IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v495y2013i7440d10.1038_nature11968.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature11968
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.

    File URL: https://libkey.io/10.1038/nature11968?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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. 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.
    3. 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.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:495:y:2013:i:7440:d:10.1038_nature11968. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.