Legume Genomics and Genetics 2026, Vol.17, No.1, 14-31 http://cropscipublisher.com/index.php/lgg 14 Research Report Open Access Comparative Genomic Analysis of Nitrogen Fixation Genes in Major Legume Crops Yuping Huang, Yunxia Chen, Hangming Lin Tropical Legume Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: hangming.lin@hitar.org Legume Genomics and Genetics, 2026 Vol.17, No.1 doi: 10.5376/lgg.2026.17.0002 Received: 10 Feb., 2026 Accepted: 12 Feb., 2026 Published: 22 Mar., 2026 Copyright © 2026 Huang 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: Huang Y.P., Chen Y.X., and Lin H.M., 2026, Comparative genomic analysis of nitrogen fixation genes in major legume crops, Legume Genomics and Genetics, 17(1): 14-31 (doi: 10.5376/lgg.2026.17.0002) Abstract Leguminous plants are capable of achieving biological nitrogen fixation through symbiotic relationships with rhizobia, thereby holding significant ecological and economic value in agricultural production. With the completion of genome sequencing for various legume crops, the systematic elucidation of the structural characteristics, evolutionary patterns, and functional divergence of nitrogen fixation-related genes-utilizing comparative genomics approaches-has emerged as a key direction in current plant molecular biology and crop genetic improvement research. Focusing on major legume crops such as soybean, pea, peanut, and alfalfa, this review systematically summarizes the molecular mechanisms underlying nitrogen fixation in legumes and the key genes regulating this process. Particular emphasis is placed on analyzing recent progress in identifying genes associated with nitrogen fixation signal recognition, nodule development regulation, and nitrogen metabolism. Building upon this foundation and integrating findings from comparative genomics studies, a comprehensive analysis is conducted regarding the evolutionary characteristics of nitrogen fixation-related genes in major legume crops, examining aspects such as gene family structure, sequence conservation, gene duplication, and phylogenetic relationships. Furthermore, using the NIN gene family-a key regulator of nitrogen fixation in soybean-as a case study, the review explores its evolutionary patterns across different legume species and its potential value for improving nitrogen fixation efficiency. Finally, this paper discusses the future prospects for applying comparative genomics in the mining of nitrogen fixation genes, the development of molecular markers, and molecular design breeding, while also offering perspectives on future directions for multi-omics integration research. The findings indicate that comparative genomics provides a crucial theoretical foundation for unraveling the mechanisms of nitrogen fixation in legumes and facilitating their genetic improvement, thereby holding significant importance for advancing the development of green agriculture. Keywords Legume crops; Biological nitrogen fixation; Comparative genomics; Nodule formation; Nitrogen fixation genes 1 Introduction Legumes occupy a pivotal position in global agriculture because they simultaneously provide high-quality plant protein and enrich soils through biological nitrogen fixation (BNF). Nitrogen is frequently the most limiting nutrient for crop production, and its industrial supply via the Haber–Bosch process is energy intensive and environmentally costly, contributing to greenhouse gas emissions, nitrate leaching, and eutrophication (Mahmud et al., 2020; Ladha et al., 2022). In contrast, symbiotic BNF in legumes relies on specialized root nodules that host nitrogen-fixing rhizobia, converting atmospheric dinitrogen into ammonia that can be assimilated by the plant (Lindström and Mousavi, 2019; Mahmud et al., 2020). Global assessments indicate that legume-based BNF supplies large quantities of nitrogen to agroecosystems, with typical fixation rates of 20–200 kg N ha-1 year-1 and average proportions of plant nitrogen derived from the atmosphere (Ndfa) around 60%–80% in many systems. These inputs not only satisfy a substantial part of the legumes’ own nitrogen demand but also improve soil fertility and nitrogen availability for subsequent or companion crops, thereby reducing dependence on synthetic fertilizers and supporting ecological intensification of cereal-based systems (Jithesh et al., 2024). As climate change, soil degradation, and the need to lower external inputs intensify, enhancing the efficiency and stability of nitrogen fixation in major legume crops has become central to sustainable agricultural development (Ladha et al., 2022; De Lima et al., 2024).
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