Integrated Transcriptomic and Metabolomic Analyses Reveal Key Regulatory Pathways Involved in Grafting in Camellia oleifera

Camellia oleifera is a significant woody oil tree species native solely to China. The bud–seedling grafting technique has been widely applied to this tree due to its significant advantages in improving propagation efficiency and shortening the growth cycle. However, the healing process and its underlying molecular regulatory mechanisms during interspecific heterografting in Camellia remain poorly understood. In this study, we established both homografting and heterografting systems using C. oleifera bud seedlings as rootstocks, grafted with scions from C. oleifera, C. meiocarpa, and C. weiningensis. We systematically investigated the response patterns and differences in metabolites and gene expression before and after grafting healing through endogenous hormone detection, LC-MS untargeted metabolomics, and transcriptomic sequencing. The results showed that the grafting survival rates between C. oleifera and the other species were high (>88%), indicating strong compatibility. Metabolomic analysis revealed that differential metabolites, such as Gibberellin A53, Sophoramine, and Morellin, accumulated significantly with prolonged grafting time, and interspecific grafting combinations exhibited specific highly expressed metabolite profiles. We integrated multi-dimensional data comprising hormone levels, differential metabolites, and DEGs. A “hormone-gene” interaction network was constructed using WGCNA. The analysis revealed that key hub genes, including CYP73A, F3H, CHS, LHCA1, and LHCB5, were significantly correlated with flavonoid biosynthesis and elevated iPR content. We hypothesize that these genes enhance graft healing capacity by regulating secondary metabolism and hormone signaling pathways. The identified candidate genes, phytohormones, and metabolites provide potential molecular markers and regulatory targets for evaluating graft compatibility, selecting suitable rootstock–scion combinations, and optimizing grafting and propagation practices in C. oleifera, providing a crucial theoretical basis for superior cultivar breeding and the investigation of graft compatibility mechanisms.