Genome-wide Association Mapping Identifies a New Arsenate Reductase Enzyme Critical for Limiting Arsenic Accumulation in Plants

Chao, Dai‐Yin; Chen, Yi; Chen, Jiugeng; Shi, Shulin; Chen, Ziru; Wang, Yuming; Danku, John; Zhao, Fang‐Jie; Salt, David E.

doi:10.1371/journal.pbio.1002009

Cited by 220 publications

(222 citation statements)

References 82 publications

(121 reference statements)

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“…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).…”

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confidence: 55%

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

Kooke¹,

Kruijer

Bours

et al. 2016

Plant Physiol.

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ORCID IDs: 0000-0002-9014-9516 (D.V.); 0000-0001-8918-0711 (J.J.B.K.).Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified.The natural phenomena of mutation and recombination that change the genetic code with each generation have given rise to the enormous genetic diversity between and within species. Through evolutionary processes, such as drift, migration, and selection, plants have accumulated a vast number of molecular polymorphisms that enabled adaptation to a wide range of environments (Kooke and Keurentjes, 2012). With the recent advancements in genetic and genomic tools, this nucleotide diversity can be fully surveyed to identify causal polymorphisms for many different plant phenotypes. This should allow the identification of molecular changes that provided evolutionary advantages and beneficial characteristics in agronomically important traits.Through selection on variation in performance, plants have adapted to different environments. Plant performance is directly determined by life history traits, such as flowering time and growth rate, which in turn depend on genetics, morphology, physiology, and the environment (Roff, 2007;Kooke et al., 2015). Understanding the regulation of plant growth and morphology is therefore essential for the comprehension of plant performance. Arabidopsis has adapted to a wide range of environments and displays an extensive variety in morphological and growth-related phenotypes. Its small genome size, the publicly available

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mentioning

confidence: 55%

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

Kooke¹,

Kruijer

Bours

et al. 2016

Plant Physiol.

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“…Technological advancements have made it possible to characterize the genetic diversity in such collections in great detail. A number of studies have shown the use of such densely genotyped natural populations in GWA mapping approaches (Cockram et al, 2010;Chan et al, 2011;Chao et al, 2014;Verslues et al, 2014). Such studies not only disclose the large amount of natural variation present in species for many traits but also hint at candidate genes causal for the observed variation.…”

Section: Discussionmentioning

confidence: 99%

“…This suggests that this gene might not be the causal gene, although the wild-type Col-0 allele in itself can already be weak or nonfunctional and additional experiments of knockout and overexpression lines of nonCol-0 alleles of this gene are needed for final determination. Because causal genes are sometimes also detected outside the LD interval of significantly associated SNPs (Chao et al, 2014), due to, among others, low linkage between causal and associated SNPs (Freedman et al, 2011), other genes in the 20-kb region around the significant SNPs (10 kb upstream and 10 kb downstream) were considered as candidates, in accordance to the average linkage distance in Arabidopsis of 10 kb (Kim et al, 2007). This resulted in the identification of a candidate gene, QUASIMODO-LIKE2 (QUL2; Smyth et al (1990).…”

Section: Preanthesis Sensitivity To Heat Stressmentioning

confidence: 99%

Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana

et al. 2015

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ORCID ID: 0000-0001-8918-0711 (J.J.B.K.)For crops that are grown for their fruits or seeds, elevated temperatures that occur during flowering and seed or fruit set have a stronger effect on yield than high temperatures during the vegetative stage. Even short-term exposure to heat can have a large impact on yield. In this study, we used Arabidopsis thaliana to study the effect of short-term heat exposure on flower and seed development. The impact of a single hot day (35°C) was determined in more than 250 natural accessions by measuring the lengths of the siliques along the main inflorescence. Two sensitive developmental stages were identified, one before anthesis, during male and female meiosis, and one after anthesis, during fertilization and early embryo development. In addition, we observed a correlation between flowering time and heat tolerance. Genome-wide association mapping revealed four quantitative trait loci (QTLs) strongly associated with the heat response. These QTLs were developmental stage specific, as different QTLs were detected before and after anthesis. For a number of QTLs, T-DNA insertion knockout lines could validate assigned candidate genes. Our findings show that the regulation of complex traits can be highly dependent on the developmental timing.

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“…An alternative explanation for the increased net efflux of As is that knockout of NIP7;1 reduces uptake of AsIII from the medium. The majority of AsV taken up by the plant will be rapidly reduced to AsIII prior to efflux from the root [3,21]. Values are mean concentrations of seed from four individuals of each genotype after growth in 150 lM AsV.…”

Section: Discussionmentioning

confidence: 99%

Arabidopsis thaliana NIP7;1 is involved in tissue arsenic distribution and tolerance in response to arsenate

Lindsay

Maathuis

2016

FEBS Letters

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The Arabidopsis aquaglyceroporin NIP7;1 is involved in uptake and tolerance to the trivalent arsenic species arsenite. Here, we show that NIP7;1 is also involved in the response to pentavalent arsenate. Loss of function of NIP7;1 improved tolerance to arsenate and reduced arsenic levels in both the phloem and xylem, resulting in altered arsenic distribution between tissues. There was no clear correlation between growth and shoot arsenic concentration. This is the first report detailing the involvement of a NIP transporter in response to arsenate. The data suggest that these proteins are relevant targets for breeding and engineering arsenic tolerance in crops.

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Genome-wide Association Mapping Identifies a New Arsenate Reductase Enzyme Critical for Limiting Arsenic Accumulation in Plants

Abstract: A genome-wide association study identifies the enzyme in plants that transforms arsenate into arsenite, allowing its extrusion into the soil and thereby controlling arsenic accumulation.

Cited by 220 publications

References 82 publications

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

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

Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana

Arabidopsis thaliana NIP7;1 is involved in tissue arsenic distribution and tolerance in response to arsenate

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