Rootstock selection shapes melon taste by divergent regulation of sugar and amino acid metabolism

Background Melon ( Cucumis melo L .) is a widely cultivated fruit globally, valued for its high nutritional content and diverse culinary uses. However, the molecular mechanisms underlying flavor enhancement mediated by grafting remain poorly understood. Objective This study aimed to elucidate the molecular regulatory mechanisms of flavor formation in melons grafted onto different rootstocks: Cucurbita moschata (QY1) and Cucumis metuliferus (ZM4). Methods Transcriptomic and metabolomic analyses were integrated to systematically dissect dynamic changes in gene expression and metabolite accumulation in grafted systems (ZM4/SG, QY1/SG). Results The two rootstocks induced distinct genetic and metabolic adaptation strategies. The ZM4 rootstock activated genes related to carbohydrate metabolism, such as sucrose-cleaving enzymes ( INV, bglX/bglB ) and nucleotide-sugar synthases ( UGDH, GAE ), promoting the accumulation of glucose and fructose and expanding UDP-sugar precursors for glycosylation. These genetic changes enhanced anabolic flux, leading to the accumulation of cell wall polysaccharides (e.g., mannan ) and high-value glycosides (e.g., vanilloyl glucose). Additionally, ZM4/SG exhibited enhanced stress resilience via activation of AKR1A1 and MIOX , resulting in increased accumulation of xylitol and trehalose-6-phosphate. In contrast, the QY1 rootstock activated energy metabolism pathways, upregulating E3.2.1.21 and MIOX to promote glycoside hydrolysis and NADPH regeneration, thereby strengthening energy metabolism. Discussion This study clarifies the mechanism of rootstock-mediated metabolic flux reprogramming: ZM4/SG coordinates hydrolytic, biosynthetic, and stress-responsive pathways to redirect carbon flux toward structural polysaccharides and high-value glycosides, providing molecular targets for improving melon aroma and flavor quality. The results align with the hypothesis that rootstocks regulate fruit quality traits and establish a working model for understanding synergistic regulatory networks between rootstocks and scions. This lays a theoretical foundation for developing precise quality modulation strategies in melons.