Comprehensive transcriptome profiling and hormonal signaling reveals important mechanism related to dwarfing effect of rootstocks on scion in Japanese apricot (Prunus mume)

•Dwarfing rootstocks are a valuable genetic resource for managing high-density plantations because it decreases the vegetative growth of scion and minimizes labor expenditures.•This study was undertaken to explore the dwarfing mechanism in Japanese apricot using RNA- sequencing.•Approximately, 1827 DEGs were found, and a comparison analysis between dwarfing and vigorous graft combinations was performed.•Alterations in the activity of hormones including IAA, ZR, GA3, ABA and BR contribute significantly to scion dwarfing.•Our research provides a foundation for the molecular mechanism of size reduction, as well as a reference for future studies related to size control of fruit crops.