GGIAR Generation Challenge Programme

(GCP)

Partnerships in modern crop breeding

for food security

November 2011

GCP in brief

Launched in August 2003

10-year framework (2004–2008; 2009–2013)

About US$15M annual budget

Via CGIAR (DFID, EC, SDC, USAID, CG Fund Council)

Bill & Melinda Gates Foundation

Target areas: Harsh drought-prone environments

Africa (SSA), S & SE Asia, LA

Mandate crops Cereals: maize, rice, sorghum, wheat,

Legumes: beans, chickpeas, cowpeas, groundnuts

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

Partnerships

GCP network

Technology

Germplasm

Breeding

Needs

CGIAR

ARIs Products/Impact

Farmer’s field

Country

programmes

NGOs

Private

sector

Germplasm

Environments

The GCP network in 2010:

200+ Institutes

Private

sector

Partnerships

EPMR panel noted that GCP community is one of the

Programme’s crucial assets. In their words: “Perhaps the

most important value of GCP thus far, is the opportunities

it has provided for people of diverse backgrounds to think

collectively about solutions to complex problems, and, in

the process, to learn from one another.”

Linking upstream with applied science

The sorghum case: From Cornell to Moi University with a

stop in Brazil

Within a decade: Plantlet under hydroponics – Gene

cloned – Favourable alleles identified – Improved

germplasm for Brazil – Improved germplasm for Kenya

Evolution of roles and responsibilities

Leader become mentors

Trainees become doers and leaders

Major achievement: GCP community

Research Themes and Logframe

Databases, Information Network

Germplasm Genes Molecular breeding

Improved germplasm in farmers’ fields

Phenotyping Phenotyping

Breeding programmes

Improved genotypes

Delivery Plans

Research Organisation (Management)

1. Integrated crop breeding

Human resources & infrastructure

3. Crop information systems

2. Comparative and applied genomics

Products

4. Capacity building

5. Product delivery

The two phases of the Programme

Phase I (2004–2008):

A combination of commissioned and competitive projects

‘Opportunistic’ and high project turn over

Establishing the GCP community

Identifying the winners and opportunities for Phase II

Phase II (2009–2013):

Mid-term activities

Focused and targeted research

Major effort in service development

Clear impact indicators by 2013 to evaluate success

A needs and bottom-up approach: Research and services

2014: Transition year

Selected major outputs

Access to genetic resources

Genotyping for 21 reference sets of CGIAR mandate crops

Substitution lines (groundnuts, rice)

Mutant collections (rice, potatoes, beans)

Synthetics (groundnuts and wheat)

MAGIC (cowpeas, rice, sorghum) NAM (rice) BCNAM, (sorghum)

Development of genomic resources

BAC libraries and EST sequences (legumes, cassava)

New markers: DArTs, SSRs and SNPs (all crops)

Identification of markers for biotic stresses

Validated markers for resistance to pests and diseases for beans,

cassava, chickpeas, cowpeas, groundnuts, maize, potatoes and rice

Selected major outputs

Identification of markers for abiotic stresses

Tolerance to Al toxicity in sorghum and salinity and phosphorus

deficiency in rice

Drought tolerance in chickpeas, cowpeas, maize, rice, wheat

New tools

GIS, bioinformatic and data management tools

Marker tool kit

Enhanced capacities in country programmes

Human capacities / Local infrastructure / Analytical power

Socioeconomic studies

Ex ante analyses MB impact in developing countries

Impact briefs

Basis: RIs are crop-, crop cluster-, and area-based

Key trait: Main focus of all the RIs is drought tolerance

Target crops/area and target countries/countries of planned research

1. Cassava: Nigeria, Ghana, Tanzania, Uganda/Brazil, Colombia

2. Legumes

Beans: Ethiopia, Kenya, Malawi, Mexico, Nicaragua, Zimbabwe

Chickpeas: Ethiopia, India, Kenya

Cowpeas: Burkina Faso, Mozambique, Senegal/USA

Groundnuts: Malawi, Senegal, Tanzania

3. Maize: China, India, Indonesia, Kenya, Thailand, The Philippines, Vietnam

4. Rice: Africa – Burkina Faso, Mali, Nigeria; Asia – Bangladesh, Cambodia,

Thailand, Vietnam, Myanmar

5. Sorghum: Mali (additional countries via CoP to be established)/Australia

6. Wheat: Africa – Ethiopia, Morocco; Asia – China, India/Australia

7. Comparative genomics to improve cereal yields in high-aluminium and low-

phosphorus soils (maize, rice, sorghum): Indonesia, Kenya, Niger/Brazil

The 7 Research Initiatives:

