Mechanism of Organic Plant Protection Technology in Controlling Apple Bitter Pit: Insights from Integrated Transcriptomic and Metabolomic Analyses

Apple bitter pit (ABP), a severe physiological disorder, severely impairs the quality and yield of the susceptible 'Qingcui' apple. This study investigated the control efficacy and mechanism of a three-in-one Organic Plant Protection Technology (OPPT) against ABP, with treatments set as control (CK), untreated diseased (UD), and OPPT-sprayed healthy groups. Results showed OPPT significantly reduced ABP incidence to 14.84%, improved fruit quality, enhanced antioxidant defense systems, mitigated oxidative damage, repaired fruit cell structural damage, and restored fruit calcium levels to the healthy level. Integrated transcriptomic and metabolomic analyses revealed OPPT reshaped fruit gene and metabolite profiles, with the flavonoid biosynthesis pathway as the core regulatory node, upregulating key genes (CHS, FLS, etc.) and promoting flavonoid metabolite accumulation. In conclusion, OPPT controls ABP via multi-dimensional regulation of phenotype, physiology, cell structure and molecular metabolism, providing a novel paradigm for the green control of apple physiological disorders and supporting sustainable apple industry development.