Rootstock selection regulates flavor quality in the scion of Citrus medica ‘Guangdong Xiangshui’: insights from LC-MS and GC-IMS metabolomic analyses

Rootstock selection is a critical horticultural practice for modulating fruit quality. This study examined the influence of grafting on pericarp antioxidant capacity, metabolite profiles, and volatile organic compounds in Citrus medica ‘Guangdong Xiangshui’. Own-rooted plants served as the control, while plants grafted onto four rootstocks—C. junos, C. grandis, Poncirus trifoliata, and P. trifoliata × C. sinensis—were evaluated. An integrated approach combining physiological measurements, untargeted metabolomics (LC-MS), and headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS) was employed. Results showed that C. junos and C. grandis rootstocks increased fruit weight and size, whereas P. trifoliata and P. trifoliata × C. sinensis enhanced pericarp antioxidant activity. Metabolomics analysis revealed that the rootstock significantly altered the metabolite profile and bioactivity of the pericarp, primarily by regulating metabolic pathways such as amino acid metabolism and flavonoid biosynthesis, thereby influencing the flavor quality. Seven differential metabolites-(R)-oxypeucedanin, neobyakangelicol, 2E,13Z-octadecadienal, quinic acid, 16β-hydroxyazadirachtin, hesperidin, and umbelliferone-were identified as potential biomarkers for rootstock and flavor evaluation. HS-GC-IMS detected 34 volatile organic compounds, with distinct rootstock-specific profiles: P. trifoliata × C. sinensis accumulated citral and linalool; C. grandis contained elevated rose oxide and (E)-2-pentenal; C. junos was richer in aldehydes and ketones; and P. trifoliata showed higher ester content. These findings elucidate the metabolic and volatile composition of the C. medica ‘Guangdong Xiangshui’ pericarp and provide new insights into rootstock-mediated regulation of fruit quality in citrus.