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

甘蓝型油菜是一个年轻的异源多倍体物种，遗传多样性有限，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，油菜近缘种之间的种间杂交经常被用来产生合成的甘蓝型油菜。人工合成的甘蓝型油菜杂种在第一次减数分裂中的基因组碰撞导致了显著的基因组变化，但在某些合成类型的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，由有益基因组改变驱动的显性效应可以促进人工合成甘蓝型油菜的杂种优势潜力，并且特定的基因组优势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表现性状相关的结构基因组变异提供了新的机会。在这项提案中，我们将生成和组合与来自高度对比的天然和合成甘蓝型油菜亲本品系之间的杂交的高级后代相关的独特的基因组和表观数据集，以及高质量的参考基因组组合，这些组合阐明了亲本和他们的F1杂交后代之间的结构性基因组变异。在中德两国领先的油菜研究小组长期合作的基础上，我们提出了一个多维的“组学”方法来研究这个杂交组合的杂种优势基础，该杂交组合在德国和中国的生长条件下都显示出异常强大的杂种优势。首先，我们将评估F1与其人工和天然甘蓝型油菜亲本(在德国和中国的对比环境中生长)的杂种优势模式，基于对高质量全基因组组装在调节性(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。其次，我们将在衍生的F2群体中识别与杂种优势有关的数量性状基因座(QTL)，在两个国家进行田间表型鉴定，并通过测序将QTL投影到双亲的组装基因组上，同时分析原始亲本及其F1的结构、调控和表观遗传学特征。最后，我们将把这些数据与之前由两个合作伙伴生成的其他重测序和表观遗传学数据集进行全面比较。总体目标是评估基因组结构变异如何影响甲基化模式、miRNA和mRNA的表达，以及它们与高度分化的异源多倍体亲本的杂种优势的关系。除了有助于对基因组进化和复杂多倍体的杂交优势是如何由染色体碰撞及其与杂种优势的关联进行总体理解之外，这些结果还将为中国、德国和世界范围内未来高产油菜杂交种的生产提供非常新颖的见解。

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.