Graft union formation involves interactions among bud signals, carbon availability, dormancy release, wound responses and non-self-communication in grapevine.

Grafting plants uses intrinsic wound-healing mechanisms to join together different organisms, yet the processes underpinning graft union formation remain poorly understood. To further our understanding of the molecular reprogramming triggered by grafting and wounding in a perennial plant, we characterised the transcriptome and metabolome of intact and wounded un-grafted scions and rootstocks, and homo- and hetero-grafts at 0 and 14 days after grafting/wounding in grapevine. We show that grafting triggered the coordinated activation of gene expression and the accumulation of lipids and phenolic compounds in comparison with intact tissues. We highlight an asymmetry in gene expression above and below the graft interface, which is in part not only due to carbon status, but also to intrinsic differences in gene expression between un-grafted scions and rootstocks, and their differential responses to wounding. We found that β-1,4-glucanases were differentially expressed in response to both wounding and grafting and demonstrated that exogenous β-1,4-glucanase application increased grafting success rate. Grafting, wounding, homo-graft and hetero-graft-specific transcriptome responses were characterised. The comprehensive experimental design of the dataset containing all necessary control samples allowed the identification of genes and metabolites potentially involved in wounding and grafting responses in an iconic grafted fruit crop. This is important because knowledge of genes regulating graft union formation could be leveraged for the selection of new, highly graft-compatible cultivars in the future.