Tree peony (Paeonia section Moutan DC.) is a unique group of precious woody species with high ornamental, medicinal, and oil value. A drought environment severely restricts their yield and quality. However, the screening and identification of miRNAs in response to drought stress of tree peony has not been reported. In this study, Paeonia ostii ‘Fengdan’ were treated with mild drought, severe drought, and rehydration, respectively. The results of phenotypic observation and physiological characteristics showed that the cell membrane of P. ostii leaves was damaged by drought stress and had a self-regulation function. Combined with multi-omics analysis (transcriptomics, miRNA, and degradome), a total of 883 miRNAs with significant differential expression were identified, and the expression regulation networks of miRNAs and target genes were constructed. A set of 19 different miRNAs was found to regulate 189 different genes. Drought-responsive miRNA–mRNA–TF modules like miR172d-ARR (Arabidopsis Response Regulator), miR396g-STAT (Signal Transducer and Activator of Transcription), and miR168-DBB (Double B-Box) were discovered. By cloning the key miRNA PomiR172d and its target gene PoARR and conducting genetic transformation to verify its function, analyzing the permeability of cell membrane and enzyme activity of ROS in transgenic plants, the molecular regulatory mechanism of the PomiR172d-PoARR module of tree peony in response to drought stress was revealed. Our studies lay the foundation for future research on the regulatory mechanism of tree peony in response to drought stress and provide a theoretical basis for the improvement and cultivation of drought-resistant varieties of tree peony.

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