Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality

PLoS Genet. 2014 Dec 11;10(12):e1004842. doi: 10.1371/journal.pgen.1004842. eCollection 2014 Dec.


As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele. This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods. Sixteen novel loci were found, including an association between Chromomethylase 2 (CMT2) and temperature seasonality where the genome-wide CHH methylation was different for the group of accessions carrying the plastic allele. Cmt2 mutants were shown to be more tolerant to heat-stress, suggesting genetic regulation of epigenetic modifications as a likely mechanism underlying natural adaptation to variable temperatures, potentially through differential allelic plasticity to temperature-stress.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological / genetics
  • Alleles
  • Arabidopsis / enzymology
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • DNA (Cytosine-5-)-Methyltransferases / genetics*
  • DNA Methylation*
  • Epigenesis, Genetic
  • Gene Expression Regulation, Plant
  • Genetic Association Studies
  • Genetic Loci
  • Genotyping Techniques
  • Polymorphism, Genetic*
  • Seasons*
  • Temperature*


  • Arabidopsis Proteins
  • DNA (Cytosine-5-)-Methyltransferases
  • chromomethylase

Grant support

This work was funded by a EURYI-award and a SSF Future Research Leader Grant to ÖC, a Swedish Research Council grant (537-2014-371) to XS and a FORMAS grant (to LH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.