Award details

Digital Cassava Genebank - Phase 1

Reference	BBS/OS/NW/000022
Principal Investigator / Supervisor	Dr Sarah Dyer
Co-Investigators / Co-Supervisors	Dr David Marshall
Institution	National Inst of Agricultural Botany
Department	National Inst of Agricultural Botany Department
Funding type	Research
Value (£)	259,156
Status	Completed
Type	Research Grant
Start date	01/12/2016
End date	31/08/2018
Duration	20 months

Abstract

1) Elucidate the genetic makeup of the global cassava collection held at the CIAT genebank. Genotyping-by-sequencing data from the DArT-seq platform will be available for 4,000 genebank accessions by the end of 2016. We will analyse these data to reveal the genetic relationships between these accessions and to provide a molecular framework for trait-association studies. 2) Assemble and deploy a foundational suite of software tools for a Digital Cassava Genebank. We will deploy the Germinate data warehouse and associated software tools for storing passport, characterisation, and GBS data, linked to Digital Object Identifiers (DOI) of genebank accessions where available. We will develop pilot software that enables Germinate to communicate with, and automatically upload data from GRIN-Global. 3) Whole-genome sequence a group of high-value accessions. We will sequence a set of frequentlyused cassava accessions, assemble reads, call variants and deploy appropriate browsing tools. 4) Capacity building and scientific exchanges. Two research staff from CIAT will visit NIAB and SRUC for training in quantitative genetics and bioinformatics applications. Two PDRAs from SRUC and NIAB will visit CIAT to take stock of passport and characterization data to be uploaded to Germinate and to demonstrate the approaches and results from the GBS data analyses.

Summary

CIAT, the International Center for Tropical Agriculture is working to modernise its Genebank. This will create a 21st century genetic-resources centre to not only conserve crop diversity but also actively develop its potential for crop improvement and climate adaptation. The Digital Cassava Genebank project will take advantage of developments in genomic, phenomic, and big-data technologies to enable a more targeted and data-driven use of genetic resources to improve the nutritional value, productivity and climate resilience of its mandate crops. Cassava (Manihot esculenta) is the third most important source of calories in the tropics. It is used for food, animal feed, starch production and biofuels, and it grows well on marginal soils and with low rainfall and few inputs, making it an essential reserve crop in times of famine. CIAT's genebank contains ~6,600 accessions of cassava and its wild relatives. Currently little is known about these accessions beyond their collection data, making it difficult to select the most appropriate materials for research and breeding. The project will explore 4,000 samples from the cassava collection held in trust at CIAT using genotyping-by-sequencing data to elucidate the genetic relationships among these accessions. In addition, whole genome sequences for an initial set of 25 high-priority accessions which span the diversity will be generated. The resulting data together with the necessary computational infrastructure and software tools are being put in place to store, visualize and share the genetic and collection data with researchers and breeders, as a foundation for the Digital Cassava Genebank. We anticipate that this project will also stimulate further collaboration and capacity-building through scientific exchanges between researchers from the UK and Colombia.

Committee	Not funded via Committee
Research Topics	Crop Science, Plant Science, Technology and Methods Development
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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