Genome-wide association analysis of aluminum tolerance related traits in rapeseed (Brassica napus L.) during germination

With the increasing acidification of soil, aluminum (Al) toxicity has become one of the most important stress factors affecting seed germination quality and crop yield. To investigate the Al tolerance on seed germination, genome-wide association analysis (GWAS) of 19,949 SNPs with genome-wide coverage was used to identify the candidate genes, which were potentially related to germinate traits of rapeseed (Brassica napus L.) under Al stress. In the experiment, 169 rapeseed cultivars (lines) were treated with AlCl3 solution of 90 ppm, and distilled water was added to the control. At the 7th day, the phenotype data, including root length and dry weight, were measured and calculated. Using the TASSEL software, Al tolerance related traits were explored in rapeseed under germination with a 60 K Brassica Illumina® Infinium SNP array. Then, the structure of the population was analyzed with the STRUCTURE software, and the genetic relationship and LD attenuation were analyzed with the software TASSEL, respectively. The GWAS of relative root length (RRL) and relative dry weight (RDW) with SNP markers were carried out under the optimal model. Meanwhile, the candidate genes were predicted based on the LD interval sequence of the associated SNP locus. Subsequently, the homologous genes of rapeseed related to Al tolerance in the target genome region were screened in Arabidopsis thaliana (L.) Heynh. The results showed that 13 SNPs were significantly associated with these two traits. Among them, 8 SNPs were significantly associated with RRL and located on chromosomes A03, A07, A09, A10, C05, C06, and C09, respectively. Five SNPs were significantly associated with RDW and located on chromosomes A03, A04, A10, C05, and C07, respectively. Afterward, fifty-nine candidate genes related to Al tolerance were identified in the LD region of these SNP loci. Four of these genes were involved in the growth regulation about organic acid, ten were involved in growth-regulating substance, eleven were related to oxidative stress, and nineteen were involved in carbon and nitrogen metabolism. The results of this study provided a theoretical basis for Al tolerance in rapeseed and laid out a foundation for further functional verification of genes and cultivation of new Al tolerant rapeseed varieties.