Legume Genomics and Genetics 2026, Vol.17, No.1, 14-31 http://cropscipublisher.com/index.php/lgg 27 efficiency, stress responses and host–rhizobium compatibility. Collectively, these efforts position comparative genomics as a central engine for both fundamental insight into the evolution of nitrogen-fixing symbioses and the rational improvement of nitrogen fixation in major legume crops. Despite substantial progress, current comparative genomic research on nitrogen fixation in legumes faces several important limitations. First, genetic and genomic characterization is heavily biased toward a few species-particularly soybean, common bean, chickpea, pea and model legumes-while many regionally important or underutilized legumes remain genomically under-resourced. Even in well-studied crops, most analyses have focused on aboveground nodulation and SNF traits under controlled or limited field environments, whereas belowground nitrogen contributions, long-term soil fertility effects and performance under diverse management systems are far less quantified. On the microbial side, although comparative genomics of rhizobia and Bradyrhizobium has revealed extensive diversity and highlighted key symbiotic islands, the functional significance of many accessory genes, secretion systems and strain-specific modules for host specificity and field-level nitrogen fixation is still poorly resolved. Second, nitrogen fixation is strongly context dependent, yet integration of genomic findings with environmental variability, microbiome complexity and agronomic management remains incomplete. Many GWAS and QTL studies report strong genotype-by-environment interactions and moderate heritability for SNF traits, complicating marker deployment and prediction of performance across sites and seasons. Comparative and functional studies often use single elite rhizobial strains and simplified conditions, which may not capture the competitive dynamics within native microbiomes that ultimately determine nodulation and fixation efficiency in farmers’ fields. Furthermore, most comparative genomic work has centered on host plants or rhizobia in isolation; truly integrative, dual-genome or community-level approaches that connect host variants, microbial genotypes and soil ecological processes are still rare. Finally, while gene editing and advanced breeding strategies are emerging, regulatory, biosafety and adoption barriers can slow the translation of genomic discoveries into widely grown varieties, particularly in low-income regions that stand to benefit most from improved biological nitrogen fixation. Future research on comparative genomics of nitrogen fixation in legumes will benefit from more comprehensive, multi-layered approaches spanning species, genomes and environments. Expansion of high-quality reference genomes, pan-genomes and diversity panels across a broader set of major and minor legumes, together with wild relatives, will help uncover hidden variation in nodulation and SNF genes and illuminate how domestication and improvement have shaped symbiotic capacities. Comparative analyses integrating structural variants, presence/absence variants and regulatory sequence diversity with functional genomics (transcriptomics, epigenomics, single-cell and spatial profiling of nodules) will be essential to dissect how conserved symbiotic modules are rewired across lineages and stress conditions. On the microbial side, large-scale comparative genomics of Bradyrhizobium and other rhizobia should be coupled with functional studies of candidate symbiosis and secretion genes to refine host-specific inoculant design and identify microbial traits that enhance competitiveness, persistence and nitrogen fixation under realistic field conditions. Equally important will be the integration of comparative genomics with systems-level modeling and breeding for sustainability. Process-based and statistical models that link genomic variation in both host and rhizobial partners to BNF outputs, crop productivity and soil nitrogen dynamics under changing climates can guide ideotype design and management strategies. Genomic selection pipelines explicitly incorporating nitrogen fixation traits, stress resilience and interactions with rhizobial communities should be developed and tested in multi-environment trials, especially in low-input systems where legumes can most reduce fertilizer dependency. Future work should also explore translational opportunities beyond classical legumes, building on comparative studies with nodulating non-legumes and attempts to transfer nitrogen-fixing capabilities or associative fixation to cereals. Finally, bridging disciplinary boundaries-linking genomics, agronomy, soil ecology, climate science and socioeconomics-will be crucial to ensure that advances in comparative genomics of nitrogen fixation translate into deployable cultivars, adapted inoculants and cropping systems that contribute tangibly to global food security and environmental sustainability.
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