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Background    B. napus  (oilseed) is an important source of edible vegetable oil, and its nutritional and economic value is determined by its fatty acid composition and content.    Results  Using the  Brassica  60 K SNP array, we performed a genome-wide association study of fatty acid composition in a population of 520 genetically diverse oilseed accessions. Using the PCA + K model in TASSEL 5.2.1, we identified 62 genomic regions that were significantly associated with the composition of seven fatty acids, and five consensus regions that mapped to the A2, A8, A9, C1, and C3 chromosomes, respectively, of the  Brassica napus  Darmor -bzh  genome. We then identified 24 orthologs of the functional candidate genes involved in fatty acid biosynthesis, excluding  BnaA.FAE1  and  BnaC.FAE1  on the A8 and C3 homologous genome blocks, which are known to have critical roles in the fatty acid biosynthesis pathway, and potential orthologs of these genes (e.g.,  LACS9 ,  KCR1 ,  FAB1 ,  LPAT4 ,  KCS17 ,  CER4 ,  TT16 , and  ACBP5 ).    Conclusions  Our results demonstrate the power of association mapping in identifying genes of interest in  B. napus  and provide insight into the genetic basis of fatty acid biosynthesis in  B. napus.  Furthermore, our findings may facilitate marker-based breeding efforts aimed at improving fatty acid composition and quality in  B. napus .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3607-8) contains supplementary material, which is available to authorized users.

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers