Integrative Transcriptomic and Metabolomic Analyses Reveal the Molecular Mechanisms Underlying Fruit Quality Formation in Watermelon

• A dynamic multi-omics atlas spanning seven key time points from fruit development through postharvest senescence in the small-fruited watermelon ‘Jingcai No. 1’ was constructed, systematically delineating the coordinated regulation of texture softening and sugar-acid metabolism. • Key candidate genes controlling flesh firmness were identified, including cell wall-modifying enzymes (e.g., PME3, PME7, CESA3) and transcription factors highly correlated with firmness (e.g., ERF113, TCP2, NAC29), providing direct targets for breeding varieties with extended shelf life. • The core regulatory network of sugar-acid metabolism was uncovered. The sucrose biosynthesis gene SPS1 was pinpointed as a key driver for sucrose accumulation. Multiple candidate transcription factors, including bHLHs (e.g., bHLH111), MYBs (e.g., MYB106), ERF071, and WRKY75, were strongly associated with sugar accumulation. • Weighted gene co-expression network analysis (WGCNA) revealed modules highly correlated with major quality traits (firmness, sucrose, malic acid, etc.) and predicted key transcriptional regulators such as ERF105, MYB32, WRKY22, and GATA15 potentially governing organic acid metabolism. • This integrative study not only elucidates the molecular mechanisms underlying watermelon fruit quality formation but also provides valuable candidate gene resources and a theoretical framework for molecular breeding aimed at improving both flavor and storability. Integrative Transcriptomic and Metabolomic Analyses Reveal the Molecular Mechanisms Underlying Fruit Quality Formation in Watermelon Abstract Flesh texture and sugar–acid composition are key determinants of watermelon fruit quality, both of which are regulated by complex, multi-gene networks. In this study, the small-fruited watermelon cultivar ‘Jingcai No. 1’ was used as experimental material. Samples were collected across seven developmental and senescence stages, and transcriptomic and metabolomic analyses were integrated to systematically elucidate the dynamic changes and regulatory mechanisms involved in texture development and sugar–acid metabolism.During fruit maturation and senescence, flesh firmness progressively decreased, whereas sucrose content increased steadily. The levels of soluble solids, fructose, glucose, citric acid, malic acid, succinic acid, and fumaric acid exhibited an overall rise followed by a decline. Several genes were closely associated with fruit texture modification, including PMEs, PGs , and CESAs . Sugar metabolism–related genes included SPS1, BAM8 , and SUS5 , while organic acid metabolism–related genes included ME1, MDH3 , and SDH1-1 . Weighted gene co-expression network analysis (WGCNA) further predicted candidate transcription factors potentially associated with fruit firmness—ERF113, TCP2, and NAC29; with sugar metabolism—bHLHs, MYBs (MYB106 and MYB54), RF2b-like, ERF071, and WRKY75; and with organic acid metabolism—ERF105, MYBs (MYB32 and MYB86), WRKY22, and GATA15. Overall, this study proposes a regulatory network framework and provides valuable candidate genes for molecular breeding aimed at improving fruit texture and flavor.