Legume Genomics and Genetics 2026, Vol.17, No.1, 14-31 http://cropscipublisher.com/index.php/lgg 16 to systematically characterize the genomic landscape of nitrogen fixation across key legumes, with the ultimate aim of informing molecular design breeding and contributing to sustainable, low-input agricultural systems. 2 Molecular Mechanisms of Nitrogen Fixation in Legumes 2.1 Signal recognition processes in nodule formation The initiation of legume–rhizobium symbiosis depends on a finely tuned molecular dialogue that allows plants to distinguish compatible nitrogen-fixing partners from the multitude of soil microbes. Root-exuded flavonoids stimulate rhizobia to express nodulation (nod) genes and synthesize lipochitooligosaccharide Nod factors, which act as key symbiotic signals guiding early infection events. In host roots, Nod factors are perceived mainly by LysM-domain receptor-like kinases at the epidermis, which trigger intracellular signaling cascades shared with other endosymbioses, including the common symbiosis pathway (SYM) initially characterized in model legumes (Roy et al., 2019). This pathway involves plasma membrane receptors, nuclear-localized ion channels, and a calcium/calmodulin-dependent protein kinase that decodes characteristic nuclear calcium oscillations to activate nodulation-specific transcriptional programs. Comparative studies show that although the core signaling components are broadly conserved among legumes, gene family expansions, promoter variation, and allelic diversity in receptor and downstream signaling genes contribute to differences in host range, infection mode, and responsiveness to environmental conditions in major crops such as soybean, common bean, and pea (Sharma et al., 2020; Tsyganov and Tsyganova, 2020). Beyond Nod factors, additional bacterial cues and secretion systems further refine host recognition and specificity. Rhizobia possess multiple protein secretion systems, including type III, IV, and VI systems, that deliver effector proteins influencing infection success, host range, and nodule number (Nelson and Sadowsky, 2015). These secretion systems, traditionally associated with pathogenicity, are increasingly recognized as central modulators of symbiotic compatibility and can either promote or block nodulation depending on host genotype. Plants in turn integrate symbiotic signaling with innate immunity, using pattern-recognition receptors and downstream defense pathways to prevent colonization by non-beneficial microbes while permitting entry of compatible rhizobia (Shumilina et al., 2023). Recent work has revealed that rhizobial tRNA-derived small RNAs (tRFs) can act as mobile signals taken up by host cells, where they hijack the RNA interference machinery to modulate expression of plant genes involved in nodule initiation and development, thereby promoting nodulation (Ren et al., 2019). These multilayered recognition and signaling processes demonstrate that early stages of nodule formation arise from a co-evolved network of small molecules, receptors, secretion systems, and regulatory RNAs, the genes for which show both strong conservation and lineage-specific diversification across legume genomes. 2.2 Nodule development and symbiotic regulatory networks Following successful signal perception, legumes coordinate rhizobial infection in epidermal/root hair cells with organogenesis in the cortex to produce nodules that house nitrogen-fixing bacteroids (Lepetit and Brouquisse, 2023). Infection threads guide bacteria through root hairs into inner tissues, while cortical cell divisions generate nodule primordia that ultimately give rise to determinate or indeterminate nodules, differing in meristem persistence and zonation (Lepetit and Brouquisse, 2023). Genetic and genomic studies over the last two decades have identified nearly 200 plant genes required for symbiotic nitrogen fixation, including receptors, ion channels, transcription factors, transporters, and enzymes that collectively orchestrate infection, nodule morphogenesis, and bacteroid accommodation (Roy et al., 2019; Tsyganov and Tsyganova, 2020). Central to this regulatory network is the transcription factor NODULE INCEPTION (NIN), which integrates upstream symbiotic and nitrogen-status signals to initiate nodule organogenesis and regulate infection thread progression (Qiao et al., 2023). Recent work demonstrated that proteolytic processing of NIN by a signal peptidase complex yields a C-terminal fragment that specifically activates genes required for symbiosome development and the transition to a nitrogen-fixing state, revealing a conserved mechanism linking early development to functional maturation. Nodule development is further shaped by systemic and local regulatory networks that balance the high carbon cost of symbiosis with whole-plant nitrogen demand. Autoregulation of nodulation (AON) is a root–shoot–root signaling loop in which early nodulation induces CLE peptide production in roots; these peptides travel to the shoot and are perceived by CLAVATA1-like leucine-rich repeat receptor kinases (e.g., HAR1/SUNN/NARK),
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