A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions

Nat Commun. 2018 Jan 31;9(1):460. doi: 10.1038/s41467-018-02839-3.

Abstract

Epigenetic variation has been proposed to facilitate adaptation to changing environments, but evidence that natural epialleles contribute to adaptive evolution has been lacking. Here we identify a retrotransposon, named "NMR19" (naturally occurring DNA methylation variation region 19), whose methylation and genomic location vary among Arabidopsis thaliana accessions. We classify NMR19 as NMR19-4 and NMR19-16 based on its location, and uncover NMR19-4 as an epiallele that controls leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE (PPH). We find that the DNA methylation status of NMR19-4 is stably inherited and independent of genetic variation. In addition, further analysis indicates that DNA methylation of NMR19-4 correlates with local climates, implying that NMR19-4 is an environmentally associated epiallele. In summary, we discover a novel epiallele, and provide mechanistic insights into its origin and potential function in local climate adaptation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acclimatization / genetics*
  • Adaptation, Physiological / genetics
  • Alleles
  • Arabidopsis / genetics
  • Arabidopsis / physiology*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • DNA Methylation
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Epigenesis, Genetic
  • Evolution, Molecular
  • Gene Expression Regulation, Plant
  • Genetic Variation
  • Hydrolases / genetics
  • Hydrolases / metabolism
  • Long Interspersed Nucleotide Elements
  • Mutation
  • Plant Leaves / genetics
  • Plant Leaves / physiology*
  • Retroelements / genetics*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • Arabidopsis Proteins
  • DDM1 protein, Arabidopsis
  • DNA-Binding Proteins
  • Retroelements
  • Transcription Factors
  • Hydrolases