Comparative transcriptome analysis provides insights into the dwarfing mechanism of pear trees

Background Dwarfism is crucial for intensive cultivation and labor-saving management in modern orchard. However, the molecular mechanisms underlying pear tree dwarfing remain largely unclear. Here, we performed comparative transcriptome analysis between dwarf pear germplasm and pear cultivar ‘Cuiguan’. Result The dwarf pear germplasm presents significantly shorter internode and branch length compared to ‘Cuiguan’. Histological analysis revealed that cortical cells in the dwarf pear germplasm are disordered and irregular, and longer than those of ‘Cuiguan’. Comparative transcriptome analysis of shoot apex from young shoots of the dwarf germplasm and ‘Cuiguan’ was conducted and a total of 13,169 differentially expressed genes (DEGs) were identified. Functional enrichment analysis revealed that function terms related to plant hormone biosynthesis and signal transduction were overrepresented in DEGs. Genes involved in brassinosteroid (BR) and gibberellin (GA) inactivation and degradation were upregulated in the dwarf germplasm. DEGs involved in transcription regulation and cell wall formation were also identified, which play potential roles in tree dwarfing. In addition, expression level of genes within the chromosomal region containing PcDw locus, which has been reported as the dominant gene controlling dwarf trait, was investigated in both the dwarf pear germplasm and ‘Cuiguan’. Based on comparative analysis, 9 genes in this region are considered to be closely associated with dwarf traits. Conclusions Overall, the results of this study provide insights for understanding the genetic and molecular mechanisms underlying pear tree dwarfing.