Epigenetic variation in the Lombardy poplar. Natural epigenetic variation in Populus nigra cv "Italica"

Between February and March 2018, cuttings from Populus nigra cv ‘Italica’ clones were collected in Europe across geographical gradients that spanned from 41° to 60°N and -5° to 25°E approximately. To cover a wide bioclimatic range, twelve sampling sites were selected such that they covered seven different Köppen-Geiger climate subtypes. In each site, cuttings were sampled in a 25 km radius and planted in a common garden setting. To assess the number of putative genotypes present in the common garden, the ramets were genotyped using the Allegro technology, a targeted genotyping-by-sequencing technique based on single primer enrichment technology. To study epigenetic variation, specifically differences in DNA methylation profiles, a subset of 164 ramets (14 ramets per sampled site) and 35 ortets (5 ortets per sampled site, in 7 sites) were sequenced using whole genome bisulfite sequencing (WGBS).