Genome-Wide Association Study of the Complex Traits in Amphidiploid Rapeseed (Brassica napus L.)

Genome-wide association study (GWAS) has been proved to be a quick and efficient method for dissecting the complex agronomic traits. Rapeseed is one of the most economically important polyploid oil crops, however, so far, no report on map-based cloning of a causal gene in a QTL of rapeseed. In this study, a recently developed 60K Brassica Infinium® SNP array was used to analyze an association panel with 472 accessions, followed by performing association mapping of seed weight, seed quality, and flowering time. As a result, two significant associations in A8 and C3 of B. napus were detected for erucic acid content and the peak SNPs were found to be only 233 kb and 128 kb away from the key genes BnaA.FAE1 and BnaC.FAE1. BnaA.FAE1 was also identified to be significantly associated with the oil content. Orthologues of A. thaliana HAG1 were identified close to four clusters of SNPs associated with glucosinolate content on A9, C2, C7 and C9. For seed weight, we detected two association signals in A7 and A9, which were consistent with previous studies of quantitative trait loci mapping. We also detected at least 33 genomic regions associated with flowering time varation in three environments. These regions distribute on 14 of 19 chromosomes, except chromosome A05, A08, A09, C01 and C09. The results indicate that our association mapping approach is available for fine mapping of the complex traits in rapeseed.