Genome-wide association study identifies candidate genes and favorable haplotypes for seed yield in Brassica napus

Oilseed rape (Brassica napus L.) is one of the most essential oil crops. Genetic improvement of seed yield (SY) is a major aim of B. napus breeding. Several studies have been reported on the genetic mechanisms of SY of B. napus. Here, a genome-wide association study (GWAS) of SY was conducted using a panel of 403 natural accessions of B. napus, with more than five million high-quality single-nucleotide polymorphisms (SNPs). A total of 1773 significant SNPs were detected associated with SY, and 783 significant SNPs were co-located with previously reported QTLs. The lead SNPs chrA01__8920351 and chrA02__4555979 were jointly detected in Trial 2_2 and Trial 2_mean value, and in Trial 1_2 and Trial 1_mean value, respectively. Subsequently, two candidate genes of BnaA01g17200D and BnaA02g08680D were identified through combining transcriptome, candidate gene association analysis, and haplotype analysis. BnaA09g10430D detected through lead SNP chrA09__5160639 was associated with SY of B. napus. Our results provide valuable information for studying the genetic control of seed yield in B. napus and valuable genes, haplotypes, and cultivars resources for the breeding of high seed yield B. napus cultivars.