Integrative Multi-Omics Reveals Quality Markers and Metabolic Pathways Across Genotype and Ripening Gradients in High-Altitude Malus

Apples from high-altitude orchards exhibit a distinctive sugar-acid balance, yet the varietal and maturity drivers remain unclear. A multi-omics survey was conducted to map sugars and acids and to resolve pathway control. Chromatography-mass spectrometry, RNA-seq, and principal component (PC) dimensionality reduction fitting analysis were integrated across <i>Malus prunifolia</i> and <i>M. asiatica</i> at 60 and 120 days after flowering (DAF). PC separated maturity on PC1 and species on PC2, and canonical correlation confirmed gene-metabolite couplings. Malate predominated but declined with ripening as sucrose rose; <i>M. prunifolia</i> at 60 DAF showed higher maltose/inositol, whereas <i>M. asiatica</i> at 120 DAF accumulated pentoses/xylitol. In <i>M. prunifolia</i> 60 vs. 120 DAF (Q60-Q120), enrichment targeted starch/sucrose plus pentose-glucuronate remodeling; in <i>M. asiatica</i> 60 vs. 120 DAF (S60-S120), fructose/mannose routes dominated with persistent wall-sugar signatures. Correlations linked succinate and pyruvate positively, and malate negatively, to hexoses, outlining an ALMT9/MDH-bridged acid-sugar switch. These maturation-anchored markers inform quality breeding and postharvest strategies.