Molecular Plant Breeding 2025, Vol.16, No.2, 105-118 http://genbreedpublisher.com/index.php/mpb 105 Feature Review Open Access Transcriptional Regulation and Gene Networks in Rice under Water Deficit Conditions Xiaoli Zhou1,3,4, Chunli Wang1,3, JiangQin 1, Xianyu Wang 1, QianZhu1,2,3, JuanLi 1,2,3, Dongsun Lee 1,2,3, Lijuan Chen1,2,3 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 State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 4 Xichang University, Xichang, 615013, Sichuan, China Corresponding email: chenlijuan@hotmail.com Molecular Plant Breeding, 2025, Vol.16, No.2 doi: 10.5376/mpb.2025.16.0011 Received: 10 Feb., 2025 Accepted: 13 Mar., 2025 Published: 21 Mar., 2025 Copyright © 2025 Zhou 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: Zhou X.L., Wang C.L., Qin J., Wang X.Y., Zhu Q., Li J., Lee D.S., and Chen L.J., 2025, Transcriptional regulation and gene networks in rice under water deficit conditions, Molecular Plant Breeding, 16(2): 105-118 (doi: 10.5376/mpb.2025.16.0011) Abstract Water scarcity is a major limiting factor in agriculture, significantly affecting crop productivity and food security. As a major food crop, rice is particularly sensitive to water stress, so it is of great significance to understand its transcriptional regulation and gene network under such conditions. This review aims to systemic synthesis the transcriptional response and gene network of rice under water deficit conditions to reveal its drought resistance mechanism. We summerized the studies on functional analysis of key drought resistance genes and validation of candidate genes using CRISPR-Cas9 technology. Additionally, the roles of abscisic acid (ABA) and other hormones in gene regulation has also been explored. Despite the inherent challenges of omics data analysis, advances in genomics and transcriptomics technology support recent research. The findings have significant practical implications for cultivating drought-resistant rice, and provide potential biotechnological applications. Future research should focus on emerging technologies and innovative strategies to further improve the resilience of crops to water scarcity. Keywords Rice; Water deficit; Transcriptional regulation; Gene networks; Drought tolerance 1 Introduction In the context of increasingly severe global climate change, water deficit has become one of the significant abiotic factors hindering the sustainable development of agriculture. Water deficit, commonly referred to as drought stress, affects various physiological and biochemical processes in plants, leading to reduced growth, development, and yield. Rice, one of the world’s most important food crops , is severely affected by water deficit, resulting in a significant decline in grain yield and quality, posing a threat to food security (Hadiarto and Tran, 2011; Gaballah et al., 2020; Sakran et al., 2022). Therefore, developing drought-tolerant rice varieties is crucial for maintaining rice production under water-limited conditions and ensuring global food security (Gaballah et al., 2020; Sakran et al., 2022). Rice, with its remarkable high-yield potential and excellent grain quality, is widely favored by farmers and consumers, becoming an indispensable precious crop in the agricultural field. However, its high sensitivity to water deficit requires us to delve deeply into its genetic and physiological responses under drought stress to better address the challenges posed by drought. Research on the transcriptional regulation and gene networks of rice under water deficit can provide a deeper understanding of drought resistance mechanisms and offer strong theoretical support for cultivating rice varieties with enhanced drought resistance (Wang et al., 2011; Chen et al., 2021). For instance, some studies have revealed key genes and regulatory pathways in rice under drought conditions, providing new insights for rice drought resistance breeding (Silva et al., 2022). In addition, researchers have comprehensively analyzed the molecular responses of rice to drought using genomics, transcriptomics, and metabolomics technologies. By comparing the gene expression differences between drought-resistant and sensitive rice varieties under drought stress, a series of genes related to drought resistance have been identified. For example, some studies have focused on key genes in the ABA signaling pathway, as ABA plays a crucial role in plant responses to drought stress (Xu et al., 2019).
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