Legume Genomics and Genetics 2025, Vol.16, No.3, 143-152 http://cropscipublisher.com/index.php/lgg 146 3.3 Symbiotic nodulation and integration with root development The symbiotic nodulation process in legumes happens through root nodule development which serves as a habitat for nitrogen-fixing rhizobia. The process of nodule formation starts when Nod factors from rhizobia initiate cell division in cortical tissue and organ formation which work alongside root development mechanisms (Luo et al., 2023; Ferguson et al., 2010; Suzaki, 2023). The development of nodules in legumes followed lateral root developmental pathways through common genetic elements and signaling mechanisms which included NIN and hormonal interactions (Soyano et al., 2019). The system regulates nodule development through autoregulation of nodulation (AON) and small peptide and microRNA feedback systems to determine proper nodule numbers and resource distribution (Djordjevic et al., 2015; Gautrat et al., 2020). 3.4 Comparative aspects with non-legume model plants While the basic organization of root developmental zones is conserved between legumes and non-legumes like Arabidopsis thaliana, legumes possess unique features. The SHR–SCR module in legumes enables cortical cytokinin response to initiate cell division in cortical cells which results in nodule organ formation that Arabidopsis lacks (Gauthier-Coles et al., 2019; Dong et al., 2020). The process of root and nodule development follows different hormonal control patterns because legumes developed unique signaling pathways to link symbiotic and environmental signals (Bensmihen, 2015; Gauthier-Coles et al., 2019; Lin et al., 2021). The distinct characteristics between these two species reveal the evolutionary changes which led to their unique root development. 4 Application of scRNA-Seq in legume root development studies 4.1 The research establishes multiple cell types which develop through distinct pathways within Legume root systems The single-cell RNA sequencing technique enables scientists to develop complete root cell atlases which help them identify every root cell type and developmental phase in legume roots. Scientists use scRNA-seq to analyze thousands of individual cells which helps them construct developmental pathways and predict cell fate transitions from stem cells to differentiated root tissues (Ryu et al., 2019; Serrano-Ron et al., 2021; Coll et al., 2024). The analysis of pseudotime enables researchers to track cell progression from meristematic zones through elongation and differentiation stages (Denyer et al., 2019; Bawa et al., 2022). 4.2 Gene expression heterogeneity and discovery of rare cell populations The scRNA-seq technique provides exceptional capabilities to detect gene expression diversity in root tissues which leads to the discovery of infrequent cell types that were unknown before. Standard bulk analysis methods lack the ability to detect two cell populations which the technology has identified as quiescent center cells and specialized epidermal cells (Ryu et al., 2019; Shaw et al., 2020). Scientists can understand root functions and developmental flexibility through the identification of these rare cell types (Shaw et al., 2020; Liao and Wang, 2023). 4.3 Insights into root meristem activity and cell cycle regulation The research delivers information about root meristem cell operations and their cell cycle management systems. High-throughput scRNA-seq has revealed root meristem molecular operations by identifying the factors which control cell cycle progression and stem cell maintenance. The analysis of cell cycle continuums and differentiation trajectories through scRNA-seq has revealed how meristematic activity relates to root growth and regeneration (Ryu et al., 2019; Liao and Wang, 2023). Scientists can use this method to observe the cell reprogramming process and root cell commitment during regeneration. 4.4 Mapping root cell-specific responses to environmental signals scRNA-seq allows for the mapping of cell-type-specific responses to environmental cues such as nutrient deficiency and abiotic stress. The analysis of gene expression at a single-cell level by scientists reveals particular root cell type reactions to environmental changes which helps them understand stress adaptation mechanisms and signaling pathways (Shaw et al., 2020; Bawa et al., 2022). The research provides essential information about how legumes change their behavior when soil nutrient availability and environmental conditions change.
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