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Outcrossing annual plants can adapt rapidly to these changes via sexual mating and DNA mutations. However, perennial and clonally reproducing plants may have developed particular mechanisms allowing them to adapt to these changes and transmit this information to their offspring. The mechanisms allowing plasticity of response could come in the form of epigenetic marks that would evolve throughout a plant’s lifetime and modulate gene expression. To study these mechanisms, we use apple (Malus domestica) as a model perennial and clonally propagated plant. Primary results indicate that a majority of DNA methylation patterns from the tree are transmitted to newly grafted plants but with specific local differences. Both the epigenomic and transcriptomic data indicate that grafted plants are at an intermediate phase between an adult tree and seedling and inherit part of the epigenomic history of their mother tree.