A comparative study of transcriptome changes in apple pulp of 3 Malus domestica genotypes developing enzymatic browning at 3 oxidation times (0, 30 min and 60 min)

Enzymatic browning (EB) endangers adaptation of apple fruit cultivars to new markets, affecting organoleptic properties and producing economic losses. The role of polyphenol oxidases and polyphenol compounds have been highlighted during thein development of EB in apple pulp. However, the regulation of apple response to EB remains to be uncovered. In this study, three apple cultivars with different EB phenotype ranging from low to high browning in apple pulp were used to study transcriptomic changes over time after fresh cutting (0, 30 and 60 minutes). This study allowed the identification of 1448 differentially expressed genes among the studied cultivars with the most significant transcriptomic changes at 60 min after cutting. The detection of a co-expressed gene cluster in a Weighed Gene Co-Expression Network Analysis correlated to EB revealed the existence of a conserved response among our genotypes covering many cell processes such as restructuration mechanisms like vesicle trafficking and cytoskeleton reorganization, lipid metabolism (crucial for both energetic and structural purposes), secondary metabolism, protein degradation and transcription regulation. Moreover, a more detailed analysis of identified WGCNA gene cluster regulatory sequences allowed detection of cis-regulatory elements belonging to CAMTA, WRKY and WUSCHEL transcription factor families, pointing out to a highly regulated stress-response that is strictly connected to innate plant immunity. These findings provide valuable insights into the molecular mechanism involved in apple fresh-cut browning and offer new potential targets for EB regulation.