This is the preprint and supplementary materials for the research article entitled “Experimental evidence for short term directional selection of epigenetic trait variation” and authored by Benoit Pujol, Mathieu Latutrie, Pierick Mouginot, Nelia Luviano- Aparicio, Jésaëlle Piquet, Sara Marin, and Stéphane Maury. This article provides direct experimental evidence of an epigenetic response to selection in plants. Theory predicts that a response to selection can rest on trait inherited epigenetic variation if this variation is inherited and stable across generations. This hypothesis is supported by population epigenetic results and evidence from the comparison of plant populations and lines that underwent selection. Our selection experiment was conducted to observe and analyze real time changes of trait values and epigenetic allele frequencies in response to selection. Here we conducted a selection experiment on a model system (Arabidopsis thaliana epigenetic Recombinant Inbred Lines: epiRILs) that allowed us to track trait and epigenomic associated changes before and after selection in a fixed genomic background. Our results show how epigenetic trait variation can act as an additional source of short-term adaptive potential in the absence of genetic variation, in accordance with the “breeding equation” and therefore under a classical quantitative genetics and selection predictive framework. Data and R protocols used for the statistical analyses are available from the ZENODO Digital Repository https://doi.org/10.5281/zenodo.7603324. The EM-seq data used in this study are available on the NCBI bioproject online repository. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA773039. There are no restrictions on data availability. Supplementary materials include Figs. S1 to S2 and Tables S1 to S6. John Pannell (University of Lausanne, Switzerland), Doyle McKey (University of Montpellier, France), Clément Lafon-Placette (Charles University in Prague, Czechia), and Fabrice Roux (Toulouse CNRS, France) provided comments during the preparation of this manuscript.