Molecular Plant Breeding 2025, Vol.16, No.2, 105-118 http://genbreedpublisher.com/index.php/mpb 110 TFs have been shown to regulate defense responses to various stresses, including drought, by forming complex co-regulatory networks with other genes. For instance, the expression of OsMYB2 is significantly upregulated under drought conditions, and this upregulation promotes the expression of multiple genes related to drought tolerance. Reducing the expression level of OsMYB2 using RNAi technology significantly decreased the drought tolerance of rice plants, demonstrating the key role of OsMYB2 in drought response (Yoo et al., 2017). 5.2 Signaling pathways involved in water deficit response Several signaling pathways are activated in response to water deficit in rice. One notable pathway involves the OsPhyB-mediated regulatory mechanism, which controls drought tolerance in rice roots. This pathway was identified through RNA-Seq analysis, revealing that OsPhyB represses the activity of ascorbate peroxidase and catalase, which are crucial for ROS processing and drought tolerance (Yoo et al., 2017). Another significant pathway involves the oxidative-mediated network, which configures early responses to stress. This network includes bZIP, ERF, and MYB TFs that respond to oxidative signals, playing a critical role in the early stages of stress response (Basu and Roychoudhury, 2021). In the complex regulatory network of rice’s response to drought, in addition to the aforementioned signaling pathways, there is also a pathway involving ABA signaling. ABA is a plant hormone that plays a central role in plants’ response to water stress. Studies have shown that ABA, by activating specific receptor proteins, initiates downstream signaling cascades to regulate the expression of a series of genes involved in processes such as water retention, stomatal closure, and root growth. For example, ABA response element-binding proteins (AREB) and positive regulatory factors (ABF) TFs play a key role in the ABA signaling pathway, activating the expression of multiple drought-related genes(Manuel et al., 2023). Additionally, calcium signaling pathways also play an important role in rice’s response to drought. Under drought conditions, changes in intracellular calcium ion concentrations can act as second messengers to activate calcium-dependent protein kinases (CDPKs) and calmodulins (CaMs). These calcium signaling molecules further regulate downstream TFs and effector proteins, thus affecting the plant’s physiological responses. For instance, OsCPK17 and OsCaM1-1 have been shown to play a positive role in rice drought resistance (Asano et al., 2012). Besides the aforementioned signaling pathways, plant hormones gibberellin (GA) and IAA also play a role in regulating rice's response to drought. Under drought conditions, the synthesis and metabolism of GA are inhibited, leading to slowed plant growth and reduced water consumption. Meanwhile, the redistribution of IAA and changes in its signaling pathways help regulate root growth and development to adapt to the water-stressed environment (Song et al., 2024). The integration of these signaling pathways helps regulate rice growth and maintain vitality under water-deficient conditions. 5.3 Integration of omics data to construct regulatory networks The construction of regulatory networks in response to water deficit in rice has been significantly advanced by the integration of various omics data. For example, the integration of transcriptome data, nucleosome-free chromatin patterns, and cis-regulatory elements has been used to infer EGRINs, which include regulatory interactions between thousands of target genes and hundreds of TFs (Wilkins et al., 2016). Additionally, the use of high-throughput expression profiling data has facilitated the construction of co-expression networks, revealing the regulatory hierarchies of MYB TFs under stress conditions. The integration of omics data, such as RNA-seq and promoter-GUS reporter systems, has also been employed to validate the expression patterns of candidate genes and monitor stress responses, further enhancing our understanding of the regulatory networks involved in drought tolerance (Chen et al., 2021). 6 Case Studies of Key Genes and Pathways 6.1 Functional analysis of key drought-responsive genes In the context of rice under water deficit conditions, several key drought-responsive genes have been identified and functionally analyzed. For instance, the study by identified 5447 putative target genes for 445 TFs involved in the response to water deficit (Volante et al., 2017). These genes are regulated through EGRINs, which coordinate gene expression in response to environmental signals (Figure 2).
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