Fact sheet 10: Experimental design for epigenetic studies

Bárbara Díez Rodríguez

Common gardens

To separate heritable epigenetic variation from non-heritable epigenetic variation (resulting from developmental plasticity in response to different environments) it is necessary to study the progeny of different natural populations and/or maternal families in a common environment, and to use the resemblance of epigenetic patterns among relatives as indication or epigenetic inheritance. To link epigenetic variation to functional phenotypic traits, it is necessary to control somehow for genetic variation. Only traits that ultimately affect fitness are relevant to the ecology and evolution of natural populations. [1]

Working with clones

Given the necessity of getting rid of genotypic variation, working with clonally reproducing plants can be a great tool to study epigenetic variation. Although some evidence suggests that changes in DNA methylation patterns can occur as a result of clonal propagation (i.e: tissue culture), in most situations these methylation patterns are inherited quite stably. By working with clones, it is easy to disregard the underlying genotypic structure, which should be the same in every individual, and focus only on the epigenetic variation. Because only stable and heritable epigenetic modifications are of interest to ecologists, small variations between clones can be accounted for by pooling samples from various individuals that are genotypically identical.[2]

1. Bossdorf O, Richards CL, Pigliucci M. Epigenetics for ecologists. Ecol Lett. 2008;11:106‑15.

2. Physiology C, Access A, Author T. Heritable epigenomic changes to the maize methylome resulting from tissue culture. Plant Cell Physiol. 2008.