Broadening the genetic diversity underpinning seed quality and yield related traits in mustard rape and oilseed rape

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Vegetable oils are an important part of the human diet, providing essential fatty acids. Amongst the most important oilseed crops, second in global production only to soybean, are the oilseed Brassica crops. These are principally the species B. napus (oilseed rape; cultivated widely in the UK) and B. juncea (mustard rape; cultivated widely in India). Both are recently-formed allotetraploids (containing the Brassica A and C genomes in the case of B. napus and the A and B genomes in the case of B. juncea), so both suffer from the complications arising from polyploidy and a lack of genetic diversity in breeding material. Broadening the genetic bases of the crops and identifying the genes underpinning trait variation are important objectives in both species.In addition to being important crops, the Brassica species represent an excellent system in which to study the evolution of genomes and the quantitative control of traits during the "diploidisation" process following polyploidy. All three diploid Brassica genomes (A, B and C) have been sequenced (those of B and C genomes are unpublished, but available under collaboration agreements). Powerful new technologies, based on Illumina transcriptome sequencing have been developed and applied to B. napus, enabling the development of a detailed gene-based genomic framework and the capability of associating, across diversity panels, trait variation with both gene sequence variation and gene expression variation.In the proposed research, 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. In doing this, we will: (1) establish genomic resources for B. juncea to match those already developed by the group of IB for B. napus, (2) analyse the evolution of the B genome relative to those of the A and C genomes, (3) establish functional genotypes for a B. juncea diversity panel and an expanded B. napus panel, (4) identify candidate genes and alleles for crop improvement and (5) promote knowledge exchange with the breeding industries to facilitate crop improvement.The proposed research builds upon ongoing activities of the applicants, involves the sharing of genetic resources and includes a strong training element. The transcriptome corresponding to the B genome will be assembled to form a unigene set using Illumina mRNAseq data obtained from B. nigra. Leaf transcriptome sequencing will be undertaken for a B. juncea DH mapping population and used, in combination with unigenes corresponding to the A and B genomes for the construction of a detailed SNP linkage map. The linkage map will be used to organise genome sequence scaffolds of the A and B genomes into pseudomolecules that will be used to define hypothetical orders of unigenes in the A and B genomes of B. juncea. The evolutionary histories of the Brassica A, B and C genomes will be analysed, as observed in the diploid species and the allotetraploids B. juncea and B. napus, since their divergence from a common ancestor. Leaf transcriptome sequencing will be undertaken for a B. juncea diversity panel and additional lines of a B. napus diversity panel, SNP variation will be scored across the respective panels and transcripts quantified across all accessions. The diversity panels will be analysed, in suitable environments, for the variation of traits prioritised in consultation with the breeding and farming industries in India and the UK and used for Associative Transcriptomics analysis. The traits are anticipated to include seed composition traits analysed in the UK (content of oil, protein, glucosinolates, erucic acid, linolenic acid, tocopherols) and resistance to various biotic and abiotic stresses analysed in India. Knowledge of the genetic bases for trait variation and markers for beneficial alleles will be generated and made available for crops.