Patterns of population epigenomic diversity

Abstract

SummaryNatural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic 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 unlinked 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 methylQTL, which revealed the first 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.

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

“…In total, 9,119 genes fulfilled our criteria across the entire sample, comprising genus-wide alignments for 25 Mb of the genome. The data were analyzed together with published SNPs from 337 A. thaliana lines [2][3][4] . In total the alignment contains 7.5 million SNPs, 6.6 million of which are biallelic.…”

DNA methylation polymorphism and stability in Chinese indica hybrid rice

“…Furthermore, they can be used to profile all forms of single methylation polymorphisms (SMPs). This broad coverage is important because CG-, CHG-, and CHH-SMPs accounted for 23%, 13% and 64% of all SMPs, respectively, in a natural Arabidopsis population [27].…”

“…This suggests a more prevalent epigenetic variation in the natural population. A recent study revealed that epigenetic variations are widespread within natural A. thaliana lines [27]. DNA methylation polymorphisms have also been observed between wild and cultivated rice [25], and between the indica and japonica subspecies of rice [23].…”

Could interallelic interactions be a key to the epigenetic aspects of fitness-trait inbreeding depression?

“…Recent experiments and discussion have, however, revitalized the old idea that epigenetic processes also impact on the phenotypic variation of complex traits and embryo development in inbred individuals (Biémont, 2010;Cheptou and Donohue, 2012;Vergeer et al, 2012;Schmitz et al, 2013;Liebl et al, 2013). However, further experiments are required if we are to decipher the precise mechanisms that underly the inbreeding/epigenetic relationship.…”