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Patterns of population epigenomic diversity

Author

Listed:
  • Robert J. Schmitz

    (Plant Biology Laboratory, The Salk Institute for Biological Studies
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Matthew D. Schultz

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies
    Bioinformatics Program, University of California at San Diego)

  • Mark A. Urich

    (Plant Biology Laboratory, The Salk Institute for Biological Studies
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Joseph R. Nery

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Mattia Pelizzola

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies
    Present address: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (ITT), Via Adamello 16, 20139 Milan, Italy.)

  • Ondrej Libiger

    (The Scripps Research Institute)

  • Andrew Alix

    (Plant Biology Laboratory, The Salk Institute for Biological Studies)

  • Richard B. McCosh

    (Plant Biology Laboratory, The Salk Institute for Biological Studies)

  • Huaming Chen

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Nicholas J. Schork

    (The Scripps Research Institute)

  • Joseph R. Ecker

    (Plant Biology Laboratory, The Salk Institute for Biological Studies
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies
    Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA)

Abstract

Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.

Suggested Citation

  • Robert J. Schmitz & Matthew D. Schultz & Mark A. Urich & Joseph R. Nery & Mattia Pelizzola & Ondrej Libiger & Andrew Alix & Richard B. McCosh & Huaming Chen & Nicholas J. Schork & Joseph R. Ecker, 2013. "Patterns of population epigenomic diversity," Nature, Nature, vol. 495(7440), pages 193-198, March.
    • Handle: RePEc:nat:nature:v:495:y:2013:i:7440:d:10.1038_nature11968
    DOI: 10.1038/nature11968
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    Citations

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    Cited by:

    1. Jie Liu & Xuehua Zhong, 2024. "Epiallelic variation of non-coding RNA genes and their phenotypic consequences," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Yibing Zeng & Julian Somers & Harrison S. Bell & Zuzana Vejlupkova & R. Kelly Dawe & John E. Fowler & Brad Nelms & Jonathan I. Gent, 2024. "Potent pollen gene regulation by DNA glycosylases in maize," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    3. Tamer Aldwairi & David J. Chevalier & Andy D. Perkins, 2021. "Exploring the Effect of Climate Factors on SNPs within FHA Domain Genes in Eurasian Arabidopsis Ecotypes," Agriculture, MDPI, vol. 11(2), pages 1-10, February.
    4. Minghui Kang & Haolin Wu & Huanhuan Liu & Wenyu Liu & Mingjia Zhu & Yu Han & Wei Liu & Chunlin Chen & Yan Song & Luna Tan & Kangqun Yin & Yusen Zhao & Zhen Yan & Shangling Lou & Yanjun Zan & Jianquan , 2023. "The pan-genome and local adaptation of Arabidopsis thaliana," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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