Epigenetic Landscape of the Citrus Greek National Germplasm Collection and Its Association with Genetic and Fitness-Related Data

Epigenetic diversity contributes to phenotypic plasticity and environmental responsiveness in Citrus spp. In this work, genome-wide DNA methylation was analyzed in 49 accessions representing six Citrus species, hybrids, varieties, and cultivars from the Greek National Germplasm Collection. Substantial variation in global DNA methylation was detected, while the epigenetic diversity indices did not differ significantly among taxa. The highest values were observed in Citrus × aurantium var. sinensis (orange) varieties (Pepi = 77.33%, Na = 1.55, h = 0.14, Iepi = 0.24), whereas the lowest were recorded in Citrus × aurantifolia (lime) (Pepi = 18.67%, Na = 0.37, h = 0.09, Iepi = 0.13), reflecting potential methylation restructuring impacted by hybridization and selection. Epigenetic and genetic diversity were significantly different. Principal coordinate analyses (PCoA) of epigenetic data revealed limited concordance to taxonomy, except for unmethylated loci, the latter exhibiting similar data to genetic (SSR) results in which groups reflected the taxonomic genealogy. Epigenetic and genetic distances were uncoupled, and associations between epigenetic diversity (Pepi, h, Iepi) and traits directly or indirectly related to fitness (fruit weight, dry matter content, ascorbic acid concentration), were weak. These findings indicate that epigenetic diversity represents an independent layer of variation in Citrus germplasm with potential relevance for breeding, conservation and environmental resilience.