title: Patterns of population epigenomic diversity.
abstract: Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.
authors: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.
authors: Robert J
authors: RJ
authors: Schmitz
authors: Matthew D
authors: MD
authors: Schultz
authors: Mark A
authors: MA
authors: Urich
authors: Joseph R
authors: JR
authors: Nery
authors: Mattia
authors: M
authors: Pelizzola
authors: Ondrej
authors: O
authors: Libiger
authors: Andrew
authors: A
authors: Alix
authors: Richard B
authors: RB
authors: McCosh
authors: Huaming
authors: H
authors: Chen
authors: Nicholas J
authors: NJ
authors: Schork
authors: Joseph R
authors: JR
authors: Ecker
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D044127:Epigenesis, Genetic / Q000235:genetics*; D057890:Epigenomics; D014644:Genetic Variation / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D015810:Linkage Disequilibrium / Q000235:genetics; D011058:Pollen / Q000235:genetics; D011110:Polymorphism, Genetic / Q000235:genetics; D040641:Quantitative Trait Loci; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D012639:Seeds / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D012333:RNA, Messenger; D018749:RNA, Plant