Genome-wide identification and expression analysis of GRF genes regulating apple tree architecture

Growth-regulating factor (GRF) proteins comprise a family of plant-specific transcription factors that play crucial roles in regulating plant architecture. However, information pertaining to the GRF gene family in apple (Malus × domestica) is limited. In the present study, 16 GRF family members were identified in the apple genome, and nine were predicted to be putative targets of apple microRNA396 (miR396). Phylogenetic and synteny analyses of MdGRF genes indicated that gene duplication events have likely contributed to the expansion and evolution of MdGRFs. Moreover, several pairs of MdGRF/AtGRF homologs were identified. The tissue-specific expression patterns of MdmiR396–MdGRF genes in different tissues and in the ArrayExpress database were subsequently characterized. The analyses indicated that they had opposing functions. Exogenous brassinolide, gibberellic acid, 1-naphthylacetic acid, and 6-benzylaminopurine increased primary shoot lengths and diameters, and elevated the expression levels of several MdGRF genes. The expression levels of MdmiR396 and MdGRF genes were reduced in the standard cultivar “Nagafu 2” compared with its short branch spur-type bud mutation “Yanfu 6,” and in the standard graft combination Nagafu 2/Nagafu 2 compared with the dwarfing graft combination Nagafu 2/“Malling 9.” Thus, MdmiR396-MdGRF may be involved in the regulation of apple tree size in response to hormone signals and in different apple varieties and grafting combinations. This work provides a basis for further functional research on MdmiR396-MdGRFs and their potential involvement in the regulation of apple tree architecture.