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

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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE39679 | GEO | 2012/07/31

SECONDARY ACCESSION(S): PRJNA171576

REPOSITORIES: GEO

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Project description:ABSTRACT: Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development, and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations, and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis thaliana accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme adenosine 5-phosphosulfate reductase 2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction and its reduced activity in the loss-of-function allele apr2-1 and the two A. thaliana accessions Hodon¨ªn (Hod) and Shahdara (Sha), leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Sha accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by four orders of magnitude across the A. thaliana species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored. genomic hybridization bulked segregant analysis Hybridizations from a set of Bulk Segregant analysis. We measured the elemental profile of 328 F2 plants from a cross between the high sulfur and selenium Arabidopsis thaliana accession Hod and the Col-0 accession, data available at www.ionomicshub.org <http://www.ionomicshub.org>). Leaves from the 57 highest and 61 lowest sulfur and selenium accumulating plants (calculated as a percentage of the Col-0 accumulation in the same growth tray) were pooled and the genomic DNA was extracted using Qiagen kits.

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

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