Molecular Soil Biology 2025, Vol.16, No.6, 287-296 http://bioscipublisher.com/index.php/msb 288 development genes and their excellent allelic variations, and discusses how to minimize the risk of yield loss during the improvement of stress resistance, providing research ideas for rice to achieve stable yield and efficient resource utilization through root system improvement. 2 Molecular Architecture of Rice Root Development 2.1 Developmental origin and structural components of the rice root system The primary/embryonic root originates from the hypocotyl and is the first root to grow in the seedling. After rice emerges from the soil, the primary root only grows for a few days before its growth slows down and its function gradually weakens. The main function of the root system will be replaced by adventitious roots. These adventitious roots mostly grow from the stem nodes and the hypocotyl, and are also called crown roots. They are responsible for absorbing water and nutrients, and also play a role in stabilizing the plant. On the primary root and the crown roots, lateral roots will continue to grow. The number of lateral roots is large, which can significantly increase the number and surface area of the roots (Meng et al., 2019). Root hairs are formed by the differentiation of epidermal cells in the mature zone. Root hairs can expand the contact area between the root and the soil, and are very important for absorbing nutrients such as phosphorus that are not easily mobile. Looking from the root tip upwards, the rice root can be divided into the root cap, meristematic zone, elongation zone and mature zone. Different regions correspond to processes such as cell division, cell elongation and cell differentiation. In the transverse structure, the rice root includes structures such as the cortex, vascular cylinder and conducting tissue. These structures facilitate the adaptation of the rice root to soil environments with strong reductivity, hypoxia or high salt content (Jiang et al., 2025). 2.2 Genetic control of root initiation, elongation, and branching Rice crown root initiation is mainly regulated by genes such as ARL1/CRL1 and CRL5, which are mostly auxin-responsive LBD or AP2/ERF transcription factors, mediating the transformation of axillary meristems into root primordia. Lateral root initiation and development depend on auxin signaling components such as AUX/IAA, ARF, and LBD, and their downstream cell cycle genes. GWAS and QTL analyses have revealed multiple genes and loci related to maximum root length and root number (Zhang et al., 2020). Root elongation is regulated by the activity of the root apical meristem and cell elongation. The OsRLR4–OsAUX1 module negatively controls primary root length by regulating auxin accumulation in the root tip and OsAUX1 transporter expression (Sun et al., 2021); overexpression of OsARD4 promotes rapid elongation of the radicle, early crown root/lateral root development, and higher root biomass (Ramanathan et al., 2018). Deep rooting and root angle are controlled by the IGT family gene DRO1 and its homologs. DRO1 and others not only affect root growth angle and depth but are also closely related to yield performance under drought and saline conditions (Kitomi et al., 2020). 2.3 Spatial and temporal expression patterns of root development genes in soil-grown rice Deep-rooting rice varieties, such as Azucena, usually show higher gene activity in the Z1 root zone. Most of these genes are related to root growth. They also affect how the root system is formed. Shallow-rooting varieties, like IR64, show a different situation. In these varieties, more genes linked to oxidative stress are turned on. This suggests that shallow roots respond more to stress in the environment (Abdirad et al., 2022). When researchers put together gene expression data from several platforms, they found hundreds of genes that mainly work in roots. Many of these genes are important for root development. They also help rice plants handle different kinds of soil stress. What is interesting is that these genes stay quite stable. This is true even when rice varieties or growing conditions change (Moon et al., 2018). As roots start to form, different root types do not follow the same rules. Radicles, crown roots, and lateral roots each show their own gene expression patterns. Their CHH methylation patterns are also not the same at the early stages. This shows that root formation is under tight methylation control. Factors such as DNG702 and DRM2 play a key role in this process. They help decide where important regulatory genes are switched on (Zhang et al., 2021). In real field soil, root growth is influenced by many outside factors. Water supply, salt levels, and soil hardness all matter. These signals affect crown root development through the ethylene–OsEIL1–OsWOX11 pathway. Through this pathway, rice plants can quickly change how many crown roots they produce and where these roots grow. This response is especially useful when the soil is compacted (Li et al., 2024).
RkJQdWJsaXNoZXIy MjQ4ODYzNA==