The Integrated Breeding

Platform: Overview

Graham McLaren

GCP-GRM

21st September 2011

Hyderabad

Vision

The IBP will provide a one-stop-shop

where breeders can access:

high-throughput breeding services,

logistics and data management tools,

an intuitive analysis pipeline,

breeding decision support tools,

support to use these facilities and

breeding communities of practice

in order to deploy molecular breeding

technology for sustainability and

development.

Integrated Breeding Platform

Breeding

Services

Support

Services

Serv

ices

Configurable Breeding Workflow System

Cyber Infrastructure

Custom

Formatted

Data

Files

Local

Database

Web Service

Data Source

High

Performance

Computer

Info

rmation S

yste

m

Port

al

SoapLab MOBY, GDPC,

BioCase/TAPIR

Data Sources

The IB Portal

A One-stop Shop for Integrated Plant Breeding

Tools and Services

The Integrated Breeding

Platform: Breeding Services

Graham McLaren

GCP-GRM

21st September 2011

Hyderabad

IBP marker services

In 2009, a new marker services concept was put in place that

uses established high-throughput genotyping services

providers to support the projected rapid growth of genotyping

needs

Transition from low throughput, low capacity, public SSR

genotyping labs to high throughput, high capacity, commercial

SNP genotyping services

6-10X reduction in genotyping costs

Identification of breeder-friendly SNP platforms that can meet the

flexible needs of MAB applications

Ability to ship leaf samples from around the world (no local DNA

extraction needed)

Fast turnover to meet tight timelines for MAS and MABC projects

Ability to integrate into the informatics tools of the IBP

IBP marker services

Chunlin He is leading marker services:

GSS consists of genotyping projects funded by the GCP

to expose NARS researchers to molecular breeding and

help get them started with MB

Marker Services provides access to genotyping services

to interested researchers to help in their MB projects

The new marker services concept based on high-throughput

SNP genotyping was implemented in 2010

Decision to focus on a single SNP genotyping provider

(KBioscience, UK)

SNP conversion to KBioscience platform almost complete

SSR genotyping support still being provided by current

labs as needed – ICRISAT, BecA and DNA Landmarks

Crops Partners # SNPs Status

Maize Converted by CIMMYT in early 2010 1250 Available for genotyping

Cowpea

University of California Riverside - Jeff

Ehlers 1122 Available for genotyping

Chickpeas ICRISAT - Rajeev Varshney 2005 Available for genotyping

Pigeonpeas ICRISAT - Rajeev Varshney 1616 Available for genotyping

Rice IRRI - Michael Thomson et al. 805

Available for genotyping

More to be added soon

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

Sorghum

EMBRAPA - Jurandir Magalhaes

CIRAD - Jean-Francois Rami 1407 Available for genotyping

Common bean USDA – Perry Cregan; CIAT – S. Beebe 1577 Conversion in progress

Wheat CIMMYT – Susanne Dreisigacker 2000 Available by end of 2011

Available SNP Markers for Genotyping

http://ibp.generationcp.org/confluence/display/MBP/Activity+3.1.2

Next steps

The GCP is planning to fingerprint 200-300 breeding

lines with all available SNPs for each crop

Lines to be chosen in collaboration with CG centers

and NARS breeders

The data will be uploaded on the IBP fingerprinting

database to facilitate the integration of molecular

breeding in the CG and NARS breeding programs

The Integrated Breeding

Platform: Data Management

and Informatics Services

Graham McLaren

GCP-GRM

21st September 2011

Hyderabad

Support Services - data

management and curation:

1. Training in Informatics and Data Management

• Eight training courses for

different crop groups in 2010/11

2. Data Management Resources Developed

3. Electronic Fieldbooks and Hand-held Devices

• Trait Ontologies, Trait Dictionaries and Trial

Templates have been developed for eight crops

• User cases trained on use of the FieldBook and

Fieldlog and Hand-held devices distributed

4. Publication of Crop Information

Support Services - analysis and

decision support:

Training courses in Analysis and Decision Support

Data Analysis Workshop, 7-11 June 2010,Zaragoza, Spain

Simulation Workshop Jan 21-23 2011, CIMMYT Mexico

Existing training material on the use of the

GenStat analytical pipeline was updated to

incorporate new developments released in

the latest version of GenStat

In parallel, a set of tutorials similar to those

for GenStat were developed for the

analytical facilities in R including Single

and multiple site analysis GxE analysis

QTL analysis QTLxE analysis and the use

of Phenotypic and Molecular Indices.

