Legume Genomics and Genetics 2026, Vol.17, No.1, 14-31 http://cropscipublisher.com/index.php/lgg 23 Network-level comparisons between soybean and model legumes further reinforce this pattern of conserved core pathways embedded in species-specific regulatory architectures. Cross-species transcriptomic profiling during nitrogen-fixing symbiosis (NFS) and arbuscular mycorrhizal symbiosis (AMS) revealed thousands of genes activated in G. max, M. truncatula and L. japonicus, with a conserved “common symbiosis” module but also soybean-specific regulatory circuits (Figure 3) (Wu et al., 2025). Figure 3 Comparative analysis of nitrogen fixation genes in legumes, highlighting conserved NFgenes across species, soybean genome duplication, shared symbiotic modules, and soybean-specific regulatory networks Co-expression based gene regulatory networks inferred using machine-learning approaches in G. max and M. truncatula highlighted shared hubs associated with symbiosis, while also identifying soybean-specific regulators, including clock components and defense-related TFs that modulate nodulation and nitrogen fixation (Li et al., 2025). Integrative genomic and transcriptomic analyses in a soybean diversity panel documented that many SNF-associated transcription factors lie within domestication sweeps, in contrast to the more structurally conserved NF core genes, indicating that breeding and domestication in soybean have acted more strongly on regulatory layers than on the underlying symbiotic machinery itself. 6.2 Evolutionary analysis of GmNIN and related gene families Although NIN itself was not the explicit focus of several genome-wide studies, insights into the evolutionary behavior of GmNIN can be inferred from comparative analyses of NF- related genes and of large transcription factor families with documented symbiotic roles. The six-legume comparison of 20 NF- related loci showed that soybean copies of core symbiosis genes generally exhibit low Ka/Ks ratios and often retain multiple paralogs, consistent with strong purifying selection and retention after WGD (Kim et al., 2013). This pattern parallels observations for soybean GATA, bZIP, BES1 and other TF gene families, in which segmental duplication associated with WGD is the primary driver of expansion and most duplicated genes display Ka/Ks < 1, indicating
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