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

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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.