integrated breeding platform (ibp): a user-friendly platform to implement the curriculum for african...
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Slides presented at University of Eldoret, Kenya, including faculty staff and students from Moi UniversityTRANSCRIPT
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)
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
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
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
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
https://www.integratedbreeding.net/
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
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
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
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
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
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
Breeding Management Trait Dictionaries
Measurement Variate
Trait property
Reporting units or scale
Measurement method
Breeding Management Trait Selector
Breeding Management Germplasm List Manager
Breeding Management IBP Fieldbook
Breeding Management Bar Code labels
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
Fieldbook connects to Android-based tablet devices for data collection in the field and laboratory
Breeding Management Tablet Devices
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
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
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
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
Genotyping Data Management
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
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
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
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
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
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
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
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
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
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