Asymmetrical Genome Evolution and its Impact on Trait Formation in Brassica Crops

Genome polyploidization has provided significant sources of genetic variation for plant adaptive evolution and new species formation. However, the way in which molecular evolution of polyploid genomes builds up genetic architecture underlying speciation is unclear and its impact imposed on trait formation involving duplicate genes is unknown. Brassica is an ideal model to address these questions and thereby we conducted comparative genome analysis of newly sequenced Brassica oleracea, B. rapa and B. napus.

 

We revealed multi-layered modes of asymmetrical subgenome evolution. These layers include: massive and asymmetrical subgenomic gene loss, asymmetrical variations in paralogous DNA sequences, expression differentiation of triplicated, α-duplicated and tandem duplicated genes, asymmetrical alternative splicing variants between the subgenomes (Liu et al. Nature Communications 5:3930, 2014) and asymmetrical homeologous exchanges (Chalhoub et al. Science, 2014), asymmetrical epigenomes and asymmetrical recombination between the genomes A and C in B. napus. The epigenomes include small RNA, DNA methylation and histone modification. Further, we used associated markers from a genome-wide association study of a large population to have revealed differences in detectable traits such as flowering time and oil content between syntenic regions of subgenomes A and C. These patterns provide new insight into genome evolution underlying speciation and trait formation and will underpin research in genetic improvement of these important crops.