Legume Genomics and Genetics 2026, Vol.17, No.1, 14-31 http://cropscipublisher.com/index.php/lgg 19 limit further nodule initiation (Chaulagain and Frugoli, 2021; Zorin et al., 2022). A complementary positive systemic pathway based on CEP peptides and the CRA2 receptor, and a miR2111–TML module, together create a balance between promotion and suppression of nodulation in response to soil nitrogen and whole-plant demand (Chaulagain and Frugoli, 2021; Cardoso-Silva et al., 2025). Comparative and transcriptomic studies in forage crops such as red clover and pea have highlighted additional developmental genes, including large families of nodule-specific cysteine-rich (NCR) peptides and PLAT-domain proteins, whose copy number and expression variation correlate with differences in nitrogen fixation efficiency and nodule traits (Figure 1) (Dinkins et al., 2022; Vlk et al., 2022). Single-cell and cell-type–specific transcriptomics in Lotus japonicus nodules identified hundreds of differentially expressed genes between infected and uninfected cells, including transcription factors and transporters with previously unknown roles, greatly expanding the set of candidates implicated in spatially patterned gene networks that sustain nodule development (Wang et al., 2022). Collectively, these findings delineate a complex, multi-layered regulatory landscape in which conserved core regulators such as NIN are complemented by lineage-specific TFs, peptides, and signaling genes that fine-tune nodule organogenesis across legume crops. Figure 1 Genes regulating nodule development (Adopted from Dinkins et al., 2022) 3.3 Functional genes for nitrogen fixation and metabolism In mature nodules, suites of functional genes from both plant and bacterial partners underpin nitrogenase activity, oxygen homeostasis, and nitrogen assimilation and export. On the plant side, leghemoglobin genes encode oxygen-binding hemoproteins that create a microaerobic environment compatible with nitrogenase while sustaining high respiration; nodule-specific expression and gene family expansion of leghemoglobins have been documented in multiple legumes, and disruption of these genes impairs nitrogen fixation (Roy et al., 2019). Single cell-type transcriptomics in L. japonicus revealed strong enrichment of genes for heme biosynthesis, leghemoglobins, and related pathways in infected cells, and functional tests showed that altering expression of haem biosynthesis regulators affected haem content, nodule coloration, and nitrogen fixation capacity. Enzymes of the carbonic anhydrase–PEPC–malate dehydrogenase pathway, which provides dicarboxylates (especially malate) as carbon and energy sources for bacteroids, are major determinants of nodule carbon metabolism, and their expression and activity respond to whole-plant nitrogen and phosphorus status (Schwember et al., 2019).
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