GRM 2013: The Integrated Breeding Platform: Overview -- G McLaren and M Sawkins

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GRM 2013: The Integrated Breeding Platform: Overview -- G McLaren and M Sawkins

  1. 1. The Integrated Breeding Platform: Overview Graham McLaren & Mark Sawkins GCP-GRM 27th September 2013 Lisbon
  2. 2. Integrated Breeding Platform  IBP - a one-stop-shop where breeders can access:  Databases (germplasm, pedigree, phenotypic, genotypic and environmental)  A configurable workflow system (CWS)  Logistics and data management tools  Breeding planning and management tools  Analytical tools  Breeding decision support tools  High throughput breeding services  Support services to use these facilities  Scientific network  Deploy integrated breeding technology for sustainability and development
  3. 3. http//www.integratedbreeding.net
  4. 4. Updates to the IBP Portal • Change of the overall look and feel to match the IBWS • The preliminary translation into Spanish, available at https://www.integratedbreeding.net/es • Numerous additions to our Biblio database, accessible from the crop community pages and to our CB resources and news pages • Development of a dedicated download page for the IBWS at https://www.integratedbreeding.net/integrated- breeding-workflow-system-1 • Development of a page for flagship marker products for IB at https://www.integratedbreeding.net/gcp-marker- products-integrated-breeding
  5. 5. Integrated Breeding Multi-year Course – IB-MYC  3 years  3 modules (Molecular breeding, Data analysis, Data management)  Target of 3 regions (WCA, ESA and S&SEA):  Broad reach (GCP community and beyond)  60 trainees per region  Breeders (senior and junior)  Master’s / PhD students
  6. 6. West & Central Africa East & Southern Africa South & Southeast Asia & Northern Africa Benin 3 Burundi 1 Algeria 2 Burkina Faso 4 Ethiopia 11 Bangladesh 9 Cameroon 2 Kenya 16 China 10 Ghana 8 Malawi 5 India 22 Ivory coast 2 Mozambique 3 Indonesia 1 Mali 11 South Africa 2 Morocco 2 Niger 3 Tanzania 11 Nepal 1 Nigeria 13 Uganda 8 Pakistan 1 Senegal 8 Zambia 1 Philippines 2 Zimbabwe 4 Thailand 2 Tunisia 1 Vietnam 1 Totals 54 62 54 Participants to IB-MYC by country
  7. 7. # Crop Region Total ESA WCA SSEA 1 Beans 19 — 1 20 2 Cassava 4 10 — 14 3 Chickpeas 8 — 15 23 4 Cowpeas 3 11 — 14 5 Groundnuts 7 3 8 18 6 Maize 11 5 4 20 7 Rice 4 12 11 27 8 Sorghum 4 11 — 15 9 Soya beans 1 1 2 4 10 Wheat 1 1 13 15 TOTALS 170 Participants to IB-MYC by crop
  8. 8. Required to complete successfully the assignments:  Data management (generate its own database using germplasm and phenotyping data)  Statistics (Analyse data of its own experimentation)  Molecular breeding (Describe steps of a MB project) Trainee evaluation From the 170 trainees:  8 did not complete any assignment  3 failed  3 missing one assignment  156 passed to Year2 (at least 2 successfully completed assignments)
  9. 9. INSTALLINGThe Integrated Breeding Workflow System
  10. 10. GETTINGSTARTED
  11. 11. REGISTERING USERS
  12. 12. THE PROJECT DASHBOARD
  13. 13. CREATING PROJECTS 1. Select your crop 2. Choose a workflow 3. Specify project members
  14. 14. MARS Workflow Project Planning Plan MARS Timelines (3) Browse Germplasm Information Browse Studies and Datasets Browse Germplasm Lists Browse Genotyping Data QTL SelectionPhenotypic Analysis Single-Site Analysis for Local Datasets Multi-Site Analysis Breeding View Standalone (All Analyses) Population Development Import Germplasm Lists (1) Manage Germplasm Lists (2) Make Crosses Manage Nurseries Field Trial Management Create Fieldbooks Genotyping Manage Genotyping Data QTL Analysis Breeding View Standalone (All Analyses) Recombination Cycle Manage Recombination Cycles (4) Make Crosses Manage Nurseries Final Breeding Decision Head-to-Head Query (coming soon) 1. Link invokes the Fieldbook with the Nursery Manager view showing; link to import germplasm list is the first entry in the menu. 2. Link leads to the List Browser tool in the Workbench 3. Link launches the freestanding Breeding Planner application 4. Launches OptiMAS
