Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana

Abstract

Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5–2 µg Cd g−1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids.

Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis

“…The currently available large populations, dense genotyping, and the advantage of homozygous lines in the mainly self-fertilizing species Arabidopsis, ought to greatly enhance the power of such studies. Indeed, GWA studies confirmed many of the previously identified genes in experimental mapping populations and mutant studies and detected a number of, to our knowledge, novel candidate genes, although this is limited for quantitative traits (Atwell et al, 2010;Brachi et al, 2010;Li et al, 2010;Todesco et al, 2010;Chan et al, 2011;Chao et al, 2012;Filiault and Maloof, 2012;Sterken et al, 2012;Yano et al, 2013;Chao et al, 2014;Meijón et al, 2014;Bac-Molenaar et al, 2015). Similar to the problem of missing heritability in human GWA studies, where individual variants cannot explain the phenotypic variation despite high heritabilities (Yang et al, 2010;Gibson, 2011;Makowsky et al, 2011), genetic variants cannot fully explain the high heritabilities in plant studies (Brachi et al, 2010;Sasaki et al, 2015).…”

Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition

“…These are sorghum homologs of Arabidopsis HMA genes in the heavy metal-transporting subfamily of the P-type ATPases. AtHMA3 participates in the vacuolar storage of Cd in Arabidopsis, and a recent study revealed that HMA3 is a major-effect locus controlling natural variation in leaf Cd (Morel et al, 2009;Chao et al, 2012). These SNP alleles could be used immediately to potentially produce sorghum seed with lowered Cd 2+ accumulation.…”

Dissection of the Control of Anion Homeostasis by Associative Transcriptomics in Brassica napus

“…The putative function of these genes was confirmed by an analysis of T-DNA lines, showing that AT has the potential to uncover new links between metabolic and/or regulatory pathways. In Arabidopsis, GWAS approaches also recovered previously known candidate genes (Aranzana et al, 2005;Atwell et al, 2010;Chan et al, 2011;Chao et al, 2012), but reports of new discoveries are still scarce (Angelovici et al, 2013;Meijón et al, 2014;Verslues et al, 2014).…”

“…The usefulness of GWAS has been demonstrated by capturing numerous well-characterized candidate genes (Aranzana et al, 2005;Atwell et al, 2010). Traits connected with the accumulation of mineral elements have also been analyzed successfully using GWAS (Atwell et al, 2010;Chao et al, 2012). Understanding the control of nutrient homeostasis is particularly important for crop plants, as it may contribute to improving NUE and the reduction of fertilizer use.…”