Legume Genomics and Genetics 2026, Vol.17, No.1, 14-31 http://cropscipublisher.com/index.php/lgg 25 now routinely reveal dozens to hundreds of loci controlling nodulation traits such as nodule number, nodule biomass, nitrogenase activity, and plant nitrogen content across chickpea, cowpea, common bean and soybean (Herridge and Rose, 2000). In chickpea, GWAS for nodulation and biological nitrogen fixation (BNF) across multiple environments identified numerous stable marker–trait associations (MTAs) for traits like number of nodules and nodule fresh weight, with several SNPs validated in independent populations, illustrating the robustness of these associations. Many MTAs lie in or near genes encoding receptors, kinases and transporters previously implicated in symbiosis, making them strong candidates for functional markers. Similarly, in cowpea, a mini-core collection genotyped at high density revealed significant associations for nodule number, nodule efficiency and nodule dry weight on multiple chromosomes, with positional candidate genes near peak markers encoding proteins associated with BNF. These discoveries have clear downstream breeding utility. Several studies emphasize that significant SNPs linked to nitrogen fixation traits can be converted into Kompetitive Allele-Specific PCR (KASP) markers to enable rapid and low-cost genotyping in breeding pipelines. Marker-assisted selection (MAS) can then be applied to stack favourable alleles for nodulation and BNF efficiency into elite backgrounds, particularly when trait heritability is moderate and environmental effects are strong, as observed for nodulation traits in cowpea and other legumes (Herridge and Rose, 2000). Reviews of legume genomics and breeding highlight that sequencing, resequencing, SNP discovery and the construction of high-density maps across major legumes provide a framework to develop marker sets tailored to nitrogen fixation traits, moving from anonymous markers to functionally annotated, trait-linked loci (Afzal et al., 2019). Integrating comparative genomics-via identification of conserved and lineage-specific symbiosis genes across species-with GWAS results further refines candidate lists and supports development of cross-species or crop-specific marker panels for nitrogen fixation efficiency (Dwivedi et al., 2014). 7.2 Molecular design breeding for nitrogen fixation-related traits The growing body of genomic resources in legumes enables “molecular design breeding,” in which alleles at multiple loci affecting nitrogen fixation are rationally combined using markers, genomic selection and genome editing. Emerging tools such as genome-wide SNP arrays, genotyping-by-sequencing, and high-density reference genomes have greatly increased the resolution of QTL mapping and GWAS for complex traits, allowing breeders to model the polygenic architecture of nodulation and BNF in silico before constructing crosses (Afzal et al., 2019). Genomic selection (GS) models, trained on multi-environment phenotypes and genome-wide markers, can capture the small-to-moderate additive effects typical of nitrogen fixation traits, thereby outperforming MAS alone when many loci contribute (Pandey et al., 2016). Comparative genomic information from model legumes and multiple crop species helps define core symbiosis networks and orthologous candidate genes, which can be prioritized in GS models or targeted for editing (Dwivedi et al., 2014). Molecular design breeding also increasingly incorporates functional validation and genome editing to create ideal ideotypes for nitrogen-efficient, climate-resilient legume varieties. Reviews of grain legume genomics stress that advances in host and rhizobial genome sequencing, combined with transcriptomics, are yielding candidate genes controlling symbiotic efficiency that can be introgressed or edited to enhance BNF under stress (Dwivedi et al., 2014; Mahto et al., 2025). For example, association studies in common bean and soybean have identified candidate genes encoding receptor-like kinases and other signaling components underlying SNF-related QTL; functional analysis using CRISPR and transcriptomics is being used to confirm causality and quantify pleiotropic effects. In chickpea, identification of key nodulation regulators such as CaNFP and its strong upregulation under favourable microbial treatments point to clear targets for genome editing to improve nodule formation and nitrogen fixation. Conceptually, molecular design breeding for nitrogen fixation will rely on integrating: (i) comparative maps of nodulation and BNF genes across legumes, (ii) trait-linked markers and genomic prediction, and (iii) precise editing or allele mining of regulatory and structural genes, with the explicit goal of optimizing both plant–microbe compatibility and whole-plant resource allocation to nodules (Dwivedi et al., 2014; Ferguson et al., 2018).
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