Integrated Breeding Platform (IBP):
A user-friendly platform to implement the
curriculum for African plant breeders and
su...
GCP in Brief
 Launched in August 2003
 10-year framework (2004–2008; 2009–2013)
 About US$15M annual budget
 Bill & Me...
Rationale for the IBP
 Large private seed companies have successfully
implemented extensive suites of integrated informat...
Vision
The IBP will provide a one-stop-shop where breeders can
access:
 high-throughput breeding services,
 logistics an...
IBP Users
 Primary target:
 NARS partners wanting to enhance the effectiveness of
their breeding programmes by integrati...
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...
Breeding Management System (BMS) –
Product Concept
 Simple and easy-to-use application containing all informatics
tools n...
List Manager Functionality
 The List Manager is at the center of all activities in the
Breeding Management System:
 Firs...
Breeding Logistics
 Once the strategy and parental material have been
identified, the breeder wants to:
 make crosses,
...
Nursery and Trial Management
 Breeding Manager configured for different crops
 Crossing manager, nursery manager, pedigr...
Field Testing
 Once populations are developed, the breeder wants to:
 select traits,
 make lists of germplasm,
 genera...
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
 Fieldbook connects to Android-based tablet devices for
data collection in the field and laboratory
Breeding Management T...
Integrated Breeding Database
 Genealogy Management System (GMS)
 Germplasm nomenclature, chronology, IP and passport dat...
Query Tools
 At the outset of a breeding cycle users want to:
 browse all germplasm information
 review existing charac...
Statistical Analysis of Phenotyping Data
 Breeding View provides easy access to the high throughput
analyses routinely re...
Genotyping
 To use molecular technologies, the breeder wants to:
 select population,
 select markers,
 genotype popula...
Genotyping Data Management
Breeding View - QTL analysis
 Single trait linkage analysis
(QTL)
 Quality control phenotypes
(summary statistics)
 Qua...
Decision support for marker implementation
 OptiMAS
 Developed at INRA, Le
Moulon
 Implementation of markers in a
MARS ...
Future Directions
 Continuous improvement of UI based on user feedback
 Additional analysis methods for expanded experim...
Implementation of the regional hubs
and support from the
Agricultural Universities
A platform for African plant breeders
N...
GIS
Centralized
Crop DB
(CGIAR)
Crop
Ontology
Crop
info
Local
Pheno
DB
Breeding
Services
Geno/Pheno
Genotyping
DB
BMS
Pred...
The Support Services
 Professional Support to be provided in three ways:
 Client-oriented breeding support primarily tar...
Central Support Team:
Managers plus ad hoc
specialists
Promotion and commercialization Team
Users from Tier 2
C&S America ...
Collaboration with Ag universities
Training the next generation of breeders for:
 Increased level of adoption of the inte...
Integrated Breeding Platform (IBP): A user-friendly platform to implement the curriculum for African plant breeders and su...
Integrated Breeding Platform (IBP): A user-friendly platform to implement the curriculum for African plant breeders and su...
Integrated Breeding Platform (IBP): A user-friendly platform to implement the curriculum for African plant breeders and su...
Integrated Breeding Platform (IBP): A user-friendly platform to implement the curriculum for African plant breeders and su...
Integrated Breeding Platform (IBP): A user-friendly platform to implement the curriculum for African plant breeders and su...
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Integrated Breeding Platform (IBP): A user-friendly platform to implement the curriculum for African plant breeders and support African plant scientists – NN Diop and A Okono

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Slides presented at Egerton University, Njoro, Kenya, in March 2014

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Integrated Breeding Platform (IBP): A user-friendly platform to implement the curriculum for African plant breeders and support African plant scientists – NN Diop and A Okono

  1. 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. 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. 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. 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. 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. 6. https://www.integratedbreeding.net/
  7. 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. 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. 9. 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
  10. 10. 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
  11. 11. 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
  12. 12. 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
  13. 13. Breeding Management Trait Dictionaries Measurement Variate Trait property Reporting units or scale Measurement method
  14. 14. Breeding Management Trait Selector
  15. 15. Breeding Management Germplasm List Manager
  16. 16. Breeding Management IBP Fieldbook
  17. 17. Breeding Management Bar Code labels
  18. 18.  Fieldbook connects to Android-based tablet devices for data collection in the field and laboratory Breeding Management Tablet Devices
  19. 19. 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
  20. 20. 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
  21. 21. 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
  22. 22. 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
  23. 23. Genotyping Data Management
  24. 24. 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
  25. 25. 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
  26. 26. 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
  27. 27. 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
  28. 28. 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
  29. 29. 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
  30. 30. 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
  31. 31. 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

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