1. The Integrated Breeding
Platform: Overview
Graham McLaren
GCP-GRM
21st September 2011
Hyderabad

2. 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.

3. Integrated Breeding Platform
Breeding
Services
Support
Services
Services
Configurable Breeding Workflow System
Cyber Infrastructure
Custom
Formatted
Data
Files
Local
Database
Web Service
Data Source
High
Performance
Computer
InformationSystem
Portal
SoapLab
MOBY, GDPC,
BioCase/TAPIR
Data Sources

4. The IB Portal
A One-stop Shop for Integrated Plant Breeding

5. Tools and Services

6. The Integrated Breeding
Platform: Breeding Services
Graham McLaren
GCP-GRM
21st September 2011
Hyderabad

7. 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

8. 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

9. 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

10. 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

11. The Integrated Breeding
Platform: Data Management
and Informatics Services
Graham McLaren
GCP-GRM
21st September 2011
Hyderabad

12. 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

13. 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.

14. The Integrated Breeding
Platform: Tools for Breeding
Logistics, Data Management,
Analysis and Decision Support
Graham McLaren
GCP-GRM
21st September 2011
Hyderabad

15. 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

16. The MARS Breeding Workflow

17. 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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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.

25. 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)

26. Application 6: Simulation Tools

27. The Integrated Breeding
Platform: Communities
Graham McLaren
GCP-GRM
21st September 2011
Hyderabad

28. 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
MolecularBreedingCommunitiesofPractice
Use Case Projects:
· Specify requirements
· Test tools and services
· Ensure Relevance
· Promote use of and
access to the Platform

29. 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

30. 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

31. 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

32. 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