An integrated transcriptomic and epigenetic analysis disclose the role of ethylene-related phytohormones during shelf life in Japanese plum (Prunus salicina L.) and apricot (Prunus armeniaca L.)

Nowadays the global fruit market is offering more diversity and novel Prunus cultivars of increased fruit quality. Most of these cultivars are characterized by a short shelf life due to its climacteric character. In this context, the current Japanese plum and apricot breeding programmes are mainly focused on fruit quality and a long shelf life. In the last few years, the mechanisms involved in the fruit ripening process and shelf life extension have been studied at transcriptomic, proteomic or metabolomic level. In Japanese plum and apricot, the role of epigenetics in the fruit ripening has not been studied in depth. Therefore, the main goal of this work was to study the postharvest behavior of plum (‘Santa Rosa’) and apricot (‘Goldrich’) cultivars upon application of an ethylene inhibitor (1-MCP) and ethylene stimulator (Ethrel^®), in order to analyze the differentially expressed genes by using RNA-Seq as well as differential DNA methylation regions in relation to the main pathways involved in fruit ripening and shelf life extension. Transcriptomic analysis showed that plant hormone signal transduction and photosynthesis were the most significative pathways for any treatment comparison in both species, while the most overexpressed genes were related to pentose and glucuronate interconversions, including pectinesterase [EC: 3.1.1.11] and polygalacturonase [EC: 3.2.1.15] in apricot and only pectinesterase in plum after Ethrel treatment. At methylation level, CG context showed the highest rate of methylated regions at 100%. A total of 12,628 and 9,249 genes showed differentially methylated regions between treatments in ‘Goldrich’ and ‘Santa Rosa’, respectively, including several genes involved in the most important pathways linked to fruit ripening such as starch and sucrose or pentose and glucuronate interconversions metabolism. These findings showed that 1-MCP and Ethrel influence the fruit ripening process inducing a differential gene expression, with a differential methylation, also evidencing that epigenetics could play an important role.