integrated breeding platform (ibp): a user-friendly platform to implement the curriculum for african...

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

http://www.generationcp.org

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


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.


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


https://www.integratedbreeding.net/

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


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


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


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


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.


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


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


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


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.


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.


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


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


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


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


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.


integrated breeding platform (ibp): a user-friendly platform to implement the curriculum for african...

Technology

african plant breeders

breeding activities

cgiar breeding programmes

molecular breeding technology

reuse of breeding d

advanced plant science

data management tools

rudimentary tools