Structural Genome Variation and Adaptive Potential in Brassica napus

Substantial genome restructuring, a well-known phenomenon in synthetic Brassica napus, may represent an accelerated form of genome evolution driven by de novo allopolyploidisation. We hypothesise that genome collisions during interspecific hybridisations accelerate Brassica molecular clocks, counteracting the loss of diversity due to intense allopolyploidisation bottlenecks and forming a key basis for natural and agricultural selection in the cultivated allopolyploid species. We are testing these hypotheses on a genome-wide scale, investigating large-scale mapping populations derived from crosses between natural and synthetic B. napus accessions. We find increasing evidence linking structural genome variation, due to homoeologous chromosome exchanges, with trait variation of relevance for oilseed rape breeding. This suggests a fundamental role of post-polyploidisation genome restructuring in the evolution and success of polyploid crops. Whole-genome resequencing of mapping parents allows identification of homoeologous chromosome rearrangements, and tracing these in segregating populations increases accuracy of B. napus genetic maps and allows associations of QTL to presence-absence and copy-number variants. Using methods to call segmental deletions and duplications from genome-wide SNP array data, we can also include copy-number and presence-absence variants in genome-wide association studies and genomic selection models. Validation of specific examples using sequence capture in large association panels demonstrates that structural genome rearrangements have played a highly significant role in creation of adaptive and agronomic diversity in B. napus, making it an important source of variation for natural and artificial selection. By moulding the B. napus pan-genome, structural variants can potentially also contribute strongly to heterotic potential.