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
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

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!