13 ERA-CAPS 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（整个基因组发生复制）和二倍体（复制的基因组稳定下来）的循环进化。这种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因素。我们对二倍体化过程的大部分理解是基于对古代多倍体事件后其结果的分析。然而，最近的结果表明，涉及二倍体化的基因组进化机制现在可能对重要作物物种的性状产生影响，即在它们祖先中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，它包括北欧主要的油料作物，油菜。品种范围广泛，既有自然形成的油菜（由油菜和甘蓝自发杂交形成的异源四倍体，是油菜籽育种遗传多样性的主要来源），也有重新合成的油菜（由同一物种在实验室诱导杂交形成），后者经历了快速的基因组变化。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界衍生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全基因组范围内对天然和再合成的油菜（包括衍生种群）的分子进化进行表征来验证这一假设，并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联系起来。我们的具体目标是：(1)建立甘蓝型油菜泛转录组，包括代表新生甘蓝型油菜基因组的有序单基因（EST组装）。(2)量化甘蓝型油菜在自然界中形成的拷贝数变异（转录序列）和同源交换的频率。(3)量化重组甘蓝型油菜中拷贝数变异（转录序列）和同源交换的频率，并将其与自然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性状变异，对该作物的一系列重要性状。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，可以对共享材料进行多学科研究。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，它将在材料的背景下做到这一点，这些材料可用于改善欧洲最重要的作物物种之一。

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 northern Europe's principal oil crop, 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 Europe's most important crop species.