Dwarfing rootstocks are a valuable genetic resource for managing high-density plantations because it decreases the vegetative growth of scion and minimizes labor expenditures. The scion architecture of grafted Japanese apricot (Prunus mume) is affected by various characteristics of the rootstocks. A leaf and root RNA-Sequencing of the two scion/rootstock combinations (LY/PM and LY/PP) was conducted to explore molecular mechanisms underlying the effect of rootstock on scion vigor and dwarfing related genes. The phenotypic observations showed that size reduction in p. mume (PM) rootstock is due to lower node number, reduced internode length, and decreased trunk diameter of the scion, while trees grafted with P. persica (PP) rootstock increased all the values of morphological index. After cutoff and pairwise comparison analysis, we retrieved 1827 differentially expressed genes (DEGs) in LY/PM and LY/PP graft combinations. The KEGG pathway analysis revealed that the most DEGs were found predominantly enriched in complex plant hormone transduction networks involving the auxin (IAA), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), brassinosteroid (BR) and gibberellic acid (GA) pathways. Several transcription factor families, such as WRKY, NAC, LBD and bZIP, might be involved in the complicated growth induction process. These findings provide a framework for exploring the molecular mechanisms underlying differential scion growth mediated by rootstock.
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