Evolution of genomes: Structure-function relationships in the polyploid crop species Brassica napus

所有植物的基因组都经历了多倍体(在此期间发生全基因组复制)和二倍化(在此期间复制的基因组稳定)的循环。这一循环代表了生物过程的遗传控制进化的基本机制，也是几乎所有作物物种多样性和表现的关键驱动因素。我们对二倍体过程的大部分理解是基于对古代多倍体事件之后二倍体过程的结果的分析。然而，最近的结果表明，二倍化所涉及的基因组进化机制可能正在影响重要作物物种的特征，即在其祖先最近的多倍体事件发生数千年后。作为具有可变基因组进化速率的复杂多倍体的模型，我们将研究甘蓝型油菜，其中包括欧洲的主要油料作物油菜。可获得的材料范围很广，既有自然界形成的甘蓝型油菜(由油菜和甘蓝属植物自发杂交形成的异源四倍体，是油菜育种的主要遗传多样性来源)，也有经历快速基因组变化的人工合成甘蓝型油菜(由同一物种在实验室诱导杂交形成)。我们假设，在重新合成的甘蓝型油菜中观察到的基因组进化代表了在自然来源的栽培甘蓝型油菜中正在进行的基因组进化的加速形式。我们的目标是通过在一大批天然和重新合成的甘蓝型油菜(包括衍生群体)中描述全基因组规模的分子进化来验证这一假设，将观察到的基因组结构变化与油菜作为作物的相关性的性状变化联系起来。我们的具体目标是：(1)建立甘蓝型油菜泛转换组，由代表新生甘蓝型油菜基因组的有序单基因(EST组件)组成。(2)量化天然形成的甘蓝型油菜的拷贝数变异(转录序列)和同源交换的频率。(3)量化在重新合成的甘蓝型油菜中存在的(转录序列的)拷贝数变异和同源交换的频率，并将其与在自然界形成的甘蓝型油菜中观察到的频率进行比较。(4)了解基因组结构进化如何影响该作物的一系列重要性状的性状变异。这项研究将由一个国际财团与来自英国、德国和法国的合作伙伴共同进行。合作伙伴是各自领域的世界领先专家，拥有互补的专业知识，能够对共享材料进行多学科调查。这些结果将为植物基因组进化的基础分子生物学提供重要的见解。重要的是，它将在可用于改良欧洲最重要的作物品种之一的材料的背景下做到这一点。

The genomes of all plants have evolved through cycles of polyploidy (during which whole genome duplication occurs) and diploidisation (during which those duplicated genomes stabilise). This cycle represents a fundamental mechanism by which the genetic control of biological processes evolve and is a key driver of diversity and performance in almost all crop species. Most of our understanding of the diploidisation process is based on analyses of its outcomes following ancient polyploidy events. Recent results, however, have suggested that the genome evolution mechanisms involved in diploidisation may be having effects on traits in important crop species now, i.e. thousands of years after the most recent polyploidy events in their ancestry.As a model for a complex polyploid with variable rates of genome evolution we will study Brassica napus, which includes the principal oilseed crop in Europe, oilseed rape. A wide range of accessions are available, of both B. napus formed in nature (an allotetraploid formed by spontaneous hybridization of B. rapa and B. oleracea species; the main source of genetic diversity for rapeseed breeding) and resynthesised B. napus (formed by induced hybridization of the same species in the laboratory), which undergoes rapid genome change. We hypothesise that the genome evolution observed in resynthesised B. napus represents an accelerated form of the genome evolution that is ongoing in cultivated B. napus derived in nature. We aim to test this hypothesis by characterising molecular evolution on a genome-wide scale in a large panel of natural and resynthesised B. napus, including derived populations, relating the observed variation in genome structure to trait variation of relevance for rapeseed as a crop. Our specific objectives are: (1) Establish the B. napus pan-transciptome, comprising ordered unigenes (EST assemblies) representing the nascent B. napus genome. (2) Quantify the frequency of copy number variation (of transcribed sequences) and homoeologous exchanges present in B. napus formed in nature. (3) Quantify the frequency of copy number variation (of transcribed sequences) and homoeologous exchanges present in resynthesised B. napus, comparing it with the frequency observed in B. napus formed in nature. (4) Understand how genome structural evolution affects trait variation, for a range of traits of importance in this crop.The research will be conducted by an international consortium with partners from UK, Germany and France. The partners are world-leading experts in their fields and have complementary expertise, enabling multidisciplinary investigation of shared material. The results will provide important insights into the fundamental molecular biology of plant genome evolution. Importantly, it will do this in the context of material that can be used for the improvement of one of the most important crop species in Europe.