Integrated metabolomic and transcriptomic analyses reveal that pectin metabolism mediates texture divergence in grape berries

Fruit firmness is a critical determinant of shelf life and consumer preference in table grapes ( Vitis vinifera L.), yet the molecular mechanisms driving texture divergence remain poorly understood. In this study, we integrated physiological, metabolomic, and transcriptomic analyses to dissect regulatory networks in soft-fleshed ‘Xiangfei’ and firm-fleshed ‘Sweet Sapphire’ cultivars during ripening. Phenotypic assessment revealed that the rapid softening in XF was associated with extensive pectin solubilization and elevated pectin methylesterase, polygalacturonase, and pectate lyase. Metabolomic profiling identified 888 differentially accumulated metabolites, highlighting a consistent accumulation of D -galacturonic acid and D -glucuronic acid in SS. K-means clustering analysis categorized these metabolites and differentially expressed genes into seven distinct clusters, which were significantly co-enriched in 6 pectin synthesis and metabolism pathways, such as pentose and glucuronate interconversions and galactose metabolism. Furthermore, weighted gene co-expression network analysis constructed a hierarchical regulatory network identifying 20 key structural genes involved in pectin metabolism, specifically GAUT , SUS6 , PMEI1 / 2 , PME1 , and PL1 . These structural genes were strongly associated with 94 transcription factors such as bHLH5 , MYB74 , ERF1 / 2 , LBD13, and NAC9 / 83 . These findings elucidate the molecular regulatory networks governing pectin metabolism and provide potential markers for improving fruit storability and extending the postharvest shelf life of table grapes. • Pectin composition and enzymatic degradation are primary determinants of texture divergence in grapes. • D -GalA and D -GlcA act as key metabolic regulators maintaining cell wall integrity and berry firmness. • Co-enrichment of DAMs and DEGs in pectin metabolic pathways underlies the variation in berry softening. • WGCNA constructs a comprehensive regulatory network of metabolism and genes during grape ripening.