  15. 15. Conventional Breeding Workflow Project Planning Browse Germplasm Information Browse Studies and Datasets Browse Germplasm Lists Browse Genotyping Data Population Development Import Germplasm Lists (1) Manage Germplasm Lists (2) Make Crosses Manage Nurseries Field Trial Management Create Fieldbooks Statistical Analysis Single-Site Analysis for Local Datasets Multi-Site Analysis Breeding View Standalone (All Analyses) Breeding Decision Head-to-Head Query (coming soon) 1. Link invokes the Fieldbook with the Nursery Manager view showing; link to import germplasm list is the first entry in the menu. 2. Link leads to the List Browser tool in the Workbench
  16. 16. MAS Workflow Project Planning Browse Germplasm Information Browse Studies and Datasets Browse Germplasm Lists Browse Genotyping Data Population Development Import Germplasm Lists (1) Manage Germplasm Lists (2) Make Crosses Manage Nurseries Field Trial Management Create Fieldbooks Statistical Analysis Single-Site Analysis for Local Datasets Multi-Site Analysis Breeding View Standalone (All Analyses) Breeding Decision Head-to-Head Query (coming soon) Genotyping Manage Genotyping Data 1. Link invokes the Fieldbook with the Nursery Manager view showing; link to import germplasm list is the first entry in the menu. 2. Link leads to the List Browser tool in the Workbench
  17. 17. MABC Workflow Project Planning Plan MABC Timelines (3) Browse Germplasm Information Browse Studies and Datasets Import Germplasm Lists (1) Manage Germplasm Lists (2) Browse Germplasm Lists Browse Genotyping Data Backcrossing Manage MABC Data Make Crosses Manage Nurseries Field Trial Management Create Fieldbooks Statistical Analysis Single-Site Analysis for Local Datasets Multi-Site Analysis Breeding View Standalone (All Analyses) Breeding Decision Head-to-Head Query (coming soon) Genotyping Manage Genotyping Data 1. Link invokes the Fieldbook with the Nursery Manager view showing; link to import germplasm list is the first entry in the menu. 2. Link leads to the List Browser tool in the Workbench 3. Link launches the freestanding Breeding Planner application
  18. 18. All Tools Menu Administration & Configuration Project Members Backup Project Restore From Backup File Project Methods Project Locations Make a Crossing Template (4) Data Management Fieldbook Genotyping Data Management System (GDMS) Project Planning Molecular Breeding Planner (MBP) (3) Germplasm Browser Germplasm List Browser Study Browser Analysis Pipeline Single site analysis for Local Datasets Multi-site Analysis for Local Datasets Breeding View Standalone (All Analyses, including QTL) QTLxE Analysis (future?) Breeding Management Germplasm Import (1) List Manager (2) Crossing Manager Nursery Manager Decision Support Molecular Breeding Decision Tool (MBDT) OptiMAS (Manage Recombination Cycles) Head-to-Head Query (coming soon) 1. Link invokes the Fieldbook with the Nursery Manager view showing; link to import germplasm list is the first entry in the menu. Future item is to develop a management tool for other templates also. 2. Link leads to the List Browser tool in the Workbench 3. Link launches the freestanding Breeding Planner application 4. Leads to the Nursery File Template portion of the Crossing Manager
  19. 19. QueryTools
  20. 20. IBP Breeders’ Queries Breeders’ Queries 1: Head to head comparisons
  21. 21. Breeders Queries to come • Query for Adapted Germplasm • Find Trait Donors • Data mining • Check for stability
  22. 22. GERMPLSM IMPORT Simplified import template
  23. 23. Wizard Process 1.Open the template 2.Specify germplasm details 3.Save the list
  24. 24. TheCrossingManager
  25. 25. IMPROVED LABEL PRINTING AND INVENTORY MANAGEMENT NurseryManager
  26. 26. MULTI-FACTORIAL TREATMENT STRUCTURES SUPORTED TheIBFieldbook

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