Award details

SeeDs of Discovery

Reference	BBS/OS/NW/000016
Principal Investigator / Supervisor	Professor Mario Caccamo
Co-Investigators / Co-Supervisors
Institution	National Inst of Agricultural Botany
Department	National Inst of Agricultural Botany Department
Funding type	Research
Value (£)	1,250,000
Status	Completed
Type	Research Grant
Start date	01/04/2016
End date	31/03/2018
Duration	23 months

Abstract

We propose to deploy a computing hardware and software platform and initiate the implementation of advanced analyses of wheat genotype and phenotype data generated by the Seeds of Discovery (SeeD) programme. The platform will integrate computing resources and expertise at TGAC, CIMMYT and NIAB with the purpose of facilitating data-intensive bioinformatics analyses to leverage data generated by SeeD and other initiatives such as the International Wheat Yield Partnership (IWYP) for the genetic improvement of wheat. This platform and the proposed research will enable the incorporation of the extensive wheat genotype and phenotype data, collected to date and in the future, with the emerging wheat reference genomes and other diversity information generated at TGAC and other international wheat research centres. These datasets will be made readily available to the community via current public and open resources such as the Wheat Information System and the Ensembl Plants browser. This will directly add value to the SeeD and IWYP programmes and enhance their benefits to the wheat breeding and scientific community. This project will address some of the current constraints limiting the exchange and value addition from “big data” generated by SeeD, IWYP and other CIMMYT and broader wheat community projects.

Summary

CIMMYT (México) hosts the largest wheat and maize seed bank in the world. Both maize and wheat provide 40% of the world’s food therefore improving these crops has a direct impact on human nutrition and health. The Seeds of Discovery (SeeD) programme (http://seedsofdiscovery. org), with funding from the Mexican Government, aims to characterise every seed in the bank using a genomic fingerprint that can be used to uniquely identify a wheat or maize variety and find correlations with other fingerprints and information such as country of origin, quality and adaptation to climate or pests. The integration of this information (to create genomic datasets) allows breeders to accelerate their work and researchers to be more targeted in their experiments. The seed bank at CIMMYT contains thousands of maize and wheat seeds so the processing of the data generated by the programme is only possible by using large computers and databases. In this BBSRC-Newton funded project, we deployed an advanced computing hardware and software platform for the analysis of large genomics datasets for wheat varieties generated from the SeeD programme. The platform integrates computing resources and bioinformatics expertise in the UK to enable crop geneticists at CIMMYT to implement sophisticated data analysis algorithms to improve the use of genetic resources for wheat and other important crops. The computing platform is distributed across the partners’ sites with hardware deployed at CIMMYT in Mexico and The Earlham Institute in UK. This hardware has been configured to be accessed remotely by researchers at CIMMYT and eventually by other scientists across the globe. We will address some of the current constraints limiting the exchange of ‘big data’ generated by SeeD, the International Wheat Yield Partnership, and other CIMMYT and broader wheat community projects. The datasets generated by this project will be made readily available to the community via current public and open resources. This will directly add value to the SeeD and other programmes to enhance the benefits to the wheat breeding and scientific community. The better use of the wheat genetic resources will directly impact on the development of new crops with better yields and better equipped to adapt to climate change.

Committee	Not funded via Committee
Research Topics	Crop Science, Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	Newton Fund - Initial Awards (NFIA) [2017]
Funding Scheme	X – not Funded via a specific Funding Scheme

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