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

Dai-Yin Chao,John Danku,Magnus Nordborg,David E Salt,Ivan Baxter,Adriano Silva,Brett Lahner,Yu S Huang,Elena Yakubova,Kirsten Bomblies

doi:10.1371/journal.pgen.1002923

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.

Highlights

Cadmium (Cd) is a significant pollutant and naturally occurring trace element that is potentially toxic to both plants and animals, including humans
We have discovered that DNA sequence changes at a single gene, which encodes the Heavy Metal ATPase 3 (HMA3), drives the variation in Cd accumulation we observe in a world-wide sample of Arabidopsis thaliana
We identified 10 major HMA3 protein variants, of which five contribute to reduce Cd accumulation in leaves of A. thaliana

Summary

Introduction

Cadmium (Cd) is a significant pollutant and naturally occurring trace element that is potentially toxic to both plants and animals, including humans. An important step for Cd to enter the human food chain is its accumulation in plant tissues, especially the aerial parts that form the majority of the food sources consumed either directly by humans or through eating meat produced from animals raised on a plant-based diet [4]. Accumulation of Cd in the aerial tissues of plants is determined by several factors, including the bioavailability of Cd in the soil, uptake from the soil solution by roots and radial transport within the root to the vascular system, translocation from the root, and storage in the above ground tissues. Xylem loading of Cd in plants requires the Heavy Metal ATPases AtHMA4 and/or AtHMA2 [7,8,9,10,11,12,13]

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