Involvement of metabolic, physiological and hormonal responses in the graft-compatible process of cucumber/pumpkin combinations was revealed through the integrative analysis of mRNA and miRNA expression.

Grafting is a widely used technique, and graft compatibility between the rootstock and scion is a prerequisite for grafting. To date, the underlying causes of graft compatibility/incompatibility remain largely unknown. Here, using cucumber (Cucumis sativus L.) grafted onto pumpkin (Cucurbita L.) rootstocks with different degrees of graft compatibility, and both self-grafting and non-grafting as controls, an integrative analysis of mRNA and miRNA expression and regulatory networks was conducted by using RNA-Seq and sRNA-Seq at 25 days after grafting (DAG). A total of 223 differentially expressed genes (DEGs) and 30 differentially expressed miRNAs (DEMs) related to graft compatibility were identified based on their fold change. Using a combination of GO annotations and KEGG pathway data, the functional annotations and pathways of DEGs and DEM targets showed that a number of metabolic, physiological and hormonal responses are involved in graft compatibility in cucumber leaves including metabolic processes (e.g., "carbohydrate metabolic processes"), nutrient transport (e.g., "sugar transport"), signal transduction (e.g., "MAPK cascade"), plant hormone signal transduction (e.g., "abscisic acid-activated signaling pathway"), transcription factors (e.g., MYB, NAC and bHLH), oxidation-reduction processes, and defense responses. The results of our comprehensive analysis suggested that compatible rootstocks might possess a greater ability for cell proliferation and a more efficient carbohydrate metabolism that promotes plant growth. In contrast, incompatible grafts induced multiple defense response-related genes and various transcription factors, likely in response to stress. Additionally, they consumed large amounts of energy, which ultimately restrained the plants normal development. This study advances our understanding of the molecular mechanisms underlying plant graft compatible/incompatible responses and provides numerous mRNA and miRNA candidates for more in-depth studies into the graft compatibility process.