Exploring the structural variant landscape in the highly dynamic genome of a recent allopolyploid crop species

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The recent allopolyploid crop species Brassica napus (oilseed rape, canola) has an unusually dynamic genome. Using long-read sequencing, we recently discovered that up to 10% of all genes in any given B. napus genotype are affected by functionally relevant, genome-wide gene conversions and deletions with high relevance for crop evolution and breeding. Because of their predominant size range (100bp~5kb), the great majority of genome-wide structural variants (SV) were undetectable by short-read sequencing in the highly-duplicated B. napus genome, hence their mechanisms and evolutionary consequences have not yet been studied. Based on robust methods developed in extensive preliminary work, we plan a detailed survey of the SV landscape in the B. napus pangenome, using long-read sequencing in 100 genetically diverse, homozygous accessions from a well-characterised global species collection. Assembly of a B. napus “Pangemome SV Atlas” will provide a valuable public tool to address the mechanisms of small-scale SV in polyploid genomes and re-visit extensive short-read datasets from previous studies. By identifying sequence motifs associated with genome-wide SV breakpoints and investigating SV patterns in the context of 3D genome structure and chromatin interactions, we aim for novel biological insight into the mechanisms underlying small-scale homoeologous exchanges, as a basis for predictive models that help to potentially harness the power of SV in breeding. In a practical case study, we will use the SV Atlas to associate SV in floweringpathway genes to ecogeographical adaptation traits. This will give novel insight into the role of SV in polyploid evolution and adaptation.