Grafting-induced metabolic reprogramming enhances flavor quality in cucumber fruits: Insights from multi-omics analysis.

Grafting enhances crop resilience, but its systemic effects on fruit flavor and nutritional quality remains unclear. This study investigated how grafting cucumber onto four Cucurbitaceae rootstocks influences fruit quality by integrating widely targeted metabolomics, volatile metabolomics, and transcriptomics. Results revealed significant alterations in non-volatile metabolites (e.g., amino acids, phenolic acids) and volatile organic compounds (e.g., aldehydes, terpenes, ketones), with heterografting markedly enhancing flavor-related compounds. Notably, pumpkin and sponge gourd rootstocks promoted free amino acid accumulation (e.g., L-arginine) and phenolic acids, while wax gourd rootstock elevated aldehydes, including key flavor contributors like (E, Z)-2,6-nonadienal and (Z)-6-nonenal. Transcriptomics identified 3814 differentially expressed genes (DEGs), enriched in amino acid biosynthesis (e.g., CsHDH, CsICD), correlating with enhanced metabolite production. Multi-omics integration demonstrated that rootstock selection modulates cucumber flavor and nutrition by regulating metabolic pathways and gene expression networks. These findings provide mechanistic insights into grafting-mediated quality improvement, supporting optimized rootstock selection for cucumber cultivation.