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Epigenetic modifications can yield information about connections between genotype, phenotype variation and environmental conditions. Bud dormancy release in temperate perennial fruit trees depends on internal and environmental signals such as cold accumulation and photoperiod. Previous investigations have noted the participation of epigenetic mechanisms in the control of this physiological process. We examined whether epigenetic modifications were modulated in MADS-box genes, potential candidates for the regulation of bud dormancy and flowering in sweet cherry ( Prunus avium  L.). We identified and cloned two MADS-box genes homologous to the already-characterized dormancy regulators DORMANCY-ASSOCIATED MADS-box (DAM3 and DAM5) from  Prunus persica  (L.) Batsch. Bisulfite sequencing of the identified genes ( PavMADS1  and  PavMADS2 ), Methylated DNA Immunoprecipitation and small RNA deep sequencing were performed to analyze the presence of DNA methylations that could be guided by non-coding RNAs in the floral buds exposed to differential chilling hours. The results obtained reveal an increase in the level of DNA methylation and abundance of matching small interference RNAs (siRNAs) in the promoter of  PavMADS1  when the chilling requirement is complete. For the first intron and 5′ UTR of  PavMADS1 , de novo DNA methylation could be associated with the increase in the abundance of 24-nt siRNA matching the promoter area. Also, in the second large intron of  PavMADS1 , maintenance DNA methylation in all cytosine contexts is associated with the presence of homologous siRNAs in that zone. For  PavMADS2 , only maintenance methylation was present in the CG context, and no matching siRNAs were detected. Silencing of  PavMADS1  and  PavMADS2  coincided with an increase in  Flowering Locus T  expression during dormancy. In conclusion, DNA methylations and siRNAs appear to be involved in the silencing of  PavMADS1  during cold accumulation and dormancy release in sweet cherry.

DNA methylation and small interference RNAs participate in the regulation of MADS-box genes involved in dormancy in sweet cherry ( Prunus avium L.)