A rootstock-oriented paradigm for fruit quality regulation in vegetables and fruit crops

Abstract Fruit quality is a fundamental component of human nutrition and a major determinant of consumer preference, creating an urgent need for sustainable strategies to improve horticultural crop quality under increasing global challenges. Conventional breeding approaches for enhancing complex quality traits are often constrained by intensive phenotyping requirements and prolonged selection cycles spanning ten years or more. Rootstock-mediated grafting provides an efficient and environmentally sustainable approach for modifying scion performance; however, the systemic mechanisms by which rootstocks regulate fruit quality remain largely unresolved. This review summarizes current advances in understanding rootstock–scion communication and proposes that rootstocks reprogram scion physiology through dynamic nutrient allocation, long-distance hormonal signaling, the transport of regulatory macromolecules (mRNAs and proteins), and the epigenetic modulation of fruit-related genes. Systematically, these interconnected pathways converge on conserved regulatory modules that ultimately define fruit quality attributes. By integrating evidence from grafted and nongrafted horticultural systems, this review establishes a conceptual framework for deciphering how rootstock-derived signals reshape scion physiology, metabolism, and gene regulation. Furthermore, future research directions are proposed, including multiomics-guided rootstock selection, AI-assisted prediction of optimal rootstock–scion combinations, and the development of engineered rootstocks for precision improvement of fruit quality. Collectively, these advances are expected to transform grafting into a predictive platform for precision horticulture and contribute to the development of climate-resilient crops with enhanced and stable fruit quality.