Accessing genotyping services for crop improvement in developing countries.

The Generation Challenge Program (GCP) experience

An initiative of the CGIAR Generation Challenge Programme (GCP)

Mark Sawkins Plant and Animal Genome 2015

San Diego, CA

What was the Generation Challenge Programme?

A CGIAR Challenge Program based at CIMMYT 10 year duration (2004-2013) closing 2014 170 million USD over 11 years Target regions – drought prone Phase I mandated crops - 18 Phase II mandated crops – 9 Cereals: maize, rice, sorghum, wheat Legumes: beans, chickpeas, cowpeas, groundnuts Roots and tubers: cassava

Research arranged around 5 themes Comparative and applied genomics, integrated crop breeding,

crop information systems, capacity building, product delivery.

Objective

To use GENETIC DIVERSITY and ADVANCED PLANT SCIENCE to IMPROVE CROPS for greater food security in

the developing world

GCP to be a broker in plant science bridging the gap between upstream and applied science

Integrated Breeding Platform (IBP) Conceived during phase II of the GCP “To improve the efficiency of plant breeding programmes in

developing countries by enabling plant breeders to access modern breeding technologies, breeding materials and related information in a centralised, integrated and practical manner”.

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

Why the Integrated Breeding Platform?

A need identified to facilitate the adoption of breeding technologies and kick start molecular breeding Access to tools and information Provide training of public sector and private sector SME

scientists in the methodologies readily available to the large private seed companies Streamline the process of data exchange (collection; analysis;

utilization) Encourage best practices in data management

Integrated Breeding Platform

Software tools Breeding Management System (BMS)

Breeding services and products Genotyping Support Services (GSS) supporting first time users

from developing country breeding programmes; Trait and metabolite, drought phenotyping and other

phenotyping services; Location analysis and climate resources online

Professional support Establishment of regional “hubs” to support and promote use of

IBP software and services. • Breeding support; Capacity building, social networks and CoPs

Technologies offered

Focus on SNP technology with understanding that some crops were not as advanced (SSR). Key partners sought for GCP clients

Why the KASP Platform?

A unique chemistry for detecting Single Nucleotide Polymorphisms (SNPs) Advantages High conversion rate Low cost Accuracy Flexibility

LGC offers a high-throughput operation with full service from DNA extraction to genotypic scores Technology well suited to Marker Assisted Breeding

(MAB) projects

Development of KASP SNPs

Each of the crop communities selected and nominated a set of about 2000 SNP sequences Crop community chose a set of 94 diverse germplasm for

the validation of assays; For the SNP conversion, each of the KASP assays was

created enough for genotyping a total of 2500 samples from the crop community

Number of SNP assays developed for each GCP crop

The number of KASP SNP markers developed by GCP for SNP genotyping

Crops SNP source No. of SNPs Maize Cornell University 1250 Cowpea University of California Riverside 1122 Chickpea ICRISAT 2068 Pigeonpea ICRISAT 1616 Rice Cornell University 2015 Cassava IITA , University of Maryland 1740 Sorghum Cornell University 1503 Common bean USDA – ARS (USA) 1497 Wheat Kansas State University 1864 Soybean USDA – ARS (USA) 1082 Groundnut ICRISAT 91

Usage statistics for LGC by GCP clients

Year Samples Datapoints Samples Datapoints2010-2011 22848 4981920 41760 53171522011-2012 31720 3817150 12712 40665742012-2013 34787 4175378 9127 33880712013-2014 43093 3922150 14463 3039257TOTAL 132448 16896598 78062 15811054

GCP (Direct) GCP (Indirect)

Distribution of Global Breeding Programs Utilizing KASP SNPs Through IBP

Genotyping Support Services (GSS)

Facilitate access by developing-world agricultural research and development organisations to genotyping technologies Provide a bridge between laboratory and field research Includes support and training in analysis for proper

interpretation of genotypic and phenotypic data Assist developing-country scientists to benefit from the

latest technologies by subcontracting genotyping work Initiated in 2006, the first three calls (2007, 2008 and

2009) were open. GCP changed its GSS strategy in 2011 to focus on developing-country partners already involved in GCP’s Research Initiatives or other projects related to capacity building.

