Comparison of fruit quality and metabolome differences between three table grape varieties and their parents

To elucidate the differences in fruit quality and metabolome between table grape hybrid varieties and their parents, this study used ‘Kyoho’ (KG) as the female parent, ‘Zaoheibao’ (ZHB) as the male parent, and their three hybrid offspring ‘Baoguang’ (BG), ‘Cuiguang’ (CG), and ‘Miguang’ (MG) as materials. Basic fruit quality traits, total phenolic and anthocyanin contents were measured, sensory evaluation was conducted, and 30 pairs of SSR fluorescent primers were employed to verify the genetic relationships between parents and offspring. Meanwhile, LC-MS/MS-based untargeted metabolomics combined with multivariate statistical analysis was used to compare the metabolic profiles of the five varieties.The results showed that CG exhibited high soluble solids content (19.26%) and low titratable acidity (3.78 g·L −1 ), demonstrating excellent sugar-acid balance; BG exhibited the highest anthocyanin content (14.56 mg/100 g); MG possessed a strong rose aroma and achieved the highest overall sensory score. SSR molecular markers confirmed that all three offspring were true hybrids, and each variety was assigned a unique SSR barcode-based molecular identity. A total of 2038 metabolites were putatively annotated by metabolomics analysis. PCA and OPLS-DA confirmed clear metabolomic separation among varieties, with flavonoids and anthocyanins identified as key differential metabolites. The up- and down-regulation patterns of metabolites in the volcano plot indicate that the inheritance from the two parents in the hybrid progeny is not simply additive. The Euclidean distance between the parents KG and ZHB was the largest (77.70), whereas the distance between CG and KG was the smallest (62.17), indicating that CG had a metabolome more similar to that of the female parent KG. KEGG enrichment analysis indicated that differential metabolites were mainly enriched in amino acid biosynthesis and flavonoid metabolism pathways. Correlation analysis revealed that flavonol glycosides showed strong positive correlations with anthocyanins and total phenolics, while WGCNA analysis revealed that anthocyanins and total phenolics exhibited divergent dynamic trends. Redundancy analysis (RDA) showed that the first two axes cumulatively explained 74.39% of the covariance, revealing an opposing differentiation pattern between appearance quality and internal quality traits at the metabolic level. In conclusion, the three hybrid cultivars exhibit distinct genetic characteristics at both the fruit-quality and metabolomic levels, and amino-acid metabolic remodeling represents a plausible factor underlying their quality divergence.