Copy-Number Variation in Flowering-Time Regulators as a Driving Force for Adaptation of Brassica napus

The allopolyploid nature of the Brassica napus genome enables exchange between different subgenomes, allowing for extensive variation within copy numbers of genes. This is expected to heavily influence traits regulated by affected genes, as demonstrated in numerous animal and plant species. To reveal if this would also prove true for flowering time regulation in B. napus, we performed deep sequencing of selected flowering regulators, captured in a diversity panel of 282 genetically divergent accessions, and determined copy number variation (CNV) by assessing coverage depth. Copies from the B. napus A subgenome were present in higher numbers than copies from the C subgenome. Some serial CNV events pointed to larger insertions or deletions. We also detected CNV events which seem to be specific for a certain morphotype, for example, a homeoelogous translocation concerning Bna.FLC on A10/C09 in swedes (B. napus ssp. napobrassica), which might be responsible for their particularly strong vernalisation requirement. The data give novel insight into the consequences of polyploidisation on pan-genomic variation, and will be very useful when considering linkage analysis and genome-wide association studies.