Genomics and Applied Biology 2024, Vol.15, No.3, 120-131 http://bioscipublisher.com/index.php/gab 120 Feature Review Open Access The Regulation Network and Mechanism of Transcriptome in Rice Response to Cold Stress: microRNA Centered FanLuo1,3,4, Mengmeng Yin 1,3,4, Xiaoli Zhou1,3,4, JuanLi 1,2,3, QianZhu1,2,3, Cui Zhang1,3, Lijuan Chen1,2,3 , Dongsun Lee 1,2,3 1 Rice Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 2 The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 3 College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 4 Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, 615013, Sichuan, China Co-corresponding authors: chenlijuan@hotmail.com; dong_east@ynu.ac.kr Genomics and Applied Biology, 2024, Vol.15, No.3 doi: 10.5376/gab.2024.15.0014 Received: 08 Mar., 2024 Accepted: 18 Apr., 2024 Published: 05 May, 2024 Copyright © 2024 Luo et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Luo F., Yin M.M., Zhou X.L., Li J., Zhu Q., Zhang C., Chen L.J., and Lee D.S., 2024, The regulation network and mechanism of transcriptome in rice response to cold stress: microRNA centered, Genomics and Applied Biology, 15(3): 120-131 (doi: 10.5376/gab.2024.15.0014) Abstract Cold stress is a significant abiotic factor that adversely affects rice (Oryza sativa) growth and productivity. This systematic review aims to elucidate the integrated regulatory networks of microRNAs (miRNAs) and transcriptome in rice response to cold stress and their underlying mechanisms. Various studies have demonstrated that miRNAs play crucial roles in regulating gene expression under cold stress by targeting specific mRNAs for degradation or translational repression. For instance, miRNAs such as osa-miR1846a/b-5p have been implicated in chilling stress tolerance by regulating genes involved in wax synthesis. Additionally, transcription factors like OsMyb4 and OsERF096 have been shown to orchestrate complex transcriptional networks that enhance cold tolerance through various signaling pathways, including those mediated by abscisic acid (ABA), jasmonic acid (JA), and reactive oxygen species (ROS). The integration of miRNA and transcriptome sequencing has revealed that miRNAs and their target genes are involved in diverse biological processes such as protein biosynthesis, redox processes, and chloroplast development, which are crucial for cold stress response. This review synthesizes current knowledge on the miRNA-mediated regulatory networks and their interaction with the transcriptome, providing insights into the molecular mechanisms underlying rice cold stress tolerance. Keywords MicroRNAs ; Cold stress; Rice (Oryza sativa); Transcriptome; Regulatory networks 1 Introduction Cold stress is a significant abiotic factor that adversely affects rice (Oryza sativa L.) growth and productivity, particularly in tropical and subtropical regions. Exposure to low temperatures can lead to various physiological and developmental issues, including leaf discoloration, reduced tiller numbers, delayed heading, and spikelet sterility, ultimately resulting in decreased yields (Jiang et al., 2019). Cold stress can also cause tissue damage and stunted growth, further limiting rice production (Lv et al., 2010). Given the importance of rice as a staple food crop for a large portion of the global population, understanding the mechanisms underlying cold stress response is crucial for developing cold-tolerant rice varieties. MiRNAs are small non-coding RNAs that play critical roles in regulating gene expression at the post-transcriptional level. They are involved in various biological processes, including stress responses (Liu et al., 2008; Lv et al., 2010; Barrera-Figueroa et al., 2012). The identification and characterization of stress-responsive miRNAs have provided insights into how plants, including rice, adapt to environmental stresses (Barrera-Figueroa et al., 2012; Jiang et al., 2019). Integrated regulatory networks involving miRNAs and transcriptome data offer a comprehensive understanding of the molecular mechanisms underlying stress responses. These networks can reveal the interactions between miRNAs and their target genes, as well as the broader regulatory pathways involved in stress adaptation (Cohen and Leach, 2019; Liu et al., 2020; Mazurier et al., 2022). By studying these integrated networks, researchers can identify key regulatory elements and potential targets for genetic manipulation to enhance stress tolerance in rice. The main purpose of this systematic study is to identify and characterize miRNAs involved in cold response in rice: This involves profiling miRNAs that are differentially expressed under cold stress conditions and validating
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