The high‐quality genome of <i>Brassica napus</i> cultivar ‘<scp>ZS</scp>11’ reveals the introgression history in semi‐winter morphotype

Abstract

Summary Allotetraploid oilseed rape ( Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B . napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi‐winter oilseed rape cultivar ‘ ZS 11’ and its comprehensive genomic comparison with the genomes of the winter‐type cultivar ‘Darmor‐ bzh ’ as well as two progenitors. The integrated BAC ‐to‐ BAC and whole‐genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high‐quality genome assembly of B . napus ‘ ZS 11’. Within a short evolutionary period (~6700 years ago), semi‐winter‐type ‘ ZS 11’ and the winter‐type ‘Darmor‐ bzh ’ maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to ‘Darmor‐ bzh ’, both two subgenomes of ‘ ZS 11’ are closely related to its progenitors, and the ‘ ZS 11’ genome harbored several specific segmental homoeologous exchanges ( HE s). Furthermore, the semi‐winter‐type ‘ ZS 11’ underwent potential genomic introgressions with B . rapa (A r ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03. FLC 3 regulating vernalization‐responsive flowering time in ‘ ZS 11’ was first experienced HE , and then underwent genomic introgression event with A r , which potentially has led to genetic differences in controlling vernalization in the semi‐winter types. Our observations improved our understanding of the genetic diversity of different B . napus morphotypes and the cultivation history of semi‐winter oilseed rape in Asia.