Patterns of population epigenomic diversity.
|Title||Patterns of population epigenomic diversity.|
|Publication Type||Journal Article|
|Year of Publication||2013|
|Authors||Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR|
|Date Published||2013 Mar 14|
|Keywords||Arabidopsis, DNA Methylation, DNA Transposable Elements, Epigenesis, Genetic, Epigenomics, Genetic Variation, Genome, Plant, Linkage Disequilibrium, Pollen, Polymorphism, Genetic, Quantitative Trait Loci, RNA, Messenger, RNA, Plant, Seeds|
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.