Genotyping Support Service (GSS)

The approach Call for small grants (up to USD 10K) Embedded in other research activities Financial and technical support for breeders in developing countries

to access molecular marker technology Access to cost-efficient outsourced genotyping services (LGC, 32m

dp) Support in experimental design and data analysis for diversity

analyses and marker implementation Impact Total about 173 projects funded; 234,000 SSR data and 3,885,000

SNP data generated, representing 18 crops for teams working in 35 countries

Most services in the areas of germplasm characterization, MTA discovery (QTL mapping) and implementation (BC, MAS)

Extension of GSS – Integrated Breeding Multiyear Course (IB-MYC)

Provide training for a core group of scientists working on GCP and non-GCP projects in three target regions West and Central Africa (WCA) Eastern and Southern Africa (ESA) South and Southeast Asia and Northern Africa (SSEA & NA).

Began in 2012 Trains scientists in modern breeding analytical tools and

methods to be able to undertake integrated breeding projects. Serve as a basis to enhance the adoption of Integrated

Breeding Platform (IBP) tools.

Extension of GSS – Integrated Breeding Multiyear Course (IB-MYC)

Supplementary activities Opportunity to initiate a small MB project was offered first to

IB–MYC trainees who had never conducted any MB, and secondly to those who had experience in MB but were not involved in a GCP project

GCP’s GSS provided support for up to 35,000 data points for projects using SNP markers and 3,500 data-points for those using SSRs (simple-sequence repeat) Project focus on QTL (quantitative trait loci) identification,

MAS (marker-assisted selection) or MABC (marker-assisted backcrossing); diversity studies and association mapping were not covered

GSS and Phase II of IBP

Access to GSS to registered users of the IBP IBP portal

Regional hubs Champion IBP tools and services in their respective regions Facilitate adoption by new users and foster strong regional

networks Work directly with local users to get feedback and inform them

of new BMS functionalities consistent with their needs.

Regional Hubs

IBP and LGC Genomics – Moving Forward Improved communication with IBP users Professional media covering sampling procedures and submission

of samples/projects Newsletter covering topics of interest to IBP clients Improved sharing and posting of news and information

Improved tools to aid decision making Pricing calculator Easier selection of SNP assays from LGC/IBP webpage Improved process of submitting projects direct from LGC/IBP

webpages Access for IBP clients to additional LGC resources (e.g.

Publications catalogue)

IBP and LGC Genomics – Moving Forward

Improvements made to sampling kits Expanding access to SNP assays Additional crops (e.g. Lentil) Additional markers

• Random markers • Diagnostic markers (publicly available SNP markers and GCP derived)

Active participation of LGC staff to IBP capacity building opportunities (e.g., training courses, workshops, meetings) Continuation of competitive pricing for IBP clients

registered on IBP portal

IBP and LGC Genomics

IBP and LGC Genomics

MTA SNP conversion

Implementable markers available in different technologies

Marker discovery projects in GCP Consultation with breeders to determine

which markers are routinely used in breeding and what technologies

In silico mapping of markers on a consensus map to identify SNP alternatives to original MTA

Diagnostic marker information will be available from IBP website and ordering through portal to LGC Genomics

Genotyping for developing countries – the GCP experience

Training essential for GCP/IBP clients The technology Where in the breeding process markers can be useful and for what

objectives Best practices in using the sampling kits and sending samples

Communication between IBP, users and genotyping service provider Regular feedback on progress of project Feedback from users on the nature of the project

Tools to improve efficiency of genotyping projects Selection of markers Submission and monitoring of projects Storage and rapid access of results for analysis and use

• E.g. customization of BMS to easily upload LGC Genomics genotyping files

Acknowledgement GSS Carmen de Vicente - initiated the GSS Humberto Gomez – GSS Coordinator Chunlin He - GSS Coordinator Ndeye Ndack Diop – GSS support

GSS and IB-MYC Theresa Fulton (Cornell) Fred van Eeuwijk (WUR) Marcos Malosetti (WUR) Xavier Delannay (GCP) Hamer Paschal Magni Bjarnason

LGC Genomics Darshna “Dusty” Vyas

Title of presentation/Author

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