Analysis of differential mRNA and miRNA expression induced by heterogeneous grafting in Gleditsia sinensis

Gleditsia sinensis Lam. is a multifaceted plant with medicinal, edible, chemical, timber, and ornamental applications. However, the effect of rootstocks on scions after grafting is still unclear. This study examined the mRNA and miRNA transcriptome among homografts, heterografts, and seedlings. GO enrichment analysis between seedlings and homograft/heterograft combinations revealed that biosynthesis, degradation, and transport were enriched. The KEGG enrichment results showed that plant hormone signal transduction and the plant MAPK signaling pathway were enriched in both seedlings and heterograft combinations. Through weighted correlation network analysis (WGCNA), the hub genes related to the content of plant hormones were obtained. Taking G. sinensis as the scion, there were 4594, 2887, 3429, and 5959 mRNAs that were specifically expressed in the grafted plants of G. sinensis/G. fera, G. sinensis/G. delavayi, G. sinensis/G. microphylla, and G. sinensis/G. japonica, respectively. The specifically expressed mRNA genes may participate in such processes and pathways as the rhythmic process, circadian rhythm, gibberellic-acid-mediated signaling pathway, and peptide-based amino acid modification. Additionally, 3, 16, 2, and 15 specifically expressed miRNAs were identified. This study examines the impact of grafting on gene expression in Gleditsia plants and establishes a foundation for the development of new resources and rootstock breeding.