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

Genome Res. 2013 Oct;23(10):1663-74. doi: 10.1101/gr.152538.112. Epub 2013 Jun 5.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / metabolism
  • Cell Division
  • Chromosome Mapping
  • Cytosine / metabolism*
  • DNA Methylation*
  • DNA Transposable Elements
  • DNA, Plant / genetics
  • DNA, Plant / metabolism*
  • DNA, Recombinant
  • Epigenesis, Genetic
  • Epigenomics*
  • Gene Expression Regulation, Plant*
  • Genes, Plant
  • Genetic Variation
  • Genome, Plant*
  • Genotype
  • Inbreeding
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci
  • Sequence Analysis
  • Soybeans / genetics*
  • Soybeans / metabolism


  • DNA Transposable Elements
  • DNA, Plant
  • DNA, Recombinant
  • Cytosine