biostudies-literatureShi HKey Research and Transformation Project of Science and Technology Department of Qinghai Province4039https://www.ebi.ac.uk/biostudies/studies/S-EPMC12691744biostudies-literatureUnknown14(23)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-QFoods (Basel, Switzerland)Integrative Multi-Omics Reveals Quality Markers and Metabolic Pathways Across Genotype and Ripening Gradients in High-Altitude &lt;i&gt;Malus&lt;/i&gt;.PMC126917442023-NK-130Tian JLi YWei CGuo THou XShi HfalseIntegrative Multi-Omics Reveals Quality Markers and Metabolic Pathways Across Genotype and Ripening Gradients in High-Altitude &lt;i&gt;Malus&lt;/i&gt;.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-Q2025-01-01T00:00:00Z2025 Nov2026-05-26T14:05:41.797Z2026-05-24T03:11:15.324ZS-EPMC126917444137597710.3390/foods14234039