Slides presented at University of Eldoret, Kenya, including faculty staff and students from Moi University

1. Integrated Breeding Platform (IBP):
A user-friendly platform to implement the
curriculum for African plant breeders and
support African plant scientists
Ndeye Ndack Diop, Capacity Building Theme Leader
Antonia Okono, Communications Manager
University of Eldoret, Kenya, March 2014
An initiative of the CGIAR
Generation
Challenge Programme (GCP)

2. GCP in Brief
 Launched in August 2003
 10-year framework (2004–2008; 2009–2013)
 About US$15M annual budget
 Bill & Melinda Gates Foundation
 CGIAR donors (DFID, EC, SDC, USAID, WB)
 Target areas: Harsh drought-prone environments
 Africa (SSA), S & SE Asia, LA
 Mandate CGIAR crops
 Cereals: Maize, rice, sorghum, wheat,
 Legumes: bean, chickpea, cowpea, groundnut
 Root and tubers: Cassava
 A CGIAR Challenge Programme hosted at CIMMYT
Main objective: To use genetic diversity and advanced plant science to improve
crops for greater food security in the developing world
GCP : A broker in plant science bridging the gap between upstream and
applied science
www.generationcp.org
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

3. Rationale for the IBP
 Large private seed companies have successfully
implemented extensive suites of integrated informatics
tools to turbocharge their breeding programs
 Implementation of this integrated informatics in public
programs lags behind, especially in developing countries
 Some tools have been developed at various CG centers, but
implementation has been uneven and they are not integrated
into a comprehensive system
 Most NARS programs still rely on rudimentary tools, from pen
and paper to Excel spreadsheets
 Small SMEs in developing countries typically do not have the
resources to acquire available commercial software or to
implement breeding IT systems on their own
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

4. 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.
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

5. IBP Users
 Primary target:
 NARS partners wanting to enhance the effectiveness of
their breeding programmes by integrating molecular
methods and end-to-end informatics pipelines
 All interested CGIAR breeding programmes and networks
 SMEs working in developing countries, without the in-
house capacity to build a breeding workflow system
 Secondary target:
 Basically anyone running breeding activities
 Both the public and the private sectors
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

6. https://www.integratedbreeding.net/

7. Overview of the
Breeding Management System
A platform for African plant breeders
N.N. Diop and A. Okono – March 2014
Image courtesy of FreeDigitalPhotos.net

8. Breeding Management System (BMS) –
Product Concept
 Simple and easy-to-use application containing all informatics
tools needed by a breeder
 Seamless flow of data between applications
 Accumulation, sharing and re-use of breeding data
 Targets routine breeding activities and will not replace
research tools
 Will allow integration of users own tools into the system
 Implementable as a standalone system
 Access central and local DB, as well as the BMS on a local PC
 Will also be implementable as a cloud-based system via
iPlant cyber-infrastructure
 For computationally intensive analyses or large data storage
needs
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

10. List Manager Functionality
 The List Manager is at the center of all activities in the
Breeding Management System:
 First screen you arrive at after opening your Breeding Program
 New left navigation menu provides direct access to all tools
 Easily build and work with the lists that are used in each stage of
the breeding cycle
 Key List Manager Features:
 Ability to browse and modify existing lists
 Ability to search for lists and germplasm entries
 Ability to create a new list dynamically by pulling from existing
lists or germplasm search results
 Expanded ability to modify list contents
 Ability to export lists for use outside of the Breeding Management
System
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

12. Nursery Management
 Breeding Manager configured for different crops
 Crossing manager, nursery manager, pedigree recording
 Focuses on population development and line selection
 Nursery advance and seed inventory tracking
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014
Breeding manager fully integrated into BMS
workbench

14. Trial Management
 IB Fieldbook
 Focuses on field trial management for germplasm evaluation
 Trait selection, field design, labels and sample tracking
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014
Field books fully integrated into BMS workbench

15. 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.
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

16. Breeding Management
Trait Dictionaries
Measurement
Variate
Trait property
Reporting
units or scale
Measurement
method

17. Breeding Management
Trait Selector

18. Breeding Management
Germplasm List Manager

19. Breeding Management
IBP Fieldbook

20. Breeding Management
Bar Code labels

21. Trial Management
 Android-based hand-held device
 Optimized for use with Samsung Galaxy tablet for field data collection
 Other Android devices can be used if preferred
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014
Field books fully integrated into BMS workbench

22.  Fieldbook connects to Android-based tablet devices for
data collection in the field and laboratory
Breeding Management Tablet Devices

23. Integrated Breeding Database
 Genealogy Management System (GMS)
 Germplasm nomenclature, chronology, IP and passport data
 Pedigrees and breeding history
 Phenotyping Data Management System (DMS)
 Germplasm characterization and evaluation data
 Annotated with Crop Research and Crop Trait Ontologies
 Genotypic Data Management System (GDMS)
 Medium density fingerprinting data
 Genotyping data for MAS and MABC
 Genotyping data for Marker-trait association analysis
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014
Databases fully integrated into BMS workbench