The Integrated Breeding

Platform: Tools for Breeding

Logistics, Data Management,

Analysis and Decision Support

Graham McLaren

GCP-GRM

21st September 2011

Hyderabad

The IBP Configurable Workflow System

Breeding Activities

Parental selection

Crossing

Population

development

Germplasm

Management

Open Project

Specify objectives

Identify team

Data resources

Define strategy

Project

Planning

Experimental Design

Fieldbook production

Data collection

Data loading

Germplasm

Evaluation

Marker selection

Fingerprinting

Genotyping

Data loading

Molecular

Analysis

Quality Assurance

Trait analysis

Genetic Analysis

QTL Analysis

Index Analysis

Data

Analysis

Selected lines

Recombines

Recombination

plans

Breeding

Decisions

MB design tool,

Cross prediction

and Strategic

simulation

Breeding Project

Planning

Breeding nursery

and pedigree

record

management

Breeding

Management

System

Trial field book

and environment

characterization

system

Field Trial

Management

System

Genotypic Data

Management

System

Statistical analysis

applications and

selection indices

Analytical

Pipeline

MABC

MAS

MARS

GWS

Decision

Support System

Breeding Applications

Lab book,

quality assurance

and diversity

analysis

Development of a Configurable Workflow System

to support Integrated Breeding

The MARS Breeding Workflow

Tool and CWS Development

1

2

3

4

5

6a 6b

Basic mock-up (MU) Stages 2&3 iteration (3–4weeks)

Functional MU: α & β prototypes

Downloadable CWS (Java, middleware)

Documentation of the structure and functionality of the tool

Graphical representation of the tool workflow annotated flow diagrams

Development of corresponding algorithms to run the analysis

Web-based CWS iPlant Cyber-infrastructure

User interactions

6c Stand-alone Tools

(Java, C ++, etc, FlapJack)

Coordination parameters for the user interface

June 2011 June 2012 June 2013

Stand-Alone CWS: Breeding

Logistics and Data Management

Workbench Admin & Configuration (CIMMYT)

Database and Middleware (CIMMYT, ICRISAT)

The Breeding Manager (CIMMYT)

Genealogy manager (IRRI)

Query Tools (IRRI)

Field Trial Management System (CIMMYT)

Environment Characterization System (GCP)

Genotypic Data Management System (ICRISAT)

+EFFICIO

+EFFICIO

+EFFICIO

Stand-Alone CWS: Analytical

Pipeline and Decision Support

R-based Analytical Pipeline

Menu Interface (IRRI)

Data Management (IRRI)

Phenotypic Data Analysis (WUR)

Molecular Genetic Analysis (WUR)

Selection Indices (CIMMYT)

Decision Support System

Breeding Decision Support (ICRISAT)

MARS Application (INRA)

Simulation Tools (UQ, CSIRO and CIMMYT)

+ VSNi

To produce

Breeding View

an analytical

Workflow for

breeding analysis

based on

GenStat

algorithms

Application 2: Field Trial Management

System

The IB FieldBook wizard takes you through eight steps

required to construct a Trial Fieldbook by merging together

a Trial Template, a Germplasm List and a Field Design

Application 4: Genotyping Data

Management System

Team established between ICRISAT and IRRI

led by Trushar Shah

to convert the ICRIS web-based genotyping system to

a stand-alone system

improve integration of the system with sample tracking

and genealogy management components

developing data loading algorithms

load data for different use case crops

improve and expand the user query interface

Application 4: Analytical Pipeline

Statistical Methodology

Experimental design

Generate basic designs with R connected to the

Fieldbook

Phenotype analysis

Genetic variance analysis, single site and multi-site

analysis available in GenStat and R

QTL analysis

QTL and QTLxE analysis tools with tutorials available in

Genstat and R

Selection Indices

Phenotype Selection Indices available in R scripts

Application 5: Decision Support

Tools

MB Design Tool (MBDT)

MBDT available for planning MB experiment with

data inputs from local files.

