Genome-wide patterns of heterotic vigour associated with allopolyploid chromosome collision

油菜（Brassica napus）是一种遗传多样性有限的年轻异源多倍体，是中国和德国的主要油料作物。为了扩大可用于育种的遗传基础，经常在相关的芸苔属物种之间进行种间杂交，以产生合成的甘蓝型油菜。合成甘蓝型油菜第一次减数分裂时的基因组碰撞导致了显著的基因组改变，但在某些合成甘蓝型油菜与天然甘蓝型油菜的杂交中可以观察到显著的杂种优势。我们假设有益的基因组改变所驱动的显性效应可以促进合成甘蓝型油菜的杂种优势潜力，并且杂种优势的特定基因组模式与异源多倍体染色体碰撞有关。现代基因组分析技术为研究和利用与作物性能性状相关的结构基因组变异提供了新的机会。在本提案中，我们将生成并结合独特的基因组和表型数据集，这些数据集与高度对比的天然和合成甘蓝型油菜亲本系杂交的高级后代相关，以及高质量的参考基因组组装，以阐明亲本与其F1杂交种之间的结构基因组差异。在中德领先油菜籽研究小组长期合作的基础上，我们提出了一种多维“组学”方法来研究该杂交品种杂种优势的基础，该杂交品种在德国和中国的生长条件下都表现出异常强大的杂种优势。首先，我们将基于高质量全基因组组装在调控（mRNA, miRNA）和表观遗传（全基因组亚硫酸盐）修饰背景下确定的结构重排的综合分析，评估F1与其合成和天然甘蓝型油菜亲本（在德国和中国的不同环境中生长）的杂种优势模式。其次，我们将在衍生的F2群体中确定有助于杂交活力的数量性状位点（QTL），在两个国家进行田间表型分析，并通过测序进行基因分型，将QTL投射到两个亲本的组装基因组上，同时分析原始亲本及其F1的结构、调控和表观遗传特征。最后，我们将与之前由两个合作伙伴生成的其他重测序和表观遗传数据集进行全面比较。总体目的是评估基因组结构变异如何影响高度分化的异源多倍体亲本的甲基化模式、miRNA和mRNA表达及其与杂种优势的关系。除了有助于了解染色体碰撞如何驱动基因组进化和复杂多倍体的杂交优势及其与杂种优势的关系外，该结果还将为未来中国、德国和世界范围内高产油菜籽杂交种的生产提供高度新颖的见解。

Rapeseed (Brassica napus), a young allopolyploid species with limited genetic diversity, is a major oil crop in both China and Germany. In order to broaden the genetic basis available for breeding, interspecific crosses between related Brassica species are frequently performed to generate synthetic B. napus forms. The genome collision in the first meiosis of synthetic B. napus hybrids results in significant genomic alterations, but remarkable heterosis can be observed in crosses between some synthetic forms and natural B. napus. We hypothesize that dominance effects driven by beneficial genome alterations can promote heterotic potential of synthetic B. napus, and that specific genomic patterns of heterotic vigour are associated with allopolyploid chromosome collision. Modern genome analysis techniques present new opportunities to investigate and exploit structural genome variation associated with crop performance traits. In this proposal we will generate and combine unique genomic and phenomic datasets associated with advanced progenies from crosses between highly contrasting natural and synthetic B. napus parental lines, along with high-quality reference genome assemblies that illuminate structural genome variation between the parents and their F1 hybrid. Building on a long-standing cooperation between leading Chinese and German rapeseed research groups, we propose a multi-dimensional "omics" approach to investigate the basis of heterosis in this cross, which shows unusually strong heterotic vigour under both German and Chinese growing conditions. Initially we will evaluate heterotic patterns of the F1 in comparison to its synthetic and natural B. napus parents (grown in contrasting environments in Germany and China), based on integrated analysis of structural rearrangements determined from high-quality whole-genome assemblies in the context of regulatory (mRNA, miRNA) and epigenetic (whole-genome bisulfite) modifications. Secondly, we will identify quantitative trait loci (QTL) contributing to hybrid vigour in a derived F2 population, with field phenotyping in both countries and genotyping-by-sequencing for projection of QTL onto the assembled genomes of the two parents accompanied by analysis in the context of structural, regulatory and epigenetic features in the original parents and their F1. Finally we will comprehensively compare the data with other resequencing and epigenetic datasets previously generated by the two partners. The overall aim is to assess how genome structural variants impact methylation patterns, miRNA and mRNA expression and their association with heterosis in highly divergent allopolyploid parents. Besides facilitating a general understanding of how genome evolution and the hybrid advantage of complex polyploids is driven by chromosome collision and its association with heterosis, the results will also provide highly novel insights for future production of high-yielding rapeseed hybrids in China, Germany and worldwide.