Comparative Profiling of Aroma Volatiles and Flavonoid Biosynthesis in Crimson Seedless, Red Globe, and Shine Muscat Table Grapes Using GC-IMS and RNA-Seq.

Table grapes are widely consumed fruits, and their quality is largely determined by aroma, texture, and the accumulation of health-promoting compounds such as flavonoids. In this study, we systematically compared the edible quality and molecular basis of flavonoid biosynthesis among three major table grape cultivars: Crimson Seedless (CRS), Red Globe (RG), and Shine Muscat (SM). An integrated approach combining physicochemical assays, Gas chromatography-ion mobility spectrometry (GC-IMS)-based volatile profiling, and transcriptome sequencing (RNA-seq) was employed. Among the three cultivars, SM exhibited superior fruit quality, characterized by the highest firmness, total soluble solids, ascorbic acid, total phenolic content, and flavonoid content, whereas CRS showed the highest titratable acidity. Volatile compound analysis revealed distinct aroma profiles among the cultivars. SM was enriched in ethanol and 2-methylbutanal, contributing sweet and fruity notes, while CRS contained higher levels of C6 aldehydes, such as hexanal and (E)-2-hexenal, which are associated with green and leafy aromas. RG exhibited a relatively simpler volatile profile with lower overall abundance. Transcriptome analysis identified 20 differentially expressed genes involved in the flavonoid biosynthetic pathway, including PAL, C4H, 4CL, CHI, F3H, F3'H, and DFR, of which ten were significantly upregulated in SM. Eight of these genes showed strong positive correlations (r > 0.8) with flavonoid content. These results provide a comprehensive understanding of the metabolic and genetic mechanisms underlying cultivar-specific quality traits and identify promising candidate genes for breeding table grapes with enhanced flavor and health-promoting properties.