A genome-wide survey of DNA methylation in hexaploid wheat

Genome Biol. 2015 Dec 10:16:273. doi: 10.1186/s13059-015-0838-3.

Abstract

Background: DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat.

Results: While the majority of methylation is conserved across all three genomes we demonstrate that differential methylation exists between the sub-genomes in approximately equal proportions. We correlate sub-genome-specific promoter methylation with decreased expression levels and show that altered growing temperature has a small effect on methylation state, identifying a small but functionally relevant set of methylated genes. Finally, we demonstrate long-term methylation maintenance using a comparison between the D sub-genome of hexaploid wheat and its progenitor Aegilops tauschii.

Conclusions: We show that tri-genome methylation is highly conserved with the diploid wheat progenitor while sub-genome-specific methylation shows more variation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Methylation*
  • DNA Transposable Elements
  • Diploidy
  • Gene Expression
  • Genome, Plant*
  • Polyploidy
  • Promoter Regions, Genetic
  • Stress, Physiological / genetics
  • Temperature
  • Triticum / genetics*

Substances

  • DNA Transposable Elements