DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
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.
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Manu J
MJ
Dubin
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Pei
P
Zhang
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Dazhe
D
Meng
Molecular and Computational Biology, University of Southern California, Los Angeles, United States.
Marie-Stanislas
MS
Remigereau
Department of Biology, University of Utah, Salt Lake City, United States.
Edward J
EJ
Osborne
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom.
Francesco
F
Paolo Casale
Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany.
Philipp
P
Drewe
Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany.
André
A
Kahles
Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany.
Geraldine
G
Jean
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Bjarni
B
Vilhjálmsson
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Joanna
J
Jagoda
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Selen
S
Irez
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Viktor
V
Voronin
Molecular and Computational Biology, University of Southern California, Los Angeles, United States.
Qiang
Q
Song
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Quan
Q
Long
Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany.
Gunnar
G
Rätsch
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom.
Oliver
O
Stegle
Department of Biology, University of Utah, Salt Lake City, United States.
Richard M
RM
Clark
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
Magnus
http://orcid.org/0000-0001-7178-9748
M
Nordborg
D000222:Adaptation, Physiological / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D018899:CpG Islands; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D004251:DNA Transposable Elements; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D013696:Temperature; D014158:Transcription, Genetic
D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements; D004248:DNA (Cytosine-5-)-Methyltransferases
DNA methylation; arabidopsis; epigenetics; evolutionary biology; genomics; local adaptation; plant biology; population genetics