Dissection of the genetic architecture of seed erucic acid content and consequences for breeding in Brassica napus L.

Oilseed rape ( Brassica napus L.) is an important oilseed crop worldwide. The seed erucic acid content (SEAC) determines the quality of the extracted rapeseed oil, with lower SEAC levels indicating higher quality oil. To elucidate the genetic mechanism underlying SEAC and identify candidate SEAC-regulatory genes, a panel of 393 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 1.6 million high-quality single-nucleotide polymorphism (SNP) markers. We identified 19 genetic regions significantly associated with SEAC using factored spectrally transformed linear mixed model (FaST-LMM), with the phenotypic variation explained (PVE) ranging from 16.67 % to 47.66 %. Additionally, a transcriptome-wide association study (TWAS) was conducted on the SEAC of this association panel, identifying 366 significantly associated genes. Eight genes were identified in both the GWAS and TWAS, and their expression levels were significantly correlated with the SEAC. A candidate gene association analysis and haplotype analysis revealed several low-SEAC haplotypes, and inbred lines combining the low-SEAC haplotypes had lower SEAC and seed glucosinolate contents but higher unsaturated fatty acids, without affecting the overall seed oil content or seed yield. A molecular marker ( Bn_C3_SEAC_Marker ) was developed based on the functional SNPs within candidate genes by using the cleaved amplified polymorphic sequence (CAPS) method. The candidate genes, favorable haplotypes, and molecular markers identified in this study will contribute to the cultivation of high-quality B. napus varieties. • Identify genes affecting B. napus seed erucic acid content by GWAS and TWAS. • Eight genes affecting B. napus seed erucic acid content was identified. • Identified six low erucic acid haplotype. • B. napus with excellent haplotypes had lower erucic acid, but other quality traits are not affected. • Developed a molecular marker for low erucic acid breeding in B. napus.