Abstract
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 Medicago truncatula 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, P-type ATPase transporters, oxidative stress response genes, and stress related UDP-glycosyltransferases. The P-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 CAX3 and PDR3, two linked adjacent genes, and leaf accumulation of Hg associated with the genes NRAMP6 and CAX9. 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.
Highlights
Heavy metals are high-density elements that can cause toxic effects when present in excess quantities
No correlation was found between leaf accumulation and relative root growth (RRG) for either metal treatment (Figure 1 and Supplementary Figure 1)
The heritability estimates and large amount of standing variation suggest that genome wide association studies (GWAS) can identify single nucleotide polymorphisms (SNPs) and genes underlying these traits due to sufficient genetic differences between genotypes, and that both tolerance and susceptibility alleles are present in the M. truncatula HapMap panel
Summary
Heavy metals are high-density elements that can cause toxic effects when present in excess quantities. Cadmium (Cd) and mercury (Hg) are two of the most toxic heavy metals to humans as Cd poisoning can cause kidney damage and osteoporosis (Järup and Åkesson, 2009), while Hg poisoning is associated with lung, kidney, muscle and brain damage (Vallee and Ulmer, 1972; Bernhoft, 2012). The predominant source of heavy metal contamination are mines, foundries, and smelters, which are often associated with high levels of contamination in surrounding soils (Tchounwou et al, 2012; Alloway, 2013). This pollution can negatively affect surrounding agricultural and natural ecosystems. Plants grown on contaminated soils may accumulate heavy metals in aerial parts such as leaf tissues and seeds and can result in severe health consequences for foraging animals and humans if these metals enter the food supply (Peralta-Videa et al, 2009)
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