Genome-wide association study exposed the pleiotropic genes for yield-related and oil quality traits in Brassica napus L.

Oilseed rape (Brassica napus L.) is an allotetraploid (AACC, 2n ​= ​38) crop, valued for its edible oil and protein content. seed yield and nutritional composition of rapeseed are influenced by its yield and oil quality traits. However, the genetic basis of yield-related and oil-quality traits remain ambiguous. A panel of 266 diversified oilseed rape accessions was genotyped using 223 simple sequence repeat (SSR) markers covering all 19 chromosomes to identify significant markers associated with yield and quality traits. Twelve yield-related and six quality traits were investigated in two consecutive years (2014 and 2015), with three replications in two environments (Changshun, CS; and Qinghe, QH). Using the model GLM with population structure and kinship (Q ​+ ​K), a total of 25 significant SSR markers (P ​< ​0.001) were detected to be associated with these twelve yield-related and six quality traits, explaining 4.56%–19.17% of the phenotypic variation for each trait. Based on these markers, BnaA03g23490D, BnaC09g46370D, BnaA07g37150D, BnaA01g32590D, and BnaC09g37280D were identified as pleiotropic genes controlling multiple traits. These candidate genes illustrated the potential for the genetic understanding of yield and oil quality traits. Most importantly, these significant markers can be used for marker-assisted breeding of oilseed rape in different environments.