Integrative Analyses of Metabolome and Transcriptome Reveal Scion–Stock Asymmetry Reduction and Shift of Sugar Metabolism During Graft Junction Formation in Malus Domestica (‘Hanfu’) Homograft

Grafting is widely used as a breeding method to enhance productivity and resilience. However, the mechanisms of graft healing remain poorly understood. In this study, we performed Malus domestica ('Hanfu') homograft and observed morphological and anatomical changes during the healing process in the graft junction within 40 days after grafting (DAG). The results showed that the healing process was divided into two phases: 0-20 days (callus proliferation phase) and 20-40 days (vascular bundle reconnection phase). During the early stage (20 DAG), gene expression exhibited asymmetry between the scion and rootstock, whereas synchronization occurred in the late stage (40 DAG). Transcriptomic and metabolomic analyses of the scion and rootstock during these two critical phases identified that differentially expressed genes (DEGs) were enriched in "Carbon fixation by Calvin cycle" and "photosynthesis-related pathways", while differentially expressed metabolites (DEMs) were clustered in "Galactose metabolism", implying a critical role of carbohydrates in grafting. Genes encoding enzymes involved in sugar biosynthesis, such as amylase (MdAMY), invertase (MdINV), galactinol synthase (MdGS), raffinose synthase (MdRS), and stachyose synthase (MdSS), were generally more highly expressed during Phase I than Phase II. In contrast, genes encoding enzymes related to sugar consumption, such as fructose kinases (MdSUS), cellulose synthases (MdCESA), and galacturonosyltransferase (MdGAUT), showed weak expression in Phase I but were strongly activated in Phase II. Glucose, sucrose, galactose, and melibiose levels increased significantly at 20 DAG compared with 0 DAG and subsequently decreased by 40 DAG. Exogenous application of 0.5% sucrose, raffinose, or melibiose significantly enhanced vascular bundle reconnection rates at 7 DAG compared with the control group (<i>p</i> < 0.01), confirming the pivotal role of sugar metabolism in graft healing.