MAS decision tool

Marker aided selection processing facilities

based on major known genes added to MBDT

MARS decision tool

OptiMAS – a tool for tracking and assembling

favorable alleles at QTL through bi- and multi-

allelic breeding populations.

Application 6: Simulation Tools

Stand-alone versions of simulation

programs available for use with manuals

and training material for:

inbred line development (QULine)

hybrid development and (QUHybred)

MARS schemes (QUMARS)

Application 6: Simulation Tools

The Integrated Breeding

Platform: Communities

Graham McLaren

GCP-GRM

21st September 2011

Hyderabad

The IBP Partnership USERS TOOLS AND SERVICES PARTNERS

Genetic Resource Support

Service

Breeding Logistics &

Data Management

Marker & Trait

Services

Analysis

Pipeline

Decision

Support Tools

Training &

Capacity Development

Accumulated Crop Information

for Predictive Breeding

CGIAR Pre-Breeding

& Breeding Projects

CGIAR Breeding

Networks

NARES Breeding

Projects

Small & Medium

Sized Enterprises

CGIAR Lead Crop

Centers:

· Set breeding standards and

procedures

· Help train external users

· Curate and Host Public

Crop Information

· Promote use and access to

the Platform

Mo

lecu

lar B

reed

ing

Co

mm

un

ities o

f Pra

ctic

e

Use Case Projects:

· Specify requirements

· Test tools and services

· Ensure Relevance

· Promote use of and

access to the Platform

14 use cases selected as first phase users of IBP

Beans  S. Beebe Africa: Ethiopia, Kenya, Tanzania, Malawi

Cassava  E. Okogbenin Africa

Chickpeas  P. Gaur Africa: Ethiopia, Kenya 

Asia: India

Cowpeas  J. Ehlers Africa: Burkina Faso, Mozambique, Senegal

Maize (DT Maize)  G. Atlin Africa: Angola, Ethiopia, Kenya, Malawi ,

Mozambique, Tanzania, Uganda, Zambia , Maize (AMDROUT) B. Vivek Asia: China, India. Thailand

Rice (STRASA) A. Kumar Sub-Saharan Africa 

South Asia

Rice (Green Super Rice) Z. Li Africa and Asia

Rice (RI) MN Ndjiondjop West Africa - Nigeria, Burkina Faso, Mali

Sorghum  J-F Rami Africa: Ethiopia, Mali

Wheat (RI, India) V. Prabhu India

Wheat (RI, China) R. Jing China

Wheat  (ACIAR) R. Trethowan Asia: India

Wheat (rust) S. Dreisigacker Asia: China 

Africa: Ethiopia, Kenya

Communities of Practice (CoP)

Use Breeding support through IBP to:

Bring together breeders and crop scientists

Share of knowledge

Initiate of MAS programmes in developing countries

Training on MAS

Training on Data management

Existing COPs

Rice in the Mekong region

Cassava in Africa

Data managers

Chickpea

Cowpea and Soybean

Future plans

Bean

Maize

Sorghum

Rice in Africa

Rice in Asia

Informatics Meetings – 23rd

Discussion on workflow for ontology and trait

dictionary curation

Linking the on-line ontology and trait dictionaries

to data management tools such as the IB

Fieldbook.

Workplan development for the Ontology project.

Tutorial of uploading data from local to central

databases.

Progress and plans for analysis and decision

support tools for Integrated breeding