Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments

Apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) are two of the most important stone fruit species, and their climacteric nature is a major determinant in terms of fruit shelf-life period. The role of the main genes involved in the ripening process of these species has been extensively studied, however there is a need to expand our molecular knowledge at epigenetic level. To achieve this, postharvest monitoring of 'Goldrich' apricots and 'Santa Rosa' Japanese plums after 1-MCP (ethylene inhibitor) and Ethrel (ethylene precursor) treatments was carried out to delve deep into the epigenetic level using Whole Genome Bisulfite Sequencing (WGBS). Results showed over 12,000 and 9,000 genes with differentially methylated regions (DMRs) in 'Goldrich' and 'Santa Rosa' cultivars respectively. 1-MCP-treated apricot 'Goldrich' exhibited more hypomethylated regions, suggesting lower methylation levels compared to Ethrel treatment. While starch and sucrose metabolism exhibited the greatest number of partially methylated genes, other pathways showcased more significant differences. Thus, 4-coumarate-CoA ligase in phenylpropanoid biosynthesis, DELLA protein in hormone signal transduction, GDP-L-fucose synthase in amino sugar metabolism, D-lactate dehydratase in pyruvate metabolism, and hydroxymethylglutaryl-CoA reductase in 'Goldrich', as well as homocysteine S-methyltransferase in the cysteine and methionine metabolism, 1-phosphatidylinositol-4-phosphate 5-kinase in the inositol phosphate metabolism, pectinesterase in the pentose and glucuronate interconversions, malate dehydrogenase in the carbon metabolism, photosystem I subunit VI in photosynthesis, and aquaporin-4 as a membrane transporter in Japanese plum showed inverse gene expression-methylation patterns. These findings reveal variations in epigenetic regulation during fruit ripening in apricot and plum, influenced by ethylene modulating treatments, suggesting significant role of DNA methylation in this process.