title: Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality.
abstract: 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.
authors.affiliation: Swedish University of Agricultural Sciences, Department of Clinical Sciences, Division of Computational Genetics, Uppsala, Sweden; Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden; University of Edinburgh, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, Edinburgh, United Kingdom.
authors.forename: Xia
authors.initials: X
authors.lastname: Shen
authors.affiliation: Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala, Sweden.
authors.forename: Jennifer
authors.initials: J
authors.lastname: De Jonge
authors.affiliation: Swedish University of Agricultural Sciences, Department of Clinical Sciences, Division of Computational Genetics, Uppsala, Sweden.
authors.forename: Simon K G
authors.initials: SK
authors.lastname: Forsberg
authors.affiliation: Swedish University of Agricultural Sciences, Department of Clinical Sciences, Division of Computational Genetics, Uppsala, Sweden.
authors.forename: Mats E
authors.initials: ME
authors.lastname: Pettersson
authors.affiliation: Swedish University of Agricultural Sciences, Department of Clinical Sciences, Division of Computational Genetics, Uppsala, Sweden.
authors.forename: Zheya
authors.initials: Z
authors.lastname: Sheng
authors.affiliation: Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala, Sweden.
authors.forename: Lars
authors.initials: L
authors.lastname: Hennig
authors.affiliation: Swedish University of Agricultural Sciences, Department of Clinical Sciences, Division of Computational Genetics, Uppsala, Sweden.
authors.forename: Örjan
authors.initials: Ö
authors.lastname: Carlborg
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000483:Alleles; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D056726:Genetic Association Studies; D056426:Genetic Loci; D060005:Genotyping Techniques; D011110:Polymorphism, Genetic; D012621:Seasons; D013696:Temperature
chemical_list: D029681:Arabidopsis Proteins; D004248:DNA (Cytosine-5-)-Methyltransferases; C112810:chromomethylase