The Integrated Breeding Platform: Overview

Graham McLaren & Mark Sawkins GCP-GRM 27th September 2013 Lisbon

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

http//www.integratedbreeding.net

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

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

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

# 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

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)

INSTALLIN

G

The Integrated Breeding Workflow System

GETTING STARTED

REGISTERING USERS

THE PROJECT DASHBOARD

CREATING PROJECTS

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

MARS Workflow

Project Planning Plan MARS Timelines (3) Browse Germplasm Information Browse Studies and Datasets Browse Germplasm Lists Browse Genotyping Data

QTL Selection

Phenotypic 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

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

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

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

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

Query Tools

IBP Breeders’ Queries

Breeders’ Queries 1: Head to head comparisons

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

GERMPLSM IMPORT

Simplified import template

Wizard Process

1.Open the template

2.Specify germplasm details

3.Save the list

The Crossing Manager

IMPROVED LABEL PRINTING AND INVENTORY MANAGEMENT

Nursery M

anager

MULTI-FACTORIAL TREATMENT STRUCTURES SUPORTED

The IB Fieldbook