Significant <scp>circRNAs</scp> , <scp>microRNAs</scp> , and Target Genes Participate in the Rooting Process of <i>Acer truncatum</i>

Acer truncatum is a multifunctional tree species widely planted worldwide with extremely high commercial value. It is not easy to take root under natural conditions, and plant growth hormone needs to be used to promote the formation of adventitious roots in stem cuttings. This study aimed to determine how non-coding RNAs and mRNAs regulate the rooting process of A. truncatum in the mode of competitive endogenous RNA interactions. Based on whole transcriptome analysis of the control and treatment (500 mg/L IBA for 30 min) groups, 133 differentially expressed mRNAs, 58 differentially expressed miRNAs, 81 differentially expressed lncRNAs, and 3 differentially expressed circRNAs were selected. Among the differentially expressed miRNAs, 34 differentially expressed miRNAs can target 100 genes. Moreover, 2105 circRNAs were identified, of which 145 interacted with rooting-related miR160, miR164, and miR171. Finally, the ciRNA46-miR164b-NAC1 regulatory network was selected. Real-time quantitative polymerase chain reaction, dual luciferase assays, and β-glucuronidase gene tissue staining experiments verified the interaction among ciRNA46-miR164b-NAC1. Overexpression experiments showed that NAC1 promoted the development of adventitious roots, whereas miR164b inhibited their development. Bimolecular fluorescence complementation and yeast two-hybrid revealed the interaction of NAC1 with SHORT-ROOT. These results explain the mechanism of action in the rooting process of A. truncatum, offering a scientific foundation for further research on its molecular mechanisms during rooting.