeding.net/

36 Analytical tools – Breeding View
Single site analysis workflow Breeding view Tool for conducting field and QTL analyses Based on Genstat Configurable steps QTL analysis workflow

37 Decision Support Finally, the breeder wants to: select lines,
predict effect of next crosses, promote lines for evaluation and release Decision Support Lastly, there are decision support tools.

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 Based on OptiMAS and MBDT

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 I hope that gives you with an idea of the tools the IBP CWS workbench provides And how they are organized based on a breeder’s workflow. Release milestones A 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.

40 Thanks!


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