Comparative Transcriptome Analysis Reveals Key miRNAs and Pathways Involved in Adventitious Root Formation in Peach

Adventitious root (AR) formation is critical for the vegetative propagation of peach rootstocks. While miRNAs are known to regulate AR development, the role of specific miRNAs and target genes in peach rootstocks remains poorly understand. In this study, we profiled the miRNAome of ‘GF677’ peach rootstock during indole-3-butyric acid (IBA)-induced AR formation. Samples were collected at key four time points (2 h, 2, 10, and 17 days) based on the dynamic changes in endogenous auxin and root morphogenesis. A total of 188 miRNAs were identified, including 60 novel miRNAs. There were 28, 45, 59, 18, 30, and 14 differentially expressed miRNAs (DEMs) in the following six comparison groups of libraries: 2 h vs. 2 d, 2 h vs. 10 d, 2 h vs. 17 d, 2 d vs. 10 d, 2 d vs. 17 d, and 10 d vs. 17 d, respectively. KEGG pathway enrichment indicated that the target genes of DEMs were predominantly associated with signal transduction and metabolism. Specifically, the plant hormone signaling and starch and sucrose metabolism pathways were enriched across all the six comparison groups, while each group exhibited a unique enriched pathway. Additionally, the functional validation of miR319, a DEM, through transgenic analysis in Arabidopsis revealed its regulatory role in AR development. Collectively, this study provides the first insights into the role of miRNAs in peach adventitious rooting, laying a theoretical foundation for improving the vegetative propagation of peach rootstock.