Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes

DNA methylation is a key epigenetic mechanism in plants, reported to be involved in regulating responses and local adaptation to abiotic and biotic stressors that could be particularly beneficial for long-lived tree species. Given that climate change is predicted to promote insect outbreaks, epigenetic studies of herbivory responses in trees may be vital for forest management and conservation. Here, we study changes in DNA methylation in response to herbivory in the clonal tree Populus nigra cv. ‘italica’ (Lombardy poplar). Cuttings were collected from three distant geographical locations (Spain, Italy, Poland), clonally replicated and grown in a common environment. We used reduced representation bisulfite sequencing to assess methylation changes between three experimental categories: (i) insect and (ii) artificial herbivory, and (iii) undamaged plants. Our results indicate that DNA methylation in poplars from different provenance, despite being genetically very similar, responded differently to experimental herbivory with plant origin accounting for 17.2% of the variation across CG, CHG, and CHH contexts. Both insect and artificial herbivory induced a significantly higher response in CHH context. When we explore loci with contrasting methylation levels (differentially methylated cytosines, DMCs), Spanish poplars were the most responsive to insect damage while Polish trees to artificial herbivory. DMCs were primarily located in gene bodies and their flanking regions (CG, CHG) or intergenic regions (CHH). Further, about one-third of DMCs obtained in CHH context were associated with transposable elements (TEs). Our findings suggest that for a better understanding of the role of the epigenetics in plant responses to herbivory we may need to take into account history of exposure, and highlight the importance of incorporating epigenetic knowledge to manage natural forests and tree plantations to help them cope with their environmental challenges.