Integrated physicochemical and metabolomic profiling reveals quality variations in red ‘Fuji’ apples from different geographical origins

The metabolic regulatory mechanisms underlying quality variations in red ‘Fuji’ apples from different geographical origins remain unclear. In this study, we systematically analyzed red ‘Fuji’ apples from four geographical origins, identifying altitude as the primary driver of their quality variations. Red ‘Fuji’ apples from higher altitudes (HA, 1013–1037 m) showed significantly higher soluble sugar, acidity, and phenolics than those from lower altitudes (LA, 675–728 m). The key aroma compound 2-methylbutyl acetate was significantly elevated in HA, contributing to their enhanced fruity aroma, whereas hexanal and 1-hexanol were identified as the predominant contributors to the characteristic grassy notes in LA. Ferulic acid was a key differential compound in PCA, with significantly higher abundance in the HA group (PC1: 11.54 %; PC2: 9.42 %). Metabolic analysis revealed that flavonoid biosynthesis pathways as primary drivers of quality variation between different geographical origins. By identifying the critical roles of flavonoid biosynthesis and aroma compound accumulation in red ‘Fuji’ apples from different regions, this study clarifies the metabolic basis for their nutritional (phenolics) and sensory (fruity/grassy notes) differences. These findings inform both cultivation strategies and marketing practices, enabling producers to leverage “high altitude” labeling to highlight the superior flavor and nutritional benefits for consumers. • First reveals Altitude-temperature determines red ‘Fuji’ apple quality variation. • High altitude red ‘Fuji’ apples exhibit enhanced fruity aroma. • Altitude regulates red ‘Fuji’ apple quality mainly via flavonoid metabolic pathway.