Legume Genomics and Genetics 2025, Vol.16, No.3, 143-152 http://cropscipublisher.com/index.php/lgg 143 Research Insight Open Access Application of Single-Cell RNA-Seq in Legume Root Development Studies Hongpeng Wang, Weichang Wu Biotechnology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, China Corresponding email: weichang.wu@cuixi.org Legume Genomics and Genetics, 2025 Vol.16, No.3 doi: 10.5376/lgg.2025.16.0015 Received: 30 Apr., 2025 Accepted: 12 Jun., 2025 Published: 29 Jun., 2025 Copyright © 2025 Wang and Wu, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wang H.P., and Wu W.C., Application of single-cell RNA-Seq in legume root development studies, Legume Genomics and Genetics, 16(3): 143-152 (doi: 10.5376/lgg.2025.16.0015) Abstract The single-cell RNA sequencing method known as scRNA-seq has revolutionized the study of plant root cellular complexity and developmental processes. The research combines modern scRNA-seq methods to study legume root development by showing how these methods help identify cell types and track cell lineages and detect short-lived cell populations. The research in Arabidopsis model systems produced complete root cell maps which revealed vital elements that regulate cell development and environmental adaptation thus enabling legume research. ScRNA-seq analysis of legumes has enabled researchers to study gene expression patterns in different cell types during root and nodule development which has enhanced our understanding of symbiotic processes and plant stress mechanisms. Single-cell plant research encounters technical barriers because of protoplasting artifacts and cell capture biases but scientists continue to develop their research through the combination of single-nucleus RNA-seq and spatial transcriptomics. The research investigates the necessity of root cell atlases that span multiple species within legumes while exploring the combination of scRNA-seq with other omics methods and their potential to develop new crop improvement approaches based on single-cell research findings. ScRNA-seq technology has the potential to revolutionize our knowledge of legume root biology which will drive major breakthroughs in plant developmental research and sustainable agricultural methods. Keywords Single-cell RNA sequencing; Legume root development; Cell type identification; Transcriptome atlas; Nitrogen fixation 1 Introduction The agricultural sector depends on legume crops including soybean and Lotus japonicus because they provide food security and improve soil fertility and support sustainable farming practices. The plants serve as a primary source for food and feed production across the world while their partnership with rhizobia allows them to transform atmospheric nitrogen into soil nutrients which reduces the need for synthetic fertilizers (D’Agostino et al., 2023). The root development of legumes serves as a vital process because their root system with nodules enables successful nutrient absorption and symbiotic relationship preservation (Sun et al., 2022). The study of root development mechanisms at cellular and molecular levels enables researchers to develop improved crops and sustainable agricultural methods. The field of plant biology has experienced a major transformation through recent transcriptomics breakthroughs because single-cell RNA sequencing (scRNA-seq) has become a revolutionary tool. The single-cell RNA sequencing method scRNA-seq provides researchers with the ability to study gene expression at the individual cell level for identifying unique cell populations and their developmental paths and environmental response patterns (Denyer et al., 2019; Ryu et al., 2019; Shulse et al., 2019; Serrano-Ron et al., 2021). The combination of scRNA-seq and sNucRNA-seq techniques has started to analyze root tissue complexity in legumes which has exposed the regulatory mechanisms that control phytohormone responses and nodulation and plant-microbe interactions (Sun et al., 2022). The new methods for extracting high-quality nuclei from difficult-to-process tissues such as root nodules became possible through technological advancements which enabled single-cell research in legumes (D’Agostino et al. 2023). The objective of this study is to synthesize current knowledge on the application of scRNA-seq in legume root development studies. The research investigates novel analytical techniques and biological discoveries through the connection between single-cell data and complete transcriptomic and gene regulatory network analyses. The
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