Rootstock selection and grafting systems affect pepino (Solanum muricatum) fruit nutritional quality and plant performance.

Pepino (Solanum muricatum) is a nutritionally valuable Solanaceae crop, but optimizing its grafting practices to improve survival, growth, and fruit quality remains a critical challenge for commercial production. In this study, we systematically evaluated four pepino scions grafted onto nine Solanaceae rootstocks-including tomato (Solanum lycopersicum), pepper (Capsicum annuum), and eggplant (Solanum melongena)-and optimized grafting parameters (cotyledon removal, grafting height, glucose pretreatment, and shading duration). We measured grafting survival, transplant success, vegetative growth, photosynthetic performance, metabolic activity, and antioxidant enzyme levels throughout early development. The optimal combination, 'Qingcanxiang' scion grafted onto eggplant rootstock 'Moshi', achieved survival rates above 90%, promoted shoot and root biomass accumulation, enhanced net Pn, and maintained elevated soluble protein and sugar contents. Multivariate analysis confirmed that genus-level taxonomic compatibility is a key determinant of graft success and physiological performance. Furthermore, heterografts improved fruit vitamin C content and sucrose accumulation while maintaining comparable yield, fruit morphology, and sensory quality. These findings provide a comprehensive and reproducible protocol for pepino grafting and practical guidance for improving growth performance, fruit quality, and stress resilience in commercial production.