Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

Abstract

Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations are thus a possible source of heritable phenotypic variation in the absence of DNA sequence change. However, attempts to assess the prevalence of stable epigenetic variation in natural and experimental populations and to quantify its impact on complex traits have been hampered by the confounding effects of DNA sequence polymorphisms. To overcome this problem as much as possible, two parents with little DNA sequence differences, but contrasting DNA methylation profiles, were used to derive a panel of epigenetic Recombinant Inbred Lines (epiRILs) in the reference plant Arabidopsis thaliana. The epiRILs showed variation and high heritability for flowering time and plant height (∼30%), as well as stable inheritance of multiple parental DNA methylation variants (epialleles) over at least eight generations. These findings provide a first rationale to identify epiallelic variants that contribute to heritable variation in complex traits using linkage or association studies. More generally, the demonstration that numerous epialleles across the genome can be stable over many generations in the absence of selection or extensive DNA sequence variation highlights the need to integrate epigenetic information into population genetics studies.

DNA methylation changes in triticale due to in vitro culture plant regeneration and consecutive reproduction

“…Contrary to marker-based approaches, high performance liquid chromatography (HPLC) has been applied in studies of DNA methylation of plants regenerated via tissue culture (Renau-Morata et al 2005;Rival et al 2013). This technique supports general information on global DNA methylation and could be applied for the evaluation of differences among plant materials that could be related to spontaneously arising off-type plants (Johannes et al 2009;Yi et al 2010).…”

The role of migration in the evolution of phenotypic switching

“…Genetically determined variation can allow offspring to be phenotypically similar to parents, while phenotypic plasticity may cause phenotypes to differ greatly within a genetic lineage. Stochastic switching can produce phenotypic variability with familial correlations intermediate between these two extremes (as is seen in the contributions of DNA methylation variation to heritability of phenotypes in the plant Arabidopsis thaliana [12]). …”

Parental epigenetic control of embryogenesis: a balance between inheritance and reprogramming?

“…For instance, studies in plants demonstrated that altered patterns of DNA methylation (so-called epialleles) can be inherited over successive generations [7], [8]. Transmission of the chromatin state of a chromosomal regulatory element through both mitosis and meiosis has been shown in Drosophila [9], [10].…”