1. The Integrated Breeding
Platform: Overview
Graham McLaren & Mark Sawkins
GCP-GRM
27th September 2013
Lisbon

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. http//www.integratedbreeding.net

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. 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. 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. # 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. 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. INSTALLINGThe Integrated Breeding Workflow System

10. GETTINGSTARTED

11. REGISTERING USERS

12. THE PROJECT DASHBOARD

13. CREATING PROJECTS
1. Select your crop
2. Choose a workflow
3. Specify project members

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. 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. 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. 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. 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. QueryTools

23. IBP Breeders’ Queries
Breeders’ Queries 1:
Head to head comparisons

24. Breeders Queries to come
• Query for Adapted Germplasm
• Find Trait Donors
• Data mining
• Check for stability

26. GERMPLSM IMPORT
Simplified
import
template

27. Wizard Process
1.Open the
template
2.Specify
germplasm
details
3.Save the
list

28. TheCrossingManager

30. IMPROVED LABEL PRINTING AND
INVENTORY MANAGEMENT
NurseryManager

31. MULTI-FACTORIAL TREATMENT
STRUCTURES SUPORTED
TheIBFieldbook