The document describes an Integrated Breeding Platform (IBP) that aims to provide a user-friendly platform and tools to support plant breeders in Africa. The IBP will provide access to high-throughput breeding services, data management tools, analysis pipelines, and decision support tools. It will also offer support and communities of practice. The core is a Breeding Management System that will integrate various tools to support the entire breeding workflow from crossing to variety release. The IBP will be implemented through regional hubs and with support from agricultural universities to train new breeders and increase adoption of integrated breeding approaches.
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Integrated Breeding Platform Provides Tools for African Plant Breeders
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
Egerton University, 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
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
9.
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
11.
12. Breeding Logistics
Once the strategy and parental material have been
identified, the breeder wants to:
make crosses,
develop populations,
track pedigrees,
track inventory,
characterize lines
A platform for African plant breeders – N.N. Diop and A. Okono – March 2014
13. Nursery and Trial 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
IB Fieldbook
Focuses on field trial management for germplasm evaluation
Trait selection, field design, labels and sample tracking
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
Breeding manager and Field books
fully integrated into BMS workbench
14.
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
21. Fieldbook connects to Android-based tablet devices for
data collection in the field and laboratory
Breeding Management Tablet Devices
22. 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
23. 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
24. 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
25.
26. 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. 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
29.
30. 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
31. 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
32. 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. 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
35. 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
36. 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