Legume Genomics and Genetics 2025, Vol.16, No.2, 81-90 http://cropscipublisher.com/index.php/lgg 81 Feature Review Open Access Identification of Key Signaling Genes in Soybean-Rhizobium Interaction Bing Wang, Xiuhua Liu, Hongwei Liu Tropical Microbial Resources Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: hongwei.liu@cuixi.org Legume Genomics and Genetics, 2025 Vol.16, No.2 doi: 10.5376/lgg.2025.16.0009 Received: 10 Feb., 2025 Accepted: 26 Mar., 2025 Published: 15 Apr., 2025 Copyright © 2025 Wang et al., 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 B., Liu X.H., and Liu H.W., 2025, Identification of key signaling genes in soybean-rhizobium interaction, Legume Genomics and Genetics, 16(2): 81-90 (doi: 10.5376/lgg.2025.16.0009) Abstract The soybean-rhizobium symbiosis plays a crucial role in sustainable agriculture, promoting biological nitrogen fixation and reducing dependence on synthetic fertilizers. This study focuses on the molecular mechanisms underlying this symbiotic relationship, with particular emphasis on the identification and characterization of key signaling genes involved in nodulation. We explore the role of nodulation factors and their perception by LysM receptor-like kinases (e.g., GmNFR1 and GmNFR5) and downstream signaling components, including calcium/calmodulin-dependent kinases and transcription factors, such as NIN and ERN1. We further discuss the functional characteristics of these genes, drawing on evidence from gene knockout, overexpression, RNAi, and CRISPR-Cas-based studies. We also highlight the integration of transcriptomics and proteomics approaches in identifying new candidate genes. Furthermore, this study explores the interplay between symbiotic signaling and other regulatory pathways, including plant hormone signaling, defense responses, and environmental cues. Using GmNARK, a key regulator of nodulation autoregulation, as an example, we delve into its negative feedback mechanism and its impact on enhancing nodulation efficiency. Finally, the biotechnological applications of these signaling genes in breeding strategies aimed at enhancing nitrogen fixation and increasing soybean yield are discussed. This study aims to comprehensively understand the signaling networks in the soybean-rhizobium symbiosis system and outline future directions for sustainable improvement of legumes using advanced genomics and synthetic biology tools. Keywords Soybean-rhizobium symbiosis; Nodulation signaling genes; LysM receptors; GmNARK; Nitrogen fixation 1 Introduction In agricultural production, soybeans (Glycine max) have a very special ability - they can coexist with rhizobia. This cooperative relationship is no simple matter. Rhizobia live in the roots of soybeans to form root nodules, helping to "convert" nitrogen in the air into ammonia that plants can use. This matter may seem minor, but it is actually remarkable: not only does it save the trouble of nitrogen fertilizer, but it also helps to cultivate the land well. However, such "cooperation" is not something that everyone can participate in; it requires matching and communication. Without that set of precise communication at the molecular level, soybeans and rhizobia would have no connection at all (Ratu et al., 2021). Interestingly, behind this mutualistic symbiosis lies a complex signal network in operation. For instance, soybeans have to first recognize the signal molecules released by rhizobia with their own receptors (such as NFR1, NFR5), namely the so-called nodular factors, before initiating subsequent physiological responses and gradually developing into the shape of rhizobia (Okazaki et al., 2013; Ma et al., 2021). However, the matter goes far beyond this. Hormones within plants, isoflavones secreted by roots, and the type III secretion system (T3SS) of rhizobia themselves are all involved, regulating the efficiency and specificity of symbiosis (Darwish et al., 2022; Chen et al., 2023). Sometimes, these factors also "fight" or "collaborate" with each other. For instance, the interaction among hormone signals, transcription factors and bacterial effector proteins is one of the key links that determine the success or failure of symbiosis (Lu et al., 2023). Based on these phenomena, we intend to review the current research progress on the key signaling genes in the interaction between soybeans and rhizobia. We do not only focus on the signal recognition step, but also discuss the effector molecules released by plants and bacteria, hormone effects, environmental interference factors, as
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