Pena-Ponton, C. | bioRxiv Science

bioRxiv2022

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

- 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.

ecology↗

bioRxiv2022

High-resolution methylome analysis in the clonal Populus nigra cv. 'Italica' reveals environmentally sensitive hotspots and drought-responsive TE superfamilies

ABSTRACT/SUMMARYO_LIDNA methylation is environment-sensitive and can mediate plant stress responses. In long-lived trees, changing environments might cumulatively shape the methylome landscape over their lifetime. However, because high-resolution methylome studies usually focus on single environments, it remains unclear to what extent the methylation responses are generic or stress-specific, and how this relates to their long-term stability. C_LIO_LIHere, we studied the methylome plasticity of a single poplar genotype, Populus nigra cv. Italica. Adult poplar trees with diverse environmental histories were clonally propagated, and the ramets exposed to experimental cold, heat, drought, herbivory, rust infection and salicylic acid treatments. Then, we identified and compared stress-induced vs. naturally occurring DNA methylation changes using whole genome bisulfite sequencing data. C_LIO_LIMethylation changes mainly targeted transposable elements and when occurring in CG/CHG contexts, the same regions were often affected by multiple stresses, indicating a generic response. Drought triggered a unique CHH hypermethylation response in transposable elements, affecting entire superfamilies and often occurring near drought-responsive genes. Stress-induced methylation variation in CG/CHG contexts showed striking overlap with methylation differences observed between trees from distinct geographical locations. C_LIO_LIAltogether, our results indicate that generic methylome stress responses can persist as epialleles in nature while some environments trigger more transient but large and specific responses, with possible functional consequences. C_LI

genomics↗