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Integrative Multi-Omics Reveals Quality Markers and Metabolic Pathways Across Genotype and Ripening Gradients in
Huiqin Shi1,2, Ting Guo3, Chenlong Wei1,4
1Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China.
Foods (Basel, Switzerland)
|December 11, 2025
Summary
High-altitude apples show unique sugar-acid profiles driven by maturity and variety. Gene-metabolite links reveal an acid-sugar switch influencing apple quality and postharvest strategies.
Area of Science:
- Plant metabolomics
- Fruit biochemistry
- High-altitude agriculture
Background:
- Apples from high-altitude regions possess a distinct sugar-acid profile.
- The specific varietal and maturity factors influencing this balance are not fully understood.
Purpose of the Study:
- To comprehensively map sugars and acids in apples.
- To identify the genetic and metabolic pathways controlling fruit composition.
- To understand the drivers of sugar-acid balance in high-altitude apples.
Main Methods:
- Multi-omics approach integrating chromatography-mass spectrometry and RNA-seq.
- Analysis of *Malus prunifolia* and *M. asiatica* at 60 and 120 days after flowering (DAF).
- Principal component (PC) analysis for dimensionality reduction and canonical correlation for gene-metabolite coupling.
Main Results:
- PC analysis separated apple samples by maturity (PC1) and species (PC2).
- Malate levels decreased as sucrose increased during ripening; specific sugar profiles varied by species and maturity.
- Gene-metabolite correlations identified an acid-sugar switch involving ALMT9 and MDH, linked to succinate, pyruvate, and malate dynamics.
Conclusions:
- Maturity and species significantly impact apple sugar and acid profiles.
- Identified key metabolic pathways and gene-metabolite interactions controlling fruit quality traits.
- Findings provide markers for apple breeding programs and postharvest management.
