Integrating genome assembly, structural variation map construction and GWAS reveal the impact of SVs on agronomic traits of Brassica napus.

key messageAn SV map of B. napus was constructed, SVs association with four agronomic traits were identified. This study provides a more systematic insight into the genetic variation of rapeseed. Rapeseed (Brassica napus L.) is one of the most major oil crops. The rapeseed genome is rich in structural variation (SV), while the functional identification and utilization of SVs are currently limited. In this study, genomes of two rapeseed accessions (4D122 and 5DH2900) were assembled, and the quality of both genomes has been improved compared to the most commonly used rapeseed reference genome ZS11. Using the long-reads sequencing data of 25 representative rapeseed accessions, an SV-map of B. napus was constructed, which contained the position and sequence information of 183,723 SVs; and combining with the long-reads data of 18 B. rapa and 26 B. oleracea accessions, an SV-map of A subgenome and C subgenome of Brassica was also constructed. Based on the SV-map, an SV-set containing 350 rapeseed accessions was constructed using resequencing data with an average sequencing depth of 25 × . SV-GWAS and SNP-GWAS revealed loci that associated with four agronomic traits of rapeseed, including glucosinolate concentrations in seeds (SGC), silique length, leaf trichomes and purple stem. Some potentially causal SVs were identified, such as SVs introduced from B. oleracea was found to may result in purple stem in rapeseed. Overall, this study provided abundant genomic resources for rapeseed, and systematically identified SVs in rapeseed genome and revealed their association with agronomic traits, lay the foundation for revealing the functions and breeding potential of SVs.