Integrated Analysis of the Metabolome and Transcriptome During Apple Ripening to Highlight Aroma Determinants in Ningqiu Apples

We investigated the dynamic changes in volatile aroma compound profiles (types and concentrations) and associated gene expression patterns in both the peel and pulp tissues of apples during fruit maturation. This study aimed to elucidate the metabolic regulatory mechanisms underlying volatile aroma biosynthesis in Malus domestica "Ningqiu" apples, thereby providing theoretical support for the comprehensive utilization of aroma resources. Our methodological framework integrated headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS), ultra-high-performance liquid chromatography-orbitrap mass spectrometry (UHPLC-OE-MS), and Illumina high-throughput sequencing to generate comprehensive metabolomic and transcriptomic profiles of peel and pulp tissues. Critical differential aroma compound classes were identified, including esters, aldehydes, alcohols, terpenoids, and ketones, with their metabolic pathways systematically mapped through KEGG functional annotation. Our findings revealed substantial transcriptomic and metabolomic divergence across carotenoid, terpenoid, and fatty acid metabolic pathways. Integrative analysis of multi-omics data revealed 26 and 31 putative biologically significant hub genes in peel and pulp tissues, respectively, putatively associated with the observed metabolic signatures. Among these, five core genes-farnesyl diphosphate synthase (<i>FDPS1.X1</i>), alcohol acyltransferases (<i>AAT1</i> and <i>AAT3</i>), alcohol dehydrogenase (<i>ADH3</i>), and carotenoid cleavage dioxygenase (<i>CCD3</i>)-were recognized as shared regulatory determinants between both tissue types. Furthermore, terpene synthase (<i>TPS7</i>) emerged as a peel-specific regulatory factor, while hydroperoxide lyase (HPL2), alcohol dehydrogenases (<i>ADH2</i> and <i>ADH4</i>), and alcohol acyltransferase (<i>AAT2</i>) were identified as pulp-exclusive modulators of metabolic differentiation. The experimental findings provide foundational insights into the molecular basis of aroma profile variation in Malus domestica "Ningqiu" and establish a functional genomics framework for precision breeding initiatives targeting fruit quality optimization through transcriptional regulatory network manipulation.