Epigenetic variation in the Lombardy poplar along climatic gradients is independent of genetic structure and persists across clonal reproduction

Abstract

- Environmental changes can trigger phenotypic variation in plants through epigenetic mechanisms, but strong genetic influences make it difficult to isolate and study epigenetic effects. Clonal trees with low genetic variation, such as the Lombardy poplar (Populus nigra cv. Italica Duroi), offer a unique system to study epigenetic variation associated with the environment. - We collected cuttings (ramets) of Lombardy poplar along a wide geographical range in Europe. We performed whole-genome-bisulfite sequencing of 164 ramets grown in a common garden and of a subset of 35 of the original parental individuals. Using historical bioclimatic data, we tested the relationship between DNA methylation and climatic gradients. - We found that average methylation levels in TEs and promoter regions correlate with biologically relevant climatic variables. Furthermore, we observed that DNA methylation was transmitted to the next clonal generation, but a fraction of the methylome changed relatively fast when comparing the parental individuals with the clonal offspring. - Our results suggest that the poplar methylome is a dynamic layer of information that can be transmitted to the clonal offspring and potentially affect how poplars acclimate to new environmental conditions.