Identification of grape miRNA revealed Vvi-miR164b involved in auxin induced root development

•Our study provides an overview of small RNA transcriptomic changes that occur.•during root development in ‘Thompson seedless’ grape and validates the role of vvimiR164b.•in grape roots in response to auxin signal. These findings lay a foundation for further exploration of candidate miRNAs and target genes in regulating root development. Root development is essential for the growth and vegetative propagation in grapevine. The proper concentration of auxin can promote root development and induce secondary roots or adventitious roots formation. MicroRNAs are involved in regulating the development of roots and played a significant role in grape adventitious roots formation. Hence, in order to verify the molecular mechanism of Indoleacetic Acid (IAA) induced grape root development, the two key time points 10, 30 d and four different IAA concentrations 0, 0.2, 1 and 5 mg/L of root development of grape tissue culture cuttings were analyzed by small RNA transcriptome. A total of 187 known miRNAs and 117 novel miRNAs which showed different expression patterns were identified. The expression levels of the differentially expressed miRNAs and target genes were confirmed by RT-qPCR, and the results showed that the expression of miRNAs and their target genes which associated with auxin signal-related (vvi-miR167, miR164 and miR160), stress response-related (vvi-miR395, miR398 miR169 and novel-miR103), cell fate transformation-, enlargement- and proliferation-related (vvi-miR399, miR166, miR319, miR3633 and miR396) were inconsistent with the RNA-seq results. Furthermore, most of the predicted target genes were negatively regulated by corresponding miRNAs. The function of vvi-miR164b was identified by gene transformation in Arabidopsis thaliana, and the number of lateral roots in transgenic lines increased significantly, suggesting that differentially expressed vvi-miR164b plays an active role in grape lateral root development. Comparison of miRNA expression patterns between the IAA treatment group and control group (CK) may provide a means to reveal the molecular mechanism of miRNA-mediated regulation of grape root development under auxin treatment. In summary, these results gave us useful information to better understanding the root development in fruit tree.