Integrated Breeding Platform (IBP)

Configurable Workflow System

Martha Narro, iPlant CollaborativeJanuary 11, 2013

Slides from Xavier Delannay and Graham McLaren, CGIAR

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

Integrated Breeding Portalhttps://www.integratedbreeding.net/

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

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

Breeding schemes

Project planning

Population development

Field trial management

Statistical analysis

Breeding decision

Breeding with marker-assisted selection (MAS)

Project planning

Population development

Field trial management

Statistical analysis

Breeding decision

Genotyping

Marker-assisted backcrossing (MABC)

Project planning

Backcrossing

Field trial management

Statistical analysis

Breeding decision

Genotyping

Marker-assisted recurrent selection (MARS)

Project planning

Population development

Field trial management

Phenotypic analysis

Final breeding decision

Genotyping

QTL analysis

QTL selection

Recombination cycle

Inventory of existing functionalityIB 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

Inventory of existing functionalityNursery 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

Inventory of existing functionalityAnalytical 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

Launching the workbench will display a splash screen.

•The Workbench Dashboard will be displayed after a successful login.

•The last opened project will be highlighted.

•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.

A breeding workflow

Query Tools

At the outset of a breeding cycle users want to: browse all germplasm

information review existing

characterization and evaluation

Project Planning

Breeding ManagementQuery browsers

Germplasm browser

Study browser

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

PopulationDevelopment

Breeding Logistics

Breeding ManagementCrossing Manager

Breeding ManagementNursery Manager

Breeding ManagementPedigree recording

Breeding ManagementInventory Manager

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 FieldTrials

Breeding ManagementTrait Dictionaries

Breeding ManagementTrait Selector

Breeding ManagementGermplasm List Manager

Breeding ManagementIBP Fieldbook

Breeding ManagementBar Code labels

Breeding ManagementTablet Devices

Fieldroid

Genotyping

To use molecular technologies, the breeder wants to: select population, select markers, genotype population, check and store

genotyping data. Genotyping

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

Availability of SNP markers at GCP for genotyping (as of August 27, 2012)Crops Partners No. of SNPs Status

MaizeConverted by CIMMYT in early 2010 1250 Available for genotyping

CowpeaUniversity of California Riverside - Jeff Ehlers 1122 Available for genotyping

Chickpeas ICRISAT - Rajeev Varshney 2068 Available for genotyping

Pigeonpeas ICRISAT - Rajeev Varshney 1616 Available for genotyping

Rice IRRI - Michael Thomson et al. 2015 Available for genotyping

Cassava IITA - Morag Ferguson, P. Rabinowicz 1740 Available for genotyping

sorghum EMBRAPA - Jurandir Magalhaes, CIRAD-Jean-Francois Rami 1503 Available for genotyping

common beanUSDA - Perry Cregan, CIAT – Stephen Beebe 1497 Available for genotyping

Wheat CIMMYT - Susane Dreisigacker

2428 Available for genotyping

SoybeanUSDA - Perry Cregan; IITA - Melaku Gedil 1082 Available for genotyping

Groundnut ICRISAT - Rajeev Varshney 91 Available for genotyping

Genotyping Data Management

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

AnalysisPipeline

The Analysis Pipeline

Analytical tools – Breeding View

Single site analysis workflow

QTL analysis workflow

Configurable steps

Finally, the breeder wants to: select lines, predict effect of next

crosses, promote lines for

evaluation and release

Decision Support

Decision Support

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

 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

Thanks!