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 and Joseph R. Ecker ()
Additional contact information
Robert J. Schmitz: Plant Biology Laboratory, The Salk Institute for Biological Studies
Matthew D. Schultz: Genomic Analysis Laboratory, The Salk Institute for Biological Studies
Mark A. Urich: Plant Biology Laboratory, The Salk Institute for Biological Studies
Joseph R. Nery: Genomic Analysis Laboratory, The Salk Institute for Biological Studies
Mattia Pelizzola: Genomic Analysis Laboratory, The Salk Institute for Biological Studies
Ondrej Libiger: The Scripps Research Institute
Andrew Alix: Plant Biology Laboratory, The Salk Institute for Biological Studies
Richard B. McCosh: Plant Biology Laboratory, The Salk Institute for Biological Studies
Huaming Chen: Genomic Analysis Laboratory, The Salk Institute for Biological Studies
Nicholas J. Schork: The Scripps Research Institute
Joseph R. Ecker: Plant Biology Laboratory, The Salk Institute for Biological Studies

Nature, 2013, vol. 495, issue 7440, 193-198

Abstract: 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.

Date: 2013
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DOI: 10.1038/nature11968

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