Comparative transcriptome analysis provides insights into the mechanism of pear dwarfing

Dwarfism is an important trait which is closely related to the efficiency of fruit orchard management and production. However, dwarfing cannot be widely applied in the cultivation of pears, especially Asian pears. Developing varieties with dwarf characteristics is a goal of paramount importance in pear breeding. In the present study, dwarf phenotype pears (DPPs) and arborescent phenotype pears (APPs) were obtained from the offspring of a cross between ‘Aiyuxiang’ and ‘Cuiguan’ pear cultivars, which exhibited dwarfed and arborescent statures, respectively. When compared with APPs, the heights of DPPs showed a 62.8% reduction, and the internode lengths were significantly shorter. Cross-grafting between DPPs and APPs demonstrated that the dwarfed phenotype of DPPs was primarily induced by the aerial portions of the plant, and independent of the root system. Observations of stem tissue sections showed that DPP cells were arranged chaotically with irregular shapes, and the average length was larger than that of the APP cells. A total of 1 401 differently expressed genes (DEGs) in shoot apices between DPPs and APPs were identified by RNA-sequencing (RNA-Seq), and these DEGs were mainly enriched in the ‘phytohormone-related pathways, cell wall metabolism and cell division’ categories. Moreover, 101 DEGs were identified as transcription factors (TFs). In DPPs, several brassinosteroids (BR) signaling and cell cycle-related genes were significantly down-regulated, while genes involved in BR and GA degradation were up-regulated. Comprehensive analysis of RNA-Seq data and stem tissue sections suggested that the dwarfed phenotype of DPPs could be primarily attributed to deficiencies in cell division. Previous work using simple sequence repeat (SSR) markers narrowed the location of the gene responsible for the dwarf phenotype of ‘Le Nain Vert’. Through combined analysis of our transcriptomic data with the SSR results, we identified four genes as promising candidates for the dwarf phenotype, among which, a DELLA gene could be the most promising. The results presented in this study provide a sound foundation for further exploration into the genetic and molecular mechanisms underlying pear dwarfing.