50% of GCP resources to RIs in Phase II

An Integrated Breeding Platform

to support reeding in the South

Overall objective To provide access to modern breeding technologies, breeding material and related information in a centralised and functional manner to improve plant breeding efficiency in developing countries.

Short-term objective To establish a minimum set of tools, data management infrastructure and services to demonstrate that molecular breeding can be efficiently applied to eight crops spread across 14 user cases

Multilateral funding for an overall budget

of US$ 20M over 5 years

Mainly Gates, DFID, EC

www.integratedbreeding.net

The IB Platform will offer:

Access to Breeding Services: • well characterised and useful genetic resources • quality, economic high throughput genotyping • sophisticated phenotype and metabolite analyses

Access to Informatics Tools: • for breeding logistics and data management • analysis and decision support for molecular breeding • accumulated public crop information of certified quality

Capacity Development - Training and support for: • planning and comparing breeding strategies • data management and curation and quality control • analysis and decision support • use of markers and molecular breeding techniques • phenotyping sites and protocols • use and protection of intellectual property

Community development • support for communities of practice by crop or discipline • facilitation of germplasm exchange

The IBP will not do breeding per se

Integrated Breeding Platform

Breeding

Services

Support

Services S

erv

ices

Configurable Breeding Workflow System

Cyber Infrastructure

Custom

Formatted

Data

Files

Local

Database

Web Service

Data Source

High

Performance

Computer

Info

rmation S

yste

m

Po

rta

l

SoapLab MOBY, GDPC,

BioCase/TAPIR

Data Sources

AA

The IBP Configurable Breeding Workflow System

Breeding Activities

Parental selection

Crossing

Population

development

Germplasm

Management

Open Project

Specify objectives

Identify team

Data resources

Define strategy

Project

Planning

Experimental Design

Fieldbook production

Data collection

Data loading

Germplasm

Evaluation

Marker selection

Fingerprinting

Genotyping

Data loading

Molecular

Analysis

Quality Assurance

Trait analysis

Genetic Analysis

QTL Analysis

Index Analysis

Data

Analysis

Selected lines

Recombines

Recombination

plans

Breeding

Decisions

Administration

Project conf.

Workbench

administration

&

configuration

Breeding

Management

System

Trial Fieldbook

Environment

characterization

system

Field Trial

Management

System

Genotypic

Data

Management

System

Sample

management

Analytical

Tools

Sel. Indices

Breeding App.

MARS App.

Cross Prediction

Simulation

Decision

Support Tools

Breeding Applications Analytical Pipeline

Breeding mana.

Genealogy mana.

Query tools

Sample mana.

Data management

Statistical analysis

Molecular Genetic

Conclusion and Perspectives

Major Challenges Today

M&E: Implement realistic workplans Clear milestones, products and timelines

Reliable Delivery Plans with clear impact indicators

Ensure delivery and sustainable use of GCP products

Product delivery strategy

Reinforce ownership by the GCP community

Partnership Balance community momentum and a focused research agenda

Data release and quality control Difficult to finish the work (time, resources)

Still not a lot of data in our Central Registry today

Quality and documentation are very variable

Change in mindset: from institutional to corporate

Conclusions

A vibrant community bridging the gap between basic and

applied agricultural science providing new tools for plant

breeding

Agile programme structure

Dynamic network of partners

Significant amount of products already been generated

Already an impact in the breeding community

Visit us: www.generationcp.org

The success of the GCP will be judged on the

quality of the science and relevance of its

products for impact on crop improvement

GCP people:

The Programme’s greatest asset!

Participants of the GCP General Research Meeting, September 2011