Genome-Wide Association Study of Cadmium Accumulation at the Seedling Stage in Rapeseed (Brassica napus L.)

Abstract

Cadmium is a potentially toxic heavy metal to human health. Rapeseed (Brassica napus L.), a vegetable and oilseed crop, might also be a Cd hyperaccumulator, but there is little information on this trait in rapeseed. We evaluated Cd accumulation in different oilseed accessions and employed a genome-wide association study to identify quantitative trait loci (QTLs) related to Cd accumulation. A total of 419 B. napus accessions and inbred lines were genotyped with a 60K Illumina Infinium SNP array of Brassica. Wide genotypic variations in Cd concentration and translocation were found. Twenty-five QTLs integrated with 98 single-nucleotide polymorphisms (SNPs) located at 15 chromosomes were associated with Cd accumulation traits. These QTLs explained 3.49–7.57% of the phenotypic variation observed. Thirty-two candidate genes were identified in these genomic regions, and they were 0.33–497.97 kb away from the SNPs. We found orthologs of Arabidopsis thaliana located near the significant SNPs on the B. napus genome, including NRAMP6 (natural resistance-associated macrophage protein 6), IRT1 (iron-regulated transporter 1), CAD1 (cadmium-sensitive 1), and PCS2 (phytochelatin synthase 2). Of them, four candidate genes were verified by qRT-PCR, the expression levels of which were significantly higher after exposure to Cd than in the controls. Our results might facilitate the study of the genetic basis of Cd accumulation and the cloning of candidate Cd accumulation genes, which could be used to help reduce Cd levels in edible plant parts and/or create more efficient hyperaccumulators.

Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

“…To determinate whether these four QTLs is specific for Pb tolerance in B. napus, comparison analysis was conducted. We found that no QTL was overlapped with previous reported Cd responsive QTLs in B. napus [23,40], although several protein such as AtHMA2 (Heavy Metal ATPases) and AtPDR8 can transport both Cd and Pb in plant [25,53]. This might be caused by the different populations used for GWAS and the large difference of genetic factors between Pb and Cd stress responses [9,54].…”

“…For further exploring genetic factors responding to Pb stress, Genome-wide association study (GWAS), a powerful tool to detect the genetic architecture of complex traits, has been widely used in rice, maize and grasses [12,[32][33][34][35][36][37][38][39]. GWAS has also been used to study HMs concentration, tolerance to Cd and other abiotic stress related quantitative trait loci (QTLs), but not the molecular mechanism of Pb tolerance in B. napus [23,[40][41][42][43].…”

Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

“…We found that no QTL was overlapped with previous reported Cd responsive QTLs in B. napus [23,41], although several protein such as AtHMA2 (Heavy Metal ATPases) and AtPDR8 can transport both Cd and Pb in plant [25,54]. This might be caused by the different populations used for GWAS and the large difference of genetic factors between Pb and Cd stress responses [9,55].…”

“…For further exploring genetic factors responding to Pb stress, Genome-wide association study (GWAS), a powerful tool to detect the genetic architecture of complex traits, has been widely used in rice, maize and grasses [32][33][34][35][36][37][38][39][40]. GWAS has also been used to study HMs concentration, tolerance to Cd and other abiotic stress related quantitative trait locus (QTL), but not the molecular mechanism of Pb tolerance in B. napus [23, [41][42][43][44].…”

Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

“…For further exploring genetic factor responding to Pb stress, Genome-wide association study (GWAS), a powerful tool to detect the genetic architecture of complex traits, has been widely used in rice, maize and grasses [30][31][32][33][34][35][36][37][38]. GWAS has also been used to study HMs concentration, tolerance to Cd and other abiotic stress related quantitative trait locus (QTL), but not the molecular mechanism of Pb tolerance in B. napus [39][40][41][42][43].…”