Abstract
Somatic hybridization represents a powerful tool for generating novel chemotypes with enhanced biosynthetic capabilities. This study provides the first comprehensive phytochemical characterization of interspecific somatic hybrids between Gentiana cruciata L. and Gentiana tibetica King ex Hook.f., two medicinally important yet regionally rare gentians. A total of 107 compounds were detected using UHPLC-DAD-ESI-MS(3), of which 31 were identified as metabolites across eight phytochemical classes. Comparative profiling revealed that all hybrids retained a conserved core of iridoids and secoiridoids while integrating lineage-specific compounds and producing hybrid-specific metabolites not detected in either parent. Despite inheriting plastids from G. tibetica, hierarchical clustering showed that the phytochemical profiles of hybrid lines were more similar to G. cruciata, the donor of the nuclear genome. Quantitative analysis of the major secoiridoids, such as gentiopicroside, swertiamarin, and sweroside, demonstrated that several hybrid lines, particularly F30A-5 and F30A-6, matched or surpassed the biosynthetic output of G. tibetica, the more productive parent. These lines also exhibited elevated antioxidant capacity, underscoring their phytochemical and functional potential. Altogether, our findings show that somatic hybridization not only preserves but may amplify the secondary metabolite capacity of the parental genotypes, offering a viable platform for sustainable in vitro production of pharmacologically relevant secoiridoids.