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Projects: Summary of Projects by Funding Source Projects awarded by BBSRC involving University of York : BB/L011751/1
Reference Number	BB/L011751/1
Title	Broadening the genetic diversity underpinning seed quality and yield related traits in mustard rape and oilseed rape
Status	Completed
Energy Categories	Not Energy Related 85%; Renewable Energy Sources(Bio-Energy, Other bio-energy) 15%;
Research Types	Basic and strategic applied research 100%
Science and Technology Fields	BIOLOGICAL AND AGRICULTURAL SCIENCES (Biological Sciences) 50%; BIOLOGICAL AND AGRICULTURAL SCIENCES (Agriculture, Veterinary and Food Science) 50%;
UKERC Cross Cutting Characterisation	Not Cross-cutting 100%
Principal Investigator	Professor I Bancroft Biology University of York
Award Type	Research Grant
Funding Source	BBSRC
Start Date	01 October 2014
End Date	30 September 2017
Duration	36 months
Total Grant Value	£535,181
Industrial Sectors	Transport Systems and Vehicles
Region	Yorkshire & Humberside
Programme	Crop Genomics and Technologies (CGAT)
Investigators	Principal Investigator	Professor I Bancroft , Biology, University of York
	Other Investigator	Dr M Trick , Computational and Systems Biology, John Innes Centre
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Objectives	The outcome of project will be new opportunities for adding value to oilseed Brassica crops (via improved seed composition) and improving their yield potential. These opportunities will be realised by breeders of oilseed/mustard rape, who will be able to design crossing strategies within each species and select alleles using molecular markers developed for polymorphisms identified in the project as being associated with the control of trait variation. Exploitation in B. napus of alleles present in the B genome of B. juncea, and exploitation in B. juncea of alleles present in the C genome of B. napus is more complex, but achievable by inter-specific crossing and marker-assisted selection of alleles captured by homoeologous recombination. In this way, knowledge and genetic resources can be exploited for crop improvement in both countries. The primary route for dissemination, knowledge exchange and commercialization will be via the lead partners in India and the UK. In the UK this will include engagements with organisations such as HGCA and via community meetings involving breeders, such as UK-BRC and OREGIN Stakeholder meetings. Contact will also be made with active UK-based companies working downstream of the breeders, such as farmers (e.g. Velcourt ltd) and processors (such as Cargill), with a view to early sharing of insights into progress and opportunities. In India, the knowledge generated through this project will be passed on to the breeders working in public sector organizations and private sector companies working on varietal development with value added products in oilseed brassicas which will ultimately benefit the farming community Once decisive insights into the first-order genetic control of key traits have been obtained, further refinement will be necessary in order to identify minor (but still important) components. This work can be undertaken by the private sector and both public and private sector in India, with advice from the academic partners in the project. This will require ramping up the genetic analysis to several hundreds of accessions. Where natural genetic variation of the type required for optimum performance has not been identified (e.g. where a gene knock-out or over-expression variant is required, but no such alleles are present in the diversity panel), induction of the necessary variation (for example by a mutagenesis approach followed by molecular selection) could be undertaken. Rapeseed breeders can undertake directly or subcontract trait analyses. Where activities such as sequence data processing are already routine, such as mRNAseq SNP identification and transcript quantification, commercial services are available, for example from the Cambridge-based company Eagle Genomics as a collaboration with U. York. A commercial service provider (Tag Genetics Ltd.) is available to undertake further association analyses for the breeders, if required.
Abstract	We aim to understand the principle genetic bases underpinning quantitative variation of an initial set of traits of importance for the commercial production of both mustard rape and oilseed rape, including: (1) Establish genomic resources for B. juncea to match those already developed for B. napus. This will involve assembly of the transcriptome of B. nigra, construction of a high density (>20,000 marker) transcriptome SNP linkage map of B. juncea and the development of DNA sequence pseudomolecules for the Brassica A and B genomes as represented in B. juncea. (2) Analyse the evolution of the B genome relative to those of the A and C genomes. This will involve comparative sequence-level analysis of sequence pseudomolecules for the Brassica A, B and C genomes as represented in B. juncea (A and B) and, from studies completed previously, B. napus (A and C). (3) Establish functional genotypes for a B. juncea diversity panel and an expanded B. napus panel. This will involve undertaking mRNAseq (using RNA from leaves) from panels of genetically diverse B. juncea and B. napus accessions, quantification of transcript abundance and SNP genotyping based on the sequence data. (4) Identify candidate genes and alleles for crop improvement. This will involve phenotypic analysis of the B. juncea and B. napus diversity panels for seed composition and yield, and Associative Transcriptomics to identify candidate genes and alleles controlling the traits and conversion of validated associations to molecular markers to assist breeding. (5) Promote knowledge exchange with the breeding industries to facilitate crop improvement. This will involve engagement with breeding, farming and processing industries in both India and UK, leading to new opportunities for adding value to oilseed Brassica crops (via improved seed composition) and improving their yield.
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Added to Database	01/12/14