Integration of mRNA-miRNA Reveals the Possible Role of PyCYCD3 in Increasing Branches Through Bud-Notching in Pear (Pyrus bretschneideri Rehd.)

Bud-notching in pear varieties with weak-branches enhances branch development, hormone distribution, and germination, promoting healthier growth and improving early yield. To examine the regulatory mechanisms of endogenous hormones on lateral bud germination in <i>Pyrus</i> spp. (cv. 'Huangguan') (<i>Pyrus bretschneideri</i> Rehd.), juvenile buds were collected from 2-year-old pear trees. Then, a comprehensive study, including assessments of endogenous hormones, germination and branching rates, RNA-seq analysis, and gene function analysis in these lateral buds was conducted. The results showed that there was no significant difference in germination rate between the control and bud-notching pear trees, but the long branch rate was significantly increased in bud-notching pear trees compared to the control (<i>p</i> < 0.05). After bud-notching, there was a remarkable increase in IAA and BR levels in the pruned section of shoots, specifically by 141% and 93%, respectively. However, the content of ABA in the lateral buds after bud-notching was not significantly different from the control. Based on RNA-seq analysis, a notable proportion of the differentially expressed genes (DEGs) were linked to the plant hormone signal transduction pathway. Notably, the brassinosteroid signaling pathway seemed to have the closest connection with the branching ability of pear with the related genes encoding <i>BRI1</i> and <i>CYCD3</i>, which showed significant differences between lateral buds. Finally, the heterologous expression of <i>PyCYCD3</i> has a positive regulatory effect on the increased <i>Arabidopsis</i> growth and branching numbers. Therefore, the <i>PyCYCD3</i> was identified as an up-regulated gene that is induced via brassinosteroid (BR) and could act as a conduit, transforming bud-notching cues into proliferative signals, thereby governing lateral branching mechanisms in pear trees.