Brassica napus is an optimum crop for repairing the heavy metal pollution of soil. To identify the associated SNP locus and candidate genes with arsenic (As) stress tolerance in B. napus, we measured and performed genome-wide association studies (GWAS) on relative root length (RRL), relative hypocotyl length (RHL), and relative fresh weight (RFW) of 140 rapeseed accessions by the Brassica 60K Illumina Infinium SNP array. In total, 15 SNPs significantly associated with RRL, 20 loci with RHL, and 35 SNP with RFW were identified, and each of SNP explained 13.31%-24.39%, 18.04%-33.82%, and 20.19%-25.06% of observed phenotypic variation, respectively. The most notable significant SNPs were located on chromosomes A02, A07, and C02, which were repeatedly detected and associated with RRL, RHL, and RFW simultaneously. Based on the rapeseed genome annotation of the linkage disequilibrium (LD) regions, we predicted 61 As resistance of candidate genes, among them, PHT3;3, PHT1;9, GST, OTC5, NRAMP1, and ZIP12, were related to the heavy metal absorbing and transporting. With the results of qRT-PCR, the PHT3;3 and PHT1;9 were obviously induced by As stress treatment in roots, hypocotyls and leaves, indicating that they were the important candidate genes related to As absorption and transport in B. napus. These results provide a reference for elucidating the regulation mechanism of candidate genes and improving agronomic traits in B. napus under As stress.
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