Stuart, TimEichten, Steven RCahn, JonathanKarpievitch, Yuliya VBorevitz, Justin OLister, Ryan2017-03-302017-03-302050-084Xhttp://hdl.handle.net/1885/114181Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation.This work was supported by the Australian Research Council (ARC) Centre of Excellence program in Plant Energy Biology CE140100008 (JOB, RL). RL was supported by an ARC Future Fellowship (FT120100862) and Sylvia and Charles Viertel Senior Medical Research Fellowship, and work in the laboratory of RL was funded by the Australian Research Council. TS was supported by the Jean Rogerson Postgraduate Scholarship. SRE was supported by an Australian Research Council Discovery Early Career Research Award (DE150101206).application/pdfCopyright Stuart et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.A. thalianaarabidopsisdna methylationchromosomesepigeneticsevolutionary biologygenesgenomicstransposable elements2016-12-0210.7554/eLife.20777