Paape Timothy, Heiniger Benjamin, Santo Domingo Miguel, Clear Michael R, Lucas M Mercedes, Pueyo José J
Brookhaven National Laboratory, Upton, NY, United States.
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
Front Plant Sci. 2022 Jan 28;12:806949. doi: 10.3389/fpls.2021.806949. eCollection 2021.
Heavy metals are an increasing problem due to contamination from human sources that and can enter the food chain by being taken up by plants. Understanding the genetic basis of accumulation and tolerance in plants is important for reducing the uptake of toxic metals in crops and crop relatives, as well as for removing heavy metals from soils by means of phytoremediation. Following exposure of seedlings to cadmium (Cd) and mercury (Hg), we conducted a genome-wide association study using relative root growth (RRG) and leaf accumulation measurements. Cd and Hg accumulation and RRG had heritability ranging 0.44 - 0.72 indicating high genetic diversity for these traits. The Cd and Hg trait associations were broadly distributed throughout the genome, indicated the traits are polygenic and involve several quantitative loci. For all traits, candidate genes included several membrane associated ATP-binding cassette transporters, -type ATPase transporters, oxidative stress response genes, and stress related UDP-glycosyltransferases. The -type ATPase transporters and ATP-binding cassette protein-families have roles in vacuole transport of heavy metals, and our findings support their wide use in physiological plant responses to heavy metals and abiotic stresses. We also found associations between Cd RRG with the genes and , two linked adjacent genes, and leaf accumulation of Hg associated with the genes and . When plant genotypes with the most extreme phenotypes were compared, we found significant divergence in genomic regions using population genomics methods that contained metal transport and stress response gene ontologies. Several of these genomic regions show high linkage disequilibrium (LD) among candidate genes suggesting they have evolved together. Minor allele frequency (MAF) and effect size of the most significant SNPs was negatively correlated with large effect alleles being most rare. This is consistent with purifying selection against alleles that increase toxicity and abiotic stress. Conversely, the alleles with large affect that had higher frequencies that were associated with the exclusion of Cd and Hg. Overall, macroevolutionary conservation of heavy metal and stress response genes is important for improvement of forage crops by harnessing wild genetic variants in gene banks such as the Medicago HapMap collection.
由于来自人类活动的污染，重金属问题日益严重，并且可以通过被植物吸收而进入食物链。了解植物中重金属积累和耐受性的遗传基础，对于减少作物及其亲缘植物对有毒金属的吸收，以及通过植物修复从土壤中去除重金属都很重要。在将幼苗暴露于镉（Cd）和汞（Hg）之后，我们使用相对根生长（RRG）和叶片积累测量进行了全基因组关联研究。Cd和Hg的积累以及RRG的遗传力范围为0.44 - 0.72，表明这些性状具有高度的遗传多样性。Cd和Hg性状关联广泛分布于整个基因组，表明这些性状是多基因的，涉及多个数量性状位点。对于所有性状，候选基因包括几个与膜相关的ATP结合盒转运蛋白、-型ATP酶转运蛋白、氧化应激反应基因以及与应激相关的UDP-糖基转移酶。-型ATP酶转运蛋白和ATP结合盒蛋白家族在重金属的液泡转运中发挥作用，我们的研究结果支持它们在植物对重金属和非生物胁迫的生理反应中广泛发挥作用。我们还发现Cd的RRG与基因和两个相邻连锁基因之间存在关联，以及Hg的叶片积累与基因和相关。当比较具有最极端表型的植物基因型时，我们使用群体基因组学方法在包含金属转运和应激反应基因本体的基因组区域中发现了显著差异。这些基因组区域中的几个在候选基因之间显示出高连锁不平衡（LD），表明它们是共同进化的。最显著单核苷酸多态性（SNP）的次要等位基因频率（MAF）和效应大小呈负相关，大效应等位基因最为罕见。这与针对增加毒性和非生物胁迫的等位基因的纯化选择一致。相反，具有较高频率的大效应等位基因与Cd和Hg的排除相关。总体而言，重金属和应激反应基因的宏观进化保守性对于通过利用基因库（如苜蓿HapMap集合）中的野生遗传变异来改良饲料作物很重要。
