Legume Genomics and Genetics 2026, Vol.17, No.1, 14-31 http://cropscipublisher.com/index.php/lgg 18 recognition of rhizobial signals and initiation of nodulation. More than 190 plant genes essential for symbiotic nitrogen fixation (SNF) have been catalogued in Medicago truncatula, Lotus japonicus, soybean (Glycine max) and common bean (Phaseolus vulgaris), many of which encode receptors and signaling proteins that mediate perception of Nod factors and downstream transduction of symbiotic signals (Chaulagain and Frugoli, 2021). LysM-domain receptor-like kinases that recognize rhizobial lipochitooligosaccharides, co-receptors such as SYMRK/DMI2, nuclear cation channels, and the calcium/calmodulin-dependent protein kinase CCaMK form the backbone of the common symbiosis pathway, and orthologous genes have been identified in all major legume crops examined (Mahmud et al., 2020). Downstream transcription factors, including NODULE INCEPTION (NIN), NIN-LIKE PROTEINS (NLPs), GRAS proteins (NSP1/NSP2), and NF-Y subunits, decode these signals to activate infection and organogenesis programs (Soyano et al., 2019). Integration of large RNA-seq datasets in soybean has shown that many of these genes belong to expanded gene families shaped by whole-genome duplication, and that nodulation-related paralogs often exhibit strong nodule- or root-specific expression, indicating functional specialization for symbiotic signaling (Cardoso-Silva et al., 2025). Beyond the canonical SYM pathway, additional signal recognition genes and regulatory modules have been uncovered in crop legumes using forward genetics, expression profiling, and functional genomics. In soybean, members of the CCR4–NOT complex, particularly GmNOT4-1, were identified as regulators of Nod factor signaling: both overexpression and knockdown of GmNOT4-1 reduced nodule number and suppressed transcription of Nod factor pathway genes, highlighting dosage-sensitive post-transcriptional control of early symbiotic signaling (Zheng et al., 2023). Studies in common bean identified SRS/STY transcription factors (PvSRS) whose expression is induced throughout symbiosis; PvSRS10 is transcriptionally activated by NF-Y and by a MADS-box factor, situating it within the NIN–NF-Y cascade that translates perception of rhizobial signals into developmental responses (Ayra et al., 2025). Comparative reviews emphasize that many of these signal recognition components are conserved across legumes but also display lineage-specific expansions and allelic variation, linked to differences in host range, infection strategy, and environmental responsiveness in crop species (Chaulagain and Frugoli, 2021). This expanding catalog of signal perception and transduction genes, derived from model and crop legumes, provides a genomic framework for engineering or enhancing signal recognition capacity in major legume crops and, potentially, in non-legume hosts. 3.2 Genes regulating nodule development Genetic dissection of nodulation has revealed a large suite of genes that regulate the transition from early signaling to nodule organogenesis and morphogenesis. Central among these is NIN, a master transcription factor whose loss abolishes nodule formation; NIN orthologs in multiple legumes have been shown to control cortical cell divisions, infection thread progression, and later steps leading to the nitrogen-fixing state (Feng et al., 2021). Recent work demonstrated that NIN is proteolytically processed by a signal peptidase complex to release a C-terminal fragment with DNA-binding activity that specifically activates genes required for symbiosome development and nitrogen fixation, and similar processing was detected in several legumes, indicating a conserved mechanism controlling the developmental transition to functional nodules (Feng et al., 2021). Downstream of NIN, NF-Y transcription factor complexes, GRAS proteins, ERF/AP2 factors, and additional TF families (including SRS/STY and MADS-domain proteins in common bean) regulate expression of genes for cell cycle control, infection thread guidance, and nodule meristem activity (Ayra et al., 2025). High-resolution single-nucleus transcriptomic atlases in soybean have further identified novel regulators of nodulation, such as GmbHLH93, GmSCL1, and the cytokinin receptor GmCRE1; knockout of GmCRE1 led to severe defects in the nitrogen fixation zone, loss of leghemoglobin expression, and almost complete loss of biological nitrogen fixation, underscoring its central role in nodule development and identity. Nodule development is strongly shaped by systemic regulatory networks that adjust nodule number and activity to plant nitrogen status, and many key genes in these pathways have now been identified in major legumes. Autoregulation of nodulation (AON) involves root-derived CLE peptides induced by early nodulation, shoot-localized CLAVATA1-like receptors (HAR1/SUNN/NARK), and downstream signaling components that
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