Genomics and Applied Biology 2024, Vol.15, No.3, 120-131 http://bioscipublisher.com/index.php/gab 122 3 MiRNAs in Rice Cold Stress Response 3.1 Identification and characterization of cold-responsive MiRNAs MiRNAs are small non-coding RNAs that play crucial roles in regulating gene expression in response to various stresses, including cold stress. In rice, several studies have identified cold-responsive miRNAs using different high-throughput sequencing techniques. For instance, a study identified 18 cold-responsive miRNAs in rice using microarrays, revealing that most of these miRNAs were down-regulated under cold stress conditions (Lv et al., 2010). Another study utilized high-throughput sequencing to identify 265 known mature miRNAs and 41 new miRNAs in wild banana, with differential expression analysis showing that some miRNAs were specific for cold treated responses (Liu et al., 2018). These findings highlight the dynamic nature of miRNA expression in response to cold stress and underscore the importance of miRNAs in the cold stress response in rice. 3.2 Functional roles of key MiRNAs The functional roles of key miRNAs in rice under cold stress have been elucidated through various studies. For example, osa-miR1320 has been shown to target the ERF transcription factor OsERF096, which negatively regulates cold stress tolerance via JA-mediated signaling pathways (Sun et al., 2022). Overexpression of miR1320 enhances cold tolerance, while its knockdown reduces cold tolerance, indicating its critical role in cold stress response. Additionally, miR396b in Poncirus trifoliata has been found to regulate cold tolerance by targeting the ACC oxidase gene, thereby modulating ethylene-polyamine homeostasis and enhancing ROS scavenging (Zhang et al., 2016). These studies demonstrate that specific miRNAs play pivotal roles in modulating key regulatory pathways and stress responses in rice under cold stress. 3.3 Regulatory mechanisms of MiRNAs in cold stress The regulatory mechanisms of miRNAs in cold stress involve complex interactions with their target genes and associated signaling pathways. For instance, miR1320 regulates cold tolerance by targeting OsERF096, which in turn affects JA-mediated signaling pathways and the expression of DREB genes involved in cold stress response (Sun et al., 2022). Similarly, miR396b modulates cold tolerance by targeting the ACC oxidase gene, leading to reduced ethylene synthesis and enhanced polyamine synthesis, which helps in ROS scavenging and stress mitigation (Zhang et al., 2016). Furthermore, the presence of hormone-responsive elements in the upstream regions of cold-responsive miRNAs suggests that hormones play a significant role in the miRNA-mediated defense system in rice (Lv et al., 2010). These regulatory mechanisms highlight the intricate network of miRNA-target interactions and their crucial roles in orchestrating the cold stress response in rice. 4 Transcriptome Dynamics under Cold Stress 4.1 Global transcriptomic changes in response to cold stress Cold stress induces significant changes in the transcriptome of rice, affecting a wide array of genes and pathways. Transcriptomic analyses have revealed that cold stress leads to the differential expression of numerous genes involved in various biological processes. For instance, the integration of miRNA and transcriptome sequencing in wild rice has shown that chilling stress results in the differential expression of miRNAs and their target genes, which are involved in protein biosynthesis, redox processes, photosynthesis, and chloroplast development (Zhao et al., 2022). Additionally, the overexpression of the OsMyb4 transcription factor (TF) in transgenic rice has been shown to alter the complexity of the transcriptional network, enhancing stress tolerance through the regulation of antioxidant capacity and metabolic processes (Park et al., 2010). 4.2 Identification of cold-responsive genes and pathways Several studies have identified specific genes and pathways that are responsive to cold stress in rice. For example, the miR1320-OsERF096 module has been identified as a key regulator of cold tolerance, with miR1320 targeting the ERF TF OsERF096, which in turn modulates hormone content and signaling pathways (Sun et al., 2022). Another study identified 18 cold-responsive miRNAs in rice, with members of the miR-167 and miR-319 families showing similar expression profiles under cold stress (Lv et al., 2010). Furthermore, the OsmiR156-OsSPL3-OsWRKY71 regulatory pathway has been shown to enhance cold stress tolerance by modulating the expression of stress-response genes (Zhou and Tang, 2018).
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