Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar

Insights into the forces that shape the plant methylome contribute to the understanding of the evolutionary significance of epigenetic diversity in plants. Previous research has mainly focused on herbaceous annual plants but it is currently unclear how much epigenetic variation is stably induced in long-lived woody perennials. There is also a need to demonstrate the role of parental environments and epigenetic variation on fitness. : We present detailed methylome analyses of the long-lived Lombardy poplar, Populus nigra cv. ‘Italica‘ Duroi. Trees of this widespread clonal cultivar descended from a common ancestor at least two centuries ago. We analyzed genome-wide methylomes of in total 29 pooled and individual DNA-samples. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts over at least two years and across vegetatively produced generations. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. We selected plant material for whole genome bisulfite sequencing (WGBS) that was described and verified as the ‘true’ Lombardy poplar previously (doi.org/10.5061/dryad.2gf700), thus representing one single genotype. We used DNA samples of individual plants to investigate the stability of the epigenome during a growing season and across vegetatively reproduced generations. The DNA samples from individual plants included i) DNA-samples from F1-ramets collected from Lombardy poplars located in Hungary, Italy, Spain and the UK, respectively, and ii) DNA-samples from second generation vegetative offspring (F2-ramets), propagated from the former F1-ramets). All ramets were grown in a common greenhouse environment in Geraardsbergen, Belgium (lat. 50,77635°, lon. 3.881007°) .