Identification and characterization of heat-responsive microRNAs at the booting stage in two rice varieties 9311 and Nagina 22

Heat stress is one of the most representative abiotic stresses that severely affect plant growth and development. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs that play important roles in abiotic stress responses in plants. Although miRNAs implicated in heat stress response have been widely reported in numerous plant species, their regulatory roles in the adaptive response to heat stress at the booting stage in two rice varieties 9311 and Nagina 22 (N22), remain largely unknown. In this study, high-throughput sequencing of eight small RNA libraries from spikelet in rice 9311 and N22 (heat stress treatments for 0, 3, 6, and 12h, rspectively) were performed for systematical identification of heat-responsive miRNAs and their expression profiling in rice. Totally, 463 known miRNAs and 123 potential novel miRNAs were identified. Of these miRNAs, a total of 90 differential expressed miRNAs were obtained with 9311 libraries as control group (N22 VS 9311), of which 54 (60.00%) upregulated and 36 (40.00%) downregulated miRNAs. To gain insight into functional significance, 2773 potential target gendss of these 90 differentially expressed miRNAs were predicted. GO enrichment showed that the predicted target genes of differentially expressed miRNAs including NAC domain-containing proteins (NACs), laccase precursor proteins (LACs), superoxide dismutase (CSD), DnaJ domain containing protein (Hsp40 or J protein), and KEGG pathway analysis showed that target genes of these differentially expressed miRNAs were significantly enriched in plant hormone signal transduction pathway. The expression levels of ten differentially expressed miRNAs and ten target genes obtained by quantitative real-time PCR (qRT-PCR) were largely consistent with the sequencing results. This study enriches the number of heat-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in rice at elevated temperatures.