Molecular Soil Biology 2025, Vol.16, No.6, 287-296 http://bioscipublisher.com/index.php/msb 287 Research insight Open Access Root Development Genes in Rice: Regulation of Root-Soil Interactions for Stress Tolerance and Yield Improvement Ruchun Chen, Dapeng Zhang Hier Rice Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: dapeng.zhang@hitar.org Molecular Soil Biology, 2025, Vol.16, No.6 doi: 10.5376/msb.2025.16.0026 Received: 21 Sep., 2025 Accepted: 26 Oct., 2025 Published: 09 Nov., 2025 Copyright © 2025 Chen and Zhang, 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: Chen R.C., and Zhang D.P., 2025, Root development genes in rice: regulation of root-soil interactions for stress tolerance and yield improvement, Molecular Soil Biology, 16(6): 287-296 (doi: 10.5376/msb.2025.16.0026) Abstract The structure and growth of the root system of rice directly affect its ability to absorb water and nutrients. In adverse environments such as drought and high salt content, the role of the root system becomes particularly significant. This study mainly collated the key genes and regulatory relationships related to the formation of the crown roots, lateral roots, changes in root length, root angles, and root hair development. By combining transcriptome, epigenetic, and population genetics research results, it analyzed the response characteristics of these root development-related genes under drought and salt stress conditions, and discussed how to utilize important root development genes and their excellent allelic variations to provide references for the improvement of rice root traits, genetic breeding, and the enhancement of resource utilization efficiency. Keywords Rice (Oryza sativa); Root development; Root-soil interaction; Stress tolerance; Yield formation 1 Introduction The root system of rice is a typical fibrous root system. It mainly consists of the radicle, the adventitious roots growing from the stem nodes, and a large number of lateral roots and root hairs. In mature plants, the adventitious roots constitute the main structure of the entire root system. The number of lateral roots and root hairs is large, which can significantly increase the contact area between the roots and the soil (Seo et al., 2020). The distribution depth, branching number, and thickness of the roots in the soil jointly determine the root system structure. If the root system is distributed deeper and has more branches, it is more likely to continuously absorb water and nitrogen from the deep soil. Hormone signaling-related genes (auxin, cytokinin, ethylene, abscisic acid, jasmonic acid, strigolactone, etc.) and their downstream transcription factors, such as RRS1-OsIAA3, OsNAC41-RoLe1-OsAGAP, OsEIL1-OsWOX11, and JAUP1, shape deeper, thicker, or more highly branched root systems by finely regulating the initiation and elongation of crown roots and lateral roots (Gao et al., 2023; Li et al., 2024). Genes related to reactive oxygen species (ROS) homeostasis, cell wall modification, and root barrier structure, such as WOX11-OsPRX130, OsDIR55, and OsHyPRP06/OsR3L1, directly affect drought and salt tolerance and ion balance by regulating the ROS gradient at the root tip, Casparian strip, and lignification barrier development, thereby altering the flux and selectivity of water and ions at the root-soil interface (Zhao et al., 2021). The regulatory modules such as DRO1, RRS1, OsNAC41-RoLe1-OsAGAP, and WOX11-OsPRX130 can alter the growth angle of roots, the length of roots, and the development of the root crown. After the root structure changes, the water absorption capacity will increase (Han et al., 2024). Under salt stress conditions, root growth is usually significantly inhibited. Salt causes osmotic stress; the accumulation of Na+ and Cl- can have toxic effects on the roots. The root tip and different types of roots are often the first sites to sense changes in salt concentration and respond. This study summarizes the structural characteristics and functional roles of the rice root system at the plant-soil interface, and summarizes the key developmental genes and regulatory modules related to root crown formation, lateral root formation, root length, root growth angle, and root zone structure. It assesses the use of important root
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