Seedbank seeds for the study of environmentally induced transgenerational epigenetic variability: A case study of barley

Abstract

Transgenerational epigenetics inheritance refers to the possibility to inherit epigenetic-based information acquired from previous generations. The design of experiments that can measure this phenomenon presents complexities. These are related mainly to difficulties in the identification of epigenetic variation components that are independent from genetic variation, and to difficulties related to the time needed to expose genetically stable plants to different environments for several generations. In this study we propose an experimental approach that takes advantage of seed material routinely produced by seedbanks in order to circumvent the abovementioned issues. By taking advantage of this freely available seed material, it is possible to evaluate epigenetic differences induced by the environment experienced by previous generations and to evaluate both the extent and the impact of epigenetic variation in crops. Seeds of two barley (Hordeum vulgare L.) cultivars, which were previously multiplied in six different seedbanks located worldwide, were grown in a common environment and the plants were evaluated at a genetic, epigenetic, and phenotypic level. Our results indicate that barley accessions multiplied in different environments displayed a comparable level of epigenetic variation, which was, however, greater than the genetic variation. Cluster analysis of methylation differences, likewise DNA differences, split the two cultivars in two distinct groups evidencing a clear link between genetic and epigenetic variation. Nevertheless, the analysis of phenotypic traits and of the CCGG sites that are variable in both cultivars suggests that there might be a possible link between previous cultivation environment and induced epigenetic changes at specific DNA regions.

The evolutionary consequences of interactions between the epigenome, the genome and the environment

“…While a large fraction of epigenetic variation, at least in plants, appears to be dependent on the genome, a smaller yet significant fraction is often found to be better explained by the environment than the underlying genetic structure. This result has been observed for DNA methylation across taxonomically diverse natural populations of plants (De Kort et al, 2020;Jueterbock et al, 2020;Martinelli et al, 2021) and animals (Aagaard et al, 2022;Chapelle & Silvestre, 2022;Johnson & Kelly, 2020). In two of the most recent comprehensive population epigenetic studies of plants, most epigenetic variation was found to be genetic in origin (~90%-95% in CG, ~70%-90% in CHG and 55%-65% in CHH), but the environment still explained a significant fraction of the observed variation (~5%-10% in CG, 10%-30% in CHG and 15%-25% in CHH; Figure 2) (Galanti et al, 2022;Sammarco et al, 2024).…”