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Elife. 2015 May 5;4:e05255. doi: 10.7554/eLife.05255.

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

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Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Molecular and Computational Biology, University of Southern California, Los Angeles, United States.
Department of Biology, University of Utah, Salt Lake City, United States.
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom.
Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany.


Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation.


DNA methylation; arabidopsis; epigenetics; evolutionary biology; genomics; local adaptation; plant biology; population genetics

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