Genome-wide association studies identify heavy metal ATPase3 as the primary determinant of natural variation in leaf cadmium in Arabidopsis thaliana

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

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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 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.
Original languageEnglish
Article numbere1002923
Number of pages14
JournalPLoS Genetics
Volume8
Issue number9
DOIs
Publication statusPublished - 6 Sep 2012

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  • Datasets

    GSE39679: eXtreme Array Mapping (XAM) for the low leaf Cd phenotype in Arabidopsis thaliana accession CS28181

    Chao, D. (Creator), Borevitz, J. O. (Creator), Atwell, S. (Creator), Huang, Y. S. (Creator), Vilhjalmsson, B. J. (Creator), Willems, G. (Creator), Horton, M. (Creator), Li, Y. (Creator), Meng, D. (Creator), Platt, A. (Creator), Tarone, A. M. (Creator), Hu, T. T. (Creator), Jiang, R. (Creator), Muliyati, N. W. (Creator), Zhang, X. (Creator), Amer, M. A. (Creator), Baxter, I. (Creator), Brachi, B. (Creator), Chory, J. (Creator), Dean, C. (Creator), Debieu, M. (Creator), de Meaux, J. (Creator), Ecker, J. R. (Creator), Faure, N. (Creator), Kniskern, J. M. (Creator), Jones, J. D. G. (Creator), Michael, T. (Creator), Nemri, A. (Creator), Roux, F. (Creator), Salt, D. (Creator), Tang, C. (Creator), Todesco, M. (Creator), Traw, M. B. (Creator), Weigel, D. (Creator), Marjoram, P. (Creator), Bergelson, J. (Creator), Nordborg, M. (Creator), Silva, A. (Creator) & Paton, G. (Data Manager), GEO, 31 Jul 2012

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