Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

  1. Joseph R. Ecker1,2,10,13
  1. 1Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
  2. 2Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
  3. 3Bioinformatics Program, University of California at San Diego, La Jolla, California 92093, USA;
  4. 4Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA;
  5. 5Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA;
  6. 6Department of Computer Science, University of Missouri, Columbia, Missouri 65211, USA;
  7. 7National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA;
  8. 8Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA;
  9. 9Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, Missouri 65211, USA;
  10. 10Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    1. 11 These authors contributed equally to this work.

    • 12 Present address: Laboratorio de Bioquímica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado De México, Mexico 54090.

    Abstract

    Cytosine DNA methylation is one avenue for passing information through cell divisions. Here, we present epigenomic analyses of soybean recombinant inbred lines (RILs) and their parents. Identification of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 RILs uncovered widespread evidence for local methylQTL. This epigenomics approach provides a comprehensive study of the patterns and heritability of methylation variants in a complex genetic population over multiple generations, paving the way for understanding how methylation variants contribute to phenotypic variation.

    Footnotes

    • 13 Corresponding authors

      E-mail ecker{at}salk.edu

      E-mail staceyg{at}missouri.edu

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.152538.112.

    • Received November 22, 2012.
    • Accepted June 5, 2013.

    This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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