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性（在此期间发生全基因组复制）和二倍体化（在此期间这些复制的基因组稳定）的循环。这一循环代表了生物过程遗传控制进化的基本机制，是几乎所有作物物种多样性和性能的关键驱动力。我们对二倍体化过程的大多数理解都是基于对古代多倍体事件后其结果的分析。 然而，最近的研究结果表明，二倍体化中涉及的基因组进化机制可能对重要作物物种的性状产生影响，即在其祖先中最近的多倍体事件发生数千年后，作为基因组进化速率可变的复杂多倍体的模型，我们将研究甘蓝型油菜，其中包括欧洲主要的油料作物油菜。B两种都有广泛的加入。自然形成的甘蓝型油菜（B. rapa和B.甘蓝物种;油菜育种遗传多样性的主要来源）和再合成的B。欧洲油菜（通过实验室中相同物种的诱导杂交形成），经历快速的基因组变化。 我们假设在再合成的B中观察到的基因组进化。欧洲油菜代表了在栽培B中正在进行的基因组进化的加速形式。自然界中的油菜。 我们的目标是通过在一个大的天然和再合成的B面板的全基因组范围内的分子进化特征来测试这一假设。油菜，包括衍生群体，将观察到的基因组结构变异与油菜作为作物的相关性状变异相关联。我们的具体目标是：（1）建立B。napus泛转录组，包括代表新生B的有序单基因（EST组装体）。油菜基因组(2)定量B中存在的拷贝数变异（转录序列）和同源异构体交换的频率。油菜是自然形成的。(3)定量再合成的B中存在的拷贝数变异（转录序列的）和同源异构体交换的频率。与B.油菜是自然形成的。(4)了解基因组结构进化如何影响该作物一系列重要性状的性状变异。该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进行。 合作伙伴是各自领域的世界领先专家，具有互补的专业知识，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，它将在可用于改善欧洲最重要的作物物种之一的材料的背景下这样做。

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.