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

植物油是人类饮食的重要组成部分，提供必需脂肪酸。在全球产量仅次于大豆的最重要的油籽作物中，有芸苔属油籽作物。这些主要是B. napus（油菜籽油菜；在英国广泛种植）和B. juncea（芥菜油菜；在印度广泛种植）。两者都是最近形成的异源四倍体（甘蓝型油菜包含芸苔A和C基因组，芥菜包含A和B基因组），因此两者都遭受多倍体和育种材料遗传多样性缺乏引起的并发症。拓宽作物的遗传基础和鉴定性状变异的基因是这两个物种的重要目标。芸苔属植物不仅是一种重要的作物，而且是研究多倍体后“二倍体化”过程中基因组进化和性状数量控制的一个很好的系统。所有三个二倍体芸苔基因组（A、B和C）都已测序（B和C基因组的测序未发表，但可通过合作协议获得）。基于Illumina转录组测序的强大新技术已经开发并应用于甘蓝型油菜，使其能够建立详细的基于基因的基因组框架，并能够跨多样性面板将性状变异与基因序列变异和基因表达变异联系起来。在拟议的研究中，我们的目标是了解支撑一组对芥菜和油菜商业生产重要的初始性状数量变异的主要遗传基础。在此过程中，我们将：(1)建立芥菜基因组资源，与IB小组已经开发的甘蓝型油菜基因组资源相匹配；(2)分析B基因组相对于A和C基因组的进化；(3)建立甘蓝型油菜多样性面板和扩展甘蓝型油菜面板的功能基因型；(4)确定作物改良的候选基因和等位基因；(5)促进与育种行业的知识交流，以促进作物改良。拟议的研究建立在申请人正在进行的活动的基础上，涉及遗传资源的共享，并包括一个强有力的培训因素。利用从黑螺旋藻中获得的Illumina mRNAseq数据，将B基因组对应的转录组组装成一个单一的基因集。将对芥菜DH定位群体进行叶片转录组测序，并将其与a和B基因组对应的unique基因结合使用，构建详细的SNP连锁图谱。该连锁图谱将用于将A和B基因组的基因组序列支架组织成假分子，这些假分子将用于定义芥菜A和B基因组中假设的单基因序列。将分析芸苔A、B和C基因组的进化历史，正如在二倍体物种和异源四倍体juncea和napus中观察到的那样，因为它们从一个共同的祖先分化而来。将对芥菜B. juncea多样性小组和甘蓝型B. napus多样性小组的其他品系进行叶片转录组测序，在各自的小组中对SNP变异进行评分，并对所有材料的转录进行量化。在适当的环境下，将对多样性小组进行分析，以与印度和英国的育种和农业行业协商，优先考虑性状的变化，并用于联合转录组学分析。预计这些性状将包括在英国分析的种子组成性状（油、蛋白质、硫代葡萄糖苷、芥酸、亚麻酸、生育酚的含量）和在印度分析的对各种生物和非生物胁迫的抗性。性状变异的遗传基础知识和有益等位基因的标记将产生并提供给作物。

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 All three diploid Brassica genomes (A, B and C) have been sequenced (those of B and C genomes are unpublished, but available under collaboration agreements).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.