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

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.解析植物镉（Cd）积累的机制，对于通过膳食及环境暴露途径降低镉对植物与人类的潜在毒性具有重要意义。本研究以全球范围内野生采集的349份拟南芥（Arabidopsis thaliana）种质株系为材料，解析其镉积累自然变异的遗传基础。在可控同质园栽培条件下，我们发现这些种质的叶片镉积累量存在4倍差异（0.5~2 μg Cd·g⁻¹干重）。本研究结合全基因组关联定位、实验F₂群体连锁定位以及转基因互补实验，证实HMA3是导致该多样化拟南芥种质群体叶片镉积累变异的唯一主效位点。对149份拟南芥种质的HMA3预测氨基酸序列进行分析，共鉴定出10种主要的天然蛋白质单倍型。上述单倍型与叶片镉积累量的关联分析及遗传互补实验结果表明，其中5种单倍型具有功能活性，剩余5种则无功能；叶片镉积累量升高与无义突变及改变两个特定氨基酸的多态性导致的HMA3功能降低密切相关。