Multi-omics approach for exploring key flavor-related metabolic pathways in different apple cultivars

This study employed a multi-omics approach, integrating transcriptomics and metabolomics, to elucidate metabolic variations in major flavor formation pathways in different apple cultivars. Pathway enrichment analysis revealed nine significant metabolic pathways associated with apple flavor biosynthesis, including the TCA cycle, starch and sucrose metabolism, and butanoate metabolism. Based on these pathways, three core metabolic networks responsible for the biosynthesis of fruity flavor, off-flavor, and sugars were elucidated. Metabolite profiling indicated that higher levels of malic, citric, and succinic acids in apples were associated with enhanced TCA cycle flux and energy metabolism, which may promote ester biosynthesis and contribute to fruity flavor formation. Transcriptomic analysis further revealed that key genes such as glyA , AGXT , and ilvE were linked to fruity ester biosynthesis, whereas xylA and malZ were associated with off-flavor aldehyde and sugar metabolism. Integration of metabolite and gene expression mapping uncovered the relationships between flavor precursors and products and provided insights into metabolic fluxes through interconnected pathways. The analytical strategy and workflow proposed herein demonstrate their effectiveness in deciphering the complex metabolic networks governing apple flavor and establish a foundation for developing apple cultivars with enhanced sensory quality. • Cultivar-specific metabolic and gene patterns explain flavor diversity in apples. • Fifty-nine metabolites across nine pathways control key apple flavor traits. • Fruity ester production was associated with glyA , AGXT , and ilvE in apples. • Off-flavor furfural and sugar generation were linked to xyIA , and malZ in apples.