Rice Genomics and Genetics 2025, Vol.16, No.3, 150-158 http://cropscipublisher.com/index.php/rgg 151 2 Genetic Factors Influencing RSA in Rice 2.1 Major RSA-related Genes Key genes such as Deeper Rooting 1 (DRO1) and Lateral Organ Boundaries Domain (LBD) genes play significant roles in root elongation and lateral root development. DRO1 is particularly notable for its influence on root depth, which is crucial for water and nutrient acquisition in rice (Panda et al., 2021; Zhao et al., 2022). LBD genes are involved in the formation of lateral roots, contributing to the overall root system architecture (RSA) by enhancing root branching and increasing the root surface area for better resource uptake (Abdirad et al., 2022). Root hair density and length are critical for nutrient absorption and soil interaction. Genes such as Xyloglucan Endotransglucosylase/Hydrolase (XTH) family members, specifically XTH19 and XTH23, have been identified to regulate lateral root development and root hair formation under stress conditions like salinity (Xu et al., 2020; Daryani et al., 2021). These genes are induced by environmental stressors and play a role in modifying root hair characteristics to adapt to changing soil conditions. Phytohormones such as auxins, cytokinins, and gibberellins are central to the regulation of RSA. Auxins are crucial for root initiation and elongation, influencing genes like AUX/IAA and PIN1b, which are involved in auxin transport and signaling (Abdirad et al., 2022; Zhao et al., 2022). Cytokinins regulate root growth by balancing cell division and differentiation, while gibberellins are involved in root elongation and lateral root formation. The interplay between these hormones creates a complex network that modulates root architecture in response to both intrinsic genetic factors and external environmental cues (Jung and McCouch, 2013; Sharma et al., 2021; Han, 2024). 2.2 Quantitative trait loci (QTLs) associated with RSA Quantitative trait loci (QTL) mapping has been instrumental in identifying regions of the genome associated with RSA traits. Studies have mapped numerous QTLs related to root traits across different rice varieties, revealing significant genetic variation that can be exploited for breeding purposes (Xiong et al., 2021). For instance, QTLs like qSOR1 and PSTOL1 have been identified for their roles in surface rooting and early root growth, respectively, under various environmental conditions (Dorlodot et al., 2007; Panda et al., 2021). Genome-wide association studies (GWAS) have provided deeper insights into the genetic basis of RSA by associating specific genetic markers with root traits across diverse rice populations. These studies have identified several candidate genes and QTLs that are conserved across different species, including rice, maize, and sorghum, highlighting the potential for cross-species genetic improvement (Wedger et al., 2019; Tripathi et al., 2020; Karnatam et al., 2023). GWAS has also facilitated the discovery of novel genes involved in root development, such as those related to drought adaptation and stress responses (Figure 1) (Abdirad et al., 2022). 2.3 Advances in molecular breeding for rsa improvement Gene editing technologies like CRISPR-Cas9 have revolutionized the field of molecular breeding by enabling precise modifications of RSA-related genes. This technology has been used to edit genes such as DRO1 and other key regulators of root development, allowing for the creation of rice varieties with optimized root systems for better resource use efficiency and stress tolerance (Panda et al., 2021; Zhao et al., 2022). Marker-assisted selection (MAS) leverages genetic markers linked to desirable RSA traits to accelerate the breeding process. By using markers associated with QTLs for root traits, breeders can select for rice varieties with improved root architecture more efficiently. This approach has been successfully applied to incorporate traits like deep rooting and enhanced lateral root formation into new rice cultivars, thereby improving their adaptability to various environmental conditions (Dorlodot et al., 2007; Jung and McCouch, 2013; Zhang et al., 2021). 3 Environmental Factors Shaping RSA in Rice 3.1 Soil properties Soil texture and compaction significantly influence the root system architecture (RSA) of rice. Different soil textures can alter the depth and spread of roots, impacting the plant's ability to access water and nutrients. For
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