Molecular Soil Biology 2025, Vol.16, No.6, 287-296 http://bioscipublisher.com/index.php/msb 289 3 Core Root Development Genes and Functional Modules 3.1 Key genes regulating root meristem maintenance and cell differentiation Several transcription factors involved in cell division and cell fate are mainly found in the root apical meristem, particularly around the quiescent center (QC). Typical examples include OsGATA6, OsGRF6, as well as genes from other transcription factor families. These genes do not stay highly expressed throughout the whole root. Instead, their expression becomes weaker as cells move away from the meristematic region and enter the elongation zone, following the developmental progression of the root. At the hormone level, ORR3, a cytokinin response regulator, is strongly expressed in young root meristems. When ORR3 is artificially overexpressed, obvious changes in root growth can be observed. The primary root becomes shorter, and the same trend is seen in adventitious roots. Meanwhile, the meristematic zone is clearly reduced in size. These observations indicate that ORR3 limits meristem activity rather than promoting it. This effect appears to be linked to cytokinin signaling and may further influence auxin synthesis, auxin transport, and processes related to cell wall metabolism (Wei et al., 2025). The RING-H2 finger protein MAL (MERISTEM ACTIVITYLESS) shows a more localized expression pattern and is mainly detected in the crown root meristem. When MAL expression is suppressed using RNAi, crown root development is strongly affected. Both root number and root length are reduced. In addition, cell division in the meristematic zone slows down. At the molecular level, changes are also observed in genes associated with cell wall metabolism and redox regulation, suggesting that MAL is required for maintaining normal meristem function (Jiang et al., 2020). 3.2 Transcription factor networks involved in rice root development The NAC transcription factor OsNAC2 is an important upstream integrator, mainly expressed in the primary root tip, crown roots, and lateral root primordia. Its overexpression inhibits primary root elongation and crown root formation, while RNAi or CRISPR knockout significantly increases primary root length and the number of crown roots. OsNAC2 can directly bind to the promoters of IAA inactivation-related genes GH3.6/GH3.8, IAA signaling gene OsARF25, and cytokinin oxidase OsCKX4, integrating auxin and cytokinin pathways, and upstream regulating CROWN ROOTLESS (CRL) and CDK-like genes (Mao et al., 2019). The LBD/ASL family member CRL1/ARL1 and its network are core modules of crown root development. Downstream genomic analysis shows that the gene regulatory network controlled by CRL1 includes a large number of auxin signaling elements, root primordia initiation factors, and genes for root meristem specification and maintenance, such as QUIESCENT-CENTER-SPECIFIC HOMEOBOX, etc. (Lavarenne et al., 2019). The WOX-LBD module refines the spatiotemporal control of crown root development. WOX11 is recruited to the LBD16 promoter region by forming a complex with the histone demethylase JMJ706, removing H3K9me2 and activating LBD16 transcription, thus promoting crown root development; while the LBD16 protein interacts with WOX11, feedback interfering with the formation of the WOX11-JMJ706 complex (Geng et al., 2024). Besides NAC, LBD, and WOX, the TOPLESS-related corepressor OsTPR1 regulates auxin distribution and sensitivity by regulating the expression of PIN family efflux carriers (OsPIN1a/b/c, OsPIN2, OsPIN5a), with its overexpression reducing and RNAi increasing lateral root density (Hou et al., 2025). 3.3 Natural genetic variation and functional diversity of root development genes Researchers used GWAS, TWAS, and eGWAS to study root traits in rice. In total, 12 root traits were analyzed using 57 rice accessions. The analysis identified several genes that are likely important for root development. One of these genes is OsENT1. This gene encodes a nucleoside transporter. The results show that OsENT1 is negatively related to several crown root and lateral root traits. In simple terms, higher OsENT1 activity is linked to weaker root development. Another gene, OsEXPA31, is an α-expansin gene. It shows a close relationship with crown root diameter. Root diameter is also affected by OsSPL14. In addition, OsDEP1 is linked to nitrogen use efficiency and drought tolerance, which are important traits under stress conditions (Wei et al., 2023). When individual genes were examined, OsRLR4 showed clear differences between wild rice and cultivated rice. This gene displays strong selection signals during domestication. Different OsRLR4 alleles have a direct impact on primary root growth. They also affect how auxin is distributed at the root tip. These findings suggest that OsRLR4 played an important role in helping rice adapt during domestication (Wang et al., 2025). Further GWAS analysis
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