Transcriptome dynamics reveals how asymmetric expression of genes promotes graft healing in Sapindus mukorossi

Grafting has been extensively utilized across various plant species to enhance productivity and stress resistance. Successful grafting necessitates an effective transport system between the rootstock and scion; otherwise, the scion may perish rapidly. Despite its widespread application, the mechanisms underlying graft formation remain poorly understood. To elucidate this process, we monitored hormone levels and genome-wide gene expression changes in grafted Sapindus mukorossi. Our observations revealed that the tissues above and below the graft exhibited asymmetry during the early stages of grafting (7, 14, 20, 30, 45 days after grafting), with the expression of numerous hormones and genes being significantly higher on one side compared to the other. This asymmetry resulted in distinct cellular activities occurring simultaneously in the tissues above and below the graft. Our findings indicate that the rootstock serves as the primary source of callus formation during grafting, while the scion is chiefly involved in the reconnection of vascular tissues. These two processes are separated in time. Subsequently, TuxNet was employed to predict the regulatory network of the tissues above and below the graft, identifying three genetic hubs that facilitate the development of the scion graft: SmHCA2, SmMYB117, and SmCKC1. Additionally, we identified two genetic hubs that promote the healing of the rootstock graft: SmHAM3 and SmSPL3. These findings provide critical insights into the hormones and genes implicated in the graft healing process of Sapindus and serve as a valuable reference for grafting research in other species.