1. Graham McLaren GCP21-II, Kampala, Uganda 19 June 2012

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. What the IBP offers Access to Breeding Services: Support services for:
well characterised and useful genetic resources
quality, economic high throughput genotyping
sophisticated phenotype and metabolite analyses
Support services for:
planning and comparing breeding strategies
data management and curation and quality control
analysis and decision support
use of markers and molecular breeding techniques
phenotyping sites and protocols
use and protection of intellectual property
Access to Informatics Tools and Resources:
for breeding logistics and data management
analysis and decision support for molecular breeding
accumulated public crop information of certified quality
Capacity and Community Development:
support for communities of practice by crop or discipline
facilitation of germplasm exchange

4. The Integrated Breeding Portal
Fred Okono
Convenient and flexible access to
Crop information
Crop breeding tools and services
Capacity building resources and opportunities
Community interaction
Relevant news and events

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

6. Crop Information Downloadable crop databases
Online crop database query interface
Trait dictionaries
Molecular markers
Other information

8. Informatics Tools for Crop Breeding
Project planning tools
Germplasm management tools
Field trial management tools
Genotypic data management tools
Data analysis tools
Breeding decision support tools
Supplementary toolbox

10. Breeding and Support Services
Breeding plan development
Genotyping & Marker
Phenotyping
Trait & Metabolite
Data Curation & Information Management
Design & Analysis
Genetic Resources
IP & Policy

12. Capacity building opportunities
Molecular breeding
Genebank management
Data analysis
Data & Information Management
Tool use – tutorials and manuals
Intellectual property and policy
eLearning System

14. Communities Blogs Forums Live chat Collaborative work
Community specific information
Bibliographic information

16. News and Events IBP Update Online news pages
Online events calendar and information pages
Social media – Facebook and Twitter

18. The Integrated Breeding Platform: Breeding Services
Xavier Delannay and Chunlin He

19. Available SNP Markers for Genotyping
Crops
Partners
# 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
2005
Pigeonpeas
1616
Rice
IRRI - Michael Thomson et al.
805
More to be added soon
Cassava
IITA - Morag Ferguson, P. Rabinowicz
1740
Sorghum
EMBRAPA - Jurandir Magalhaes CIRAD - Jean-Francois Rami
1407
Common bean
 USDA – Perry Cregan; CIAT – S. Beebe
1577
Conversion in progress
Wheat
 CIMMYT – Susanne Dreisigacker
2000
Available by end of 2011

20. Next steps
The GCP is planning to fingerprint 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

21. The Integrated Breeding Platform: Data Management and Informatics Services
Arllet Portugal

22. 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
Trait Ontologies, Trait Dictionaries and Trial Templates have been developed for eight crops
3. Electronic Fieldbooks and Hand-held Devices
User cases trained on use of the FieldBook and Fieldlog and Hand-held devices distributed
4. Publication of Crop Information

23. Support Services - analysis and decision support
Support Services - analysis and decision support. Fred van Eeuwijk and Marcos Malosetti, WUR:
Training courses in Analysis and Decision Support
Data Analysis Workshop, 7-11 June 2010,Zaragoza, Spain
Simulation Workshop Jan , 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.

24. The Integrated Breeding Platform: Tools for Breeding Logistics, Data Management, Analysis and Decision Support
Graham McLaren

25. The IBP Configurable Workflow System Breeding Applications
Development of a Configurable Workflow System
to support Integrated Breeding
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
Evaluation
Marker selection
Fingerprinting
Genotyping
Molecular
Analysis
Quality Assurance
Trait analysis
Genetic Analysis
QTL Analysis
Index Analysis
Data
Selected lines
Recombines
Recombination
plans
Breeding
Decisions
MB design tool,
Cross prediction
and Strategic
simulation
Breeding Project
Breeding nursery
and pedigree
record
management
System
Trial field book
and environment
characterization
system
Field Trial
Genotypic Data
Statistical analysis
applications and
selection indices
Analytical
Pipeline
MABC
MAS
MARS
GWS
Decision
Support System
Breeding Applications
Lab book,
quality assurance
and diversity
analysis

26. The MARS Breeding Workflow

27. 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

28. 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.

29. The Integrated Breeding Platform: Communities
Ndeye Ndack Diop

30. 14 use cases selected as first phase users of IBP30

31. 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
Having in mind GCP sun set it is important for GCP to identify and implement way to make available GCP research products to a large number of scientists in the world. CoP has been identify as one way to get there but also as a user case of the IBP.

32. Existing COPs Future plans 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