Metabolite accumulation pathway of watercore in apple fruit: An integrative transcriptome and metabolome analysis

• Metabolomics and transcriptomics characteristic of watercore was analyzed. • Genes (8761) and metabolites (529) were differentially changed due to watercore. • Watercore caused sugar metabolism and Ca 2+ signal transduction genes change. • Accumulation of sorbitol was emerged as a prominent feature in watercored tissues. • Possible biosynthesis pathways related to watercore formation were elucidated. The distinctive morphology and flavor of watercored apples have drawn significant interest, yet the molecular mechanisms differentiating watercored and non-watercored tissues remain unclear. This study investigates the pathways involved in apple watercore formation by integrating metabolomic and transcriptomic data. Our findings revealed that sugar metabolism was prioritized enriched in watercored apple, including highly accumulated sorbitol. Up-regulated expression of sorbitol dehydrogenase showed no relationship between its activity and watercore formation. Watercore induced up-regulated expression levels of sucrose synthesis-related genes (e.g., sucrose-phosphate phosphatase), whereas it inhibited the expression of glucose decomposition-related genes (hexokinase). Additionally, significantly higher calcium content was detected in watercored apples. Furthermore, plant-pathogen interaction was down-regulated. Watercore was also associated with the expression level of genes related to defense and cold stress. These findings offer new insights into the molecular basis of watercore, laying the groundwork for targeted postharvest interventions to improve apple quality and storage resilience.