Legume Genomics and Genetics 2025, Vol.16, No.3, 143-152 http://cropscipublisher.com/index.php/lgg 150 analysis of thousands of individual cells through scRNA-seq has enabled researchers to study how different cell types react to environmental signals and identify essential factors that control root development and cell differentiation and symbiotic processes. The application of scRNA-seq technology produces results which extend past legume research to create a new approach for studying plant development. The development of methods to detect cell states and transitions in complex tissues has enabled scientists to study plant stem cell maintenance and regeneration and environmental stress adaptation. Scientists employ integrated single-cell analysis techniques that combine spatial transcriptomics with epigenomics to examine plant development by analyzing both spatial and temporal patterns. ScRNA-seq technology shows promising applications for enhancing agricultural practices in legume crops. The technology enables researchers to discover cell-type-specific gene expression patterns and regulatory networks which leads to new targets for breeding and genetic engineering to boost nutrient uptake and stress resistance and symbiotic performance. Single-cell methods and technical solution advancements will establish scRNA-seq as a core analytical method for studying legume biology and crop research which will propel sustainable agricultural development. ScRNA-seq has revolutionized legume root development research through its discoveries which now benefit both plant science and agricultural practices. Future research on legume crops will gain from continuous method development and combined research approaches which will open up fresh opportunities for their advancement. Acknowledgments We would like to sincerely thank the reviewers and editors for their valuable comments and constructive suggestions. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References AlJanahi A., Danielsen M., and Dunbar C., 2018, An introduction to the analysis of single-cell RNA-sequencing data, Molecular Therapy, Methods & Clinical Development, 10: 189-196. https://doi.org/10.1016/j.omtm.2018.07.003 Andrews T., Kiselev V., McCarthy D., and Hemberg M., 2020, Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data, Nature Protocols, 16: 1-9. https://doi.org/10.1038/s41596-020-00409-w Bacher R., and Kendziorski C., 2016, Design and computational analysis of single-cell RNA-sequencing experiments, Genome Biology, 17: 63. https://doi.org/10.1186/s13059-016-0927-y Baran-Gale J., Chandra T., and Kirschner K., 2017, Experimental design for single-cell RNA sequencing, Briefings in Functional Genomics, 17: 233-239. https://doi.org/10.1093/bfgp/elx035 Bawa G., Liu Z., Yu X., Qin A., and Sun X., 2022, Single-Cell RNA sequencing for plant research: insights and possible benefits, International Journal of Molecular Sciences, 23(9): 4497. https://doi.org/10.3390/ijms23094497 Bensmihen S., 2015, Hormonal control of lateral root and nodule development in legumes, Plants, 4(3): 523-547. https://doi.org/10.3390/plants4030523 Boualem A., Laporte P., Jovanovic M., Laffont C., Plet J., Combier J., Niebel A., Crespi M., and Frugier F., 2008, MicroRNA166 controls root and nodule development in Medicago truncatula, The Plant Journal, 54(5): 876-887. https://doi.org/10.1111/j.1365-313X.2008.03448.x Cervantes-Pérez S., Thibivilliers S., Laffont C., Farmer A., Frugier F., and Libault M., 2022, Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume, Molecular Plant, 15(12): 1868-1888. https://doi.org/10.1016/j.molp.2022.10.021 Chen Z., Wang L., Cardoso J., Zhu S., Liu G., Rao I., and Lin Y., 2023, Improving phosphorus acquisition efficiency through modification of root growth responses to phosphate starvation in legumes, Frontiers in Plant Science, 14: 1094157. https://doi.org/10.3389/fpls.2023.1094157 Coll N., Moreno-Risueno M., Strader L., Goodnight A., and Sozzani R., 2024, Advancing our understanding of root development: technologies and insights from diverse studies, Plant Physiology, 197(2): kiae605. https://doi.org/10.1093/plphys/kiae605
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