Table_3_Genome-Wide Association Study of Cadmium Accumulation at the Seedling Stage in Rapeseed (Brassica napus L.).XLSX

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.

镉（Cadmium）是一种对人体健康存在潜在毒性的重金属。甘蓝型油菜（Brassica napus L.）作为兼具蔬菜与油料用途的作物，有可能成为镉超富集植物，但目前关于该性状在油菜中的相关研究信息仍较为匮乏。本研究对不同油料油菜种质的镉积累特性开展了系统评价，并通过全基因组关联分析（genome-wide association study）筛选与镉积累相关的数量性状位点（quantitative trait loci, QTL）。研究采用60K Illumina Infinium甘蓝型油菜单核苷酸多态性（single-nucleotide polymorphism, SNP）芯片，对419份甘蓝型油菜种质及自交系进行基因分型。结果显示，供试材料的镉浓度与镉转运能力均存在广泛的基因型差异。本研究共鉴定到25个与镉积累性状相关的QTL，这些位点整合了98个SNP，分布于15条染色体上，可解释3.49%~7.57%的表型变异。在上述基因组区域内共筛选得到32个候选基因，它们与对应SNP的物理距离介于0.33~497.97 kb之间。我们在甘蓝型油菜基因组中显著SNP位点附近，发现了拟南芥（Arabidopsis thaliana）的同源基因，包括NRAMP6（天然抗性相关巨噬细胞蛋白6，natural resistance-associated macrophage protein 6）、IRT1（铁调控转运蛋白1，iron-regulated transporter 1）、CAD1（镉敏感蛋白1，cadmium-sensitive 1）以及PCS2（植物螯合肽合酶2，phytochelatin synthase 2）。其中4个候选基因通过qRT-PCR（实时荧光定量PCR，quantitative real-time PCR）验证，结果显示镉处理组的基因表达水平显著高于对照组。本研究结果可为解析镉积累的遗传机制、克隆镉积累候选基因提供理论支撑，亦可用于降低作物可食用部分的镉含量，或培育更高效的镉超富集植物。