Computational Molecular Biology 2025, Vol.15, No.5, 227-234 http://bioscipublisher.com/index.php/cmb 227 Research Insight Open Access Genome-Wide Identification of Drought-Responsive miRNAs in Maize Using Deep Sequencing and Network Analysis Jin Zhou, Minli Xu Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding author: minli.xu@hitar.org Computational Molecular Biology, 2025, Vol.15, No.5 doi: 10.5376/cmb.2025.15.0022 Received: 11 Jul., 2025 Accepted: 22 Aug., 2025 Published: 13 Sep., 2025 Copyright © 2025 Zhou and Xu, 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.6 Preferred citation for this article: Zhou J., and Xu M.L., 2025, Genome-wide identification of drought-responsive miRNAs in maize using deep sequencing and network analysis, Computational Molecular Biology, 15(5): 227-234 (doi: 10.5376/cmb.2025.15.0022) Abstract Drought stress is one of the main abiotic factors restricting corn production worldwide. microRNA (miRNA), as a key post-transcriptional regulatory factor, plays a significant role in the process of plants responding to adverse stress. This study utilized deep sequencing technology and network analysis methods to systematically identify miRNAs in corn that respond to drought stress, analyze their regulatory network mechanisms, and construct miRNA expression profiles of corn seedlings under drought treatment and normal irrigation conditions through high-throughput small RNA sequencing technology. A total of 312 known mirnas and 74 newly predicted mirnas were identified, among which 51 were significantly differentially expressed under drought stress. Further, the target genes were predicted through bioinformatics methods, and GO annotation and KEGG pathway enrichment analysis were conducted. The results showed that these mirnas were mainly involved in biological processes such as plant hormone signal transduction (such as the ABA pathway), oxidative stress response, and transcriptional regulation. This study comprehensively depicted the miRNA map of corn in response to drought stress and established a mirNA-mediated gene regulatory network framework, providing a theoretical basis for in-depth understanding of the molecular mechanism of corn drought resistance and potential target resources for molecular design breeding. KeywordsCorn (Zeamays); Drought stress; microRNA (miRNA); Deep sequencing; Gene regulatory network 1 Introduction Corn (Zea mays L.), this seemingly ordinary crop, actually occupies an irreplaceable position in the global food and feed system. Whether it is for human consumption, livestock consumption, or raw materials used in industry, it deserves a place on the list. But there are also many problems, especially in today's increasingly unstable climate. Abiotic stresses like drought, which are often discussed, are almost the "invisible killers" in all corn-growing areas and have a very direct impact on plant growth and final yield (Tang et al., 2022). Worse still, with global warming, the frequency and intensity of droughts are both on the rise (Liu et al., 2019), which forces people to start thinking about a more realistic problem: How to cultivate drought-resistant corn varieties? In recent years, molecular biology has developed rapidly, and research on drought resistance mechanisms has become increasingly in-depth. miRNA (microRNA), a small non-coding RNA, is not the most prominent role, but it plays a considerable behind-the-scenes role in regulating plants' responses to stress (Singroha et al., 2021). In corn bodies, they regulate a series of processes including abscisic acid signaling, reactive oxygen species scavenging, root development, etc. (Aravind et al., 2017; Jiao et al., 2022), playing a "bridging" role in enhancing drought resistance. With the aid of high-throughput sequencing and bioinformatics analysis, researchers have screened out many mirnas and their target genes related to drought, and have also sketched out a preliminary regulatory network map (Zhakypbek et al., 2025). But to be honest, these pictures are far from complete. There are still many aspects that remain unclear up to now, such as the specific responses of different tissues or the differential regulation among genotypes. This study utilized deep sequencing and network analysis techniques to conduct a comprehensive genome-wide identification of mirnas responding to drought in maize. It reviewed the current research progress on drought stress and miRNA functions in maize and provided a detailed introduction to the experimental design and analysis methods. By integrating transcriptome and small RNA sequencing data, this study aims to clarify the regulatory networks involved in drought adaptation and the key miRNA-mRNA modules. The research results are expected
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