24. Query Tools
 At the outset of a breeding cycle users want to:
 browse all germplasm information
 review existing characterization and evaluation
 search for adapted germplasm
 perform head to head comparisons
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

25. Statistical Analysis of Phenotyping Data
 Breeding View provides easy access to the high throughput
analyses routinely required by breeders
 The same interface can be used to access procedures in
Genstat or R-scripts and allows analyses to be configured
 Single site analysis is available for complete and incomplete
block designs as well as row-column designs and spatial
analysis. New designs are being added at each update,
 Analyses can be run in batches over environments and traits,
 Two-stage multi-site analysis is available for GxE and stability
analysis with or without grouping of environments,
 Single pass meta analysis of unbalanced site by season data
is being incorporated.
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014
Tools to be fully integrated into the BMS by June 2014

27. Genotyping
 To use molecular technologies, the breeder wants to:
 select population,
 select markers,
 genotype population,
 check and store genotyping data.
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

28. Genotyping Data Management

29. Breeding View - QTL analysis
 Single trait linkage analysis
(QTL)
 Quality control phenotypes
(summary statistics)
 Quality control marker data
 QTL detection – genome wide
scan using single and
composite IM
 Output includes profile plots and
tables
 Results available for automatic
viewing in Flapjack
 HTML report of QTL results
 Multiple trait sequential analysis
 QTL results for each trait
combined
 Single Flapjack view for all traits

31. Decision support for 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
MAS and MABC context

32. Future Directions
 Continuous improvement of UI based on user feedback
 Additional analysis methods for expanded experimental
designs and genetic analysis
 Seed inventory management system
 LAN based deployment available in January, cloud
based deployment available in June
 Data will be stored in a single shareable database with
user access roles
 Off-line capability will be supported by a data cache
which will synchronize when a connection is available
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

33. Implementation of the regional hubs
and support from the
Agricultural Universities
A platform for African plant breeders
N.N. Diop and A. Okono – March 2014
Image courtesy of FreeDigitalPhotos.net

34. GIS
Centralized
Crop DB
(CGIAR)
Crop
Ontology
Crop
info
Local
Pheno
DB
Breeding
Services
Geno/Pheno
Genotyping
DB
BMS
Predictive markers
Crop Simple traits
Atlas
Capacity
Building
Elearning
Communities
of Practice
Social
Network
Forum
Problem
solving
Professional and Technical Support Service: Central team and Regional Hubs
Protocols
Access to Germplasm and Genetic resources
IBP Core business
Manuals
Tutorials
DM good
practice
policy
DB Breeding information Services Info/Knowledge
Courses
IBP: Components and Products

35. The Support Services
 Professional Support to be provided in three ways:
 Client-oriented breeding support primarily targeting developing-country
breeders
 Capacity building support to provide professional and comprehensive
training in orientation to, and using, the tools
 Interaction with peers through social networks and CoPs
 Technical Support to be provided at two levels to all users:
 Level 1: installation technical support
• To overcome any difficulties in downloading, installing and getting started
with the BMS and related tools
 Level 2: operational technical support
• for users that might encounter problems in day-to-day use of the BMS and
related tools
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014
Considering the nature of IBP and the very diverse potential users of the BMS,
it is critical to provide a top-quality support services to ensure sustainable
adoption

36. Central Support Team:
Managers plus ad hoc
specialists
Promotion and commercialization Team
Users from Tier 2
C&S America African Asia
(Europe, North America)
DB/DM
BMS CB
Breeding
Coordinate and facilitate
access to IBP tools and
services
User Feedback to impact
on IBWS development and
implementation

37. Perspectives for IBP
 Phase 2
 Recommended by BMGF to be used in some of the
agricultural projects
 Likely to be funded
 Host
 Regional hubs will be the engine that will drive IBP to
provide localised and contextualised CB and support
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

38. Collaboration with Ag universities
Training the next generation of breeders for:
 Increased level of adoption of the integrated management
of breeding data and digitisation of the breeding programs
 Link newly trained breeders to existing data, efficiency in
their use, link with a community
How?:
 Incorporate a portion of the tools and some of the
integrated breeding concepts in the curriculum at
University and Breeding College level
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014

39. Steps taken
 In selection process of IB-MYC candidates, deliberate mix of
scientists and lecturers in view of future trainers to take care
of regional, national or awareness training
 Endorsement of BMGF for the use of IBP tools in the “Web-
based plant breeding curriculum project”.
 Collaboration with UC-Davis on the use of IBP tools in their
Plant Breeding Academy training programmes
 Collaboration with University of Illinois on the “Soybean
Innovation Laboratory project, SIL” to train African Soybean
breeders.
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014