Beyond population genetics: natural epigenetic variation in wild cherry (Prunus avium)

The epigenetic structure in wild plant populations remains largely unknown despite the substantial interest in evaluating epigenetic diversity in non-model organisms living in nature. The forces that shape natural epigenetic variation continue to be elusive and the potential challenge of neo-Darwinian evolutionary theory is still an open question. In this work, we estimated epigenetic diversity and differentiation within and between five natural wild cherry (Prunus avium L.) populations in northern Greece. By using a combination of either EcoRI/HpaII, or EcoRI/MspI restriction enzymes, we found low epigenetic polymorphism and weak epigenetic structure. In total, 324 methylation-sensitive amplified polymorphic (MSAP) marker bands were detected across 93 wild cherry individuals examined. They represented 272 methylation-susceptible and 52 non-methylated epiloci. The total 5'-CCGG-methylation level, ranged from 37.05 to 59.39 %, presenting an overall mean of 49.67 % and the difference among populations was significant. The relative levels of full-methylation (m-subepiloci), hemi-methylation (h-subepiloci), and non-methylation (n-subepiloci), presented an overall mean of 47.07, 30.99, and 21.92 % respectively. Most of the epigenetic variation (97 %) resided within populations (Phi(ST)=0.017; p<0.001). Epigenetic and genetic diversity did not differ significantly and were not significantly correlated. Epigenetic variation was not congruent to genetic variation that was assessed in the same populations and individuals by inter simple sequence repeat (ISSR) markers and by the S-locus. This study supports the thesis that epigenetic variation is uncoupled from genetic variation. It presents a first insight into the partitioning of epigenetic diversity within and among natural wild cherry populations.