Watercore is a physiological disorder of apple expressed as fluid deposition in intercellular spaces. We analysed the watercore prone cultivar \u27Fuji\u27 to establish a link between enzymatic response and fluid accumulation in the fruit. Individual phenolic content, selected enzyme activities of the phenylpropanoid pathway, sugars and organic acids were quantified in watercore affected flesh and peel. In addition, transcriptome sequencing was performed to obtain a first insight into molecular mechanisms underlying the physiological disorder. Sampled material included: peel (HP) and flesh from healthy fruit (H), peel from watercore affected fruit (WP), healthy flesh from fruit with watercore (HW) and watercore flesh (WW) from fruit with watercore. A sorbitol increase in watercore affected apple was observed not only in the flesh but also in the peel. Moreover, two phenolic groups (hydroxycinnamic acids and flavonols) were significantly affected by watercore and their content was higher in WP in comparison to HP. Dihydrochalcone content was the highest in WW flesh. This was supported by RNA-seq data, which indicated a generally increased expression of genes from the early flavonoid pathway, sorbitol metabolism and polyphenol oxidases. Among the phenylpropanoid pathway enzymes analysed, phloretin 2′-O-glycosyltransferase was the only one exhibiting altered activity
