Patterns of population epigenomic diversity
Robert J. Schmitz, Matthew D. Schultz, Mark A. Urich, Joseph R. Nery, Mattia Pelizzola, Ondrej Libiger, Andrew Alix, Richard B. McCosh, Huaming Chen, Nicholas J. Schork & Joseph R. Ecker
Affiliations Contributions Corresponding author
Nature 495, 193–198 (14 March 2013) doi:10.1038/nature11968
Received 05 July 2012 Accepted 30 January 2013 Published online 06 March 2013
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.
Subject terms: Epigenomics
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