Legume Genomics and Genetics 2026, Vol.17, No.1, 14-31 http://cropscipublisher.com/index.php/lgg 26 7.3 Nitrogen fixation research and sustainable agricultural development Enhanced biological nitrogen fixation in legumes is central to sustainable agricultural systems that reduce dependence on synthetic fertilizers, lower greenhouse gas emissions, and maintain soil fertility. Global meta-analyses and quantitative reviews show that nitrogen derived from the atmosphere (Ndfa) in legumes can range from 5%–99%, with averages near 68% across crops, and around 0.84 kg fixed N per kg total shoot N when belowground contributions are included, underscoring the large potential contribution of legumes to system-level N budgets. Other reviews of legume-driven BNF highlight multiple ecosystem services: improved soil structure, residual nitrogen benefits for subsequent crops, break-crop effects on pests and diseases, and enhanced biodiversity in rotation, intercropping, green manuring and alley-cropping systems (Lindström and Mousavi, 2019). Under organic and low-input systems, BNF is often the principal N source; systematic reviews indicate that optimizing species choice, cropping practice and biomass production is crucial to maximize Ndfa and stabilize yields under variable climate and sanitary conditions. However, realizing this potential at scale requires aligning genetic gains in nitrogen fixation with agronomic, environmental and socioeconomic realities. Meta-analyses and reviews emphasize that BNF is highly sensitive to ecological context-soil fertility, climate, stand composition and rhizobial compatibility-so that local testing and adaptive management are essential. Climate change adds further constraints, as high temperatures and drought can drastically reduce nodulation and N fixation, calling for breeding of stress-tolerant, high-BNF varieties and the development of climate-smart management strategies. Comparative genomics and breeding for symbiotic efficiency, when coupled with improved inoculant technologies and microbiome management, can help produce cultivars that fix more nitrogen reliably across environments, thereby reducing fertilizer needs and associated emissions (Mahmud et al., 2020). Ultimately, sustained investment in nitrogen fixation research-from gene discovery and marker development to breeding and systems-level evaluation-will be crucial for designing diversified, legume-rich cropping systems that contribute meaningfully to global food security while staying within planetary nitrogen boundaries (Jhu and Oldroyd, 2023). 8 Summary and Outlook Comparative genomics has established that key nitrogen fixation and nodulation genes are widely conserved across major legume crops, despite extensive genome duplication, polyploidy and divergence. Cross-species analyses of core nodulation and symbiotic signaling components, coupled with synteny and orthology mapping, show that a common set of regulatory and structural genes underpins nodule organogenesis, rhizobial infection, bacteroid differentiation and nodule metabolism in both model and crop legumes. Sequence-level comparisons of nitrogen fixation (NF) genes in multiple legumes highlight predominantly purifying selection and retention of duplicated copies, underscoring their essential role in legume biology. At the same time, pan-genomic and transcriptomic studies reveal substantial diversification in gene copy number, expression patterns and regulatory networks, particularly among transcription factors and receptors modulating nodulation and symbiotic nitrogen fixation (SNF). Parallel comparative genomics of rhizobial symbionts demonstrates large, open pan-genomes, extensive accessory gene content and multiple configurations of nodulation and nif clusters, with no simple core “symbiome,” but instead a spectrum of genetic strategies for establishing effective symbioses. These genomic foundations have been translated into practical tools for dissecting natural variation in nitrogen fixation traits. High-density reference genomes, resequencing of diversity panels and genome-wide association studies (GWAS) have identified numerous loci associated with nodulation, nodule biomass, nitrogenase activity and plant nitrogen status in cowpea, soybean, common bean, chickpea and other legumes, frequently implicating receptors, kinases, transporters and regulatory genes. Many trait-linked SNPs can be converted into efficient markers (e.g., KASP) to support marker-assisted selection, and are increasingly integrated with transcriptome-wide association, eQTL mapping and chromatin accessibility data to pinpoint causal genes and cis-regulatory variants. Advances in functional genomics-including CRISPR/Cas-mediated editing, detailed nodule transcriptomics, and cross-species comparative analyses of nodulation genes-are clarifying the roles of key regulators such as NIN, CaNFP, FEN1 and multiple transcription factor families in controlling symbiotic
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