| Summary: | In many plant species, flowering is promoted by the cold treatment or vernalization. The mechanism of vernalization-induced flowering has been extensively studied in <i>Arabidopsis</i> but remains largely unknown in legumes. The orthologs of the <i>FLC</i> gene, a major regulator of vernalization response in <i>Arabidopsis</i>, are absent or non-functional in the vernalization-sensitive legume species. Nevertheless, the legume integrator genes <i>FT</i> and <i>SOC1</i> are involved in the transition of the vernalization signal to meristem identity genes, including <i>PIM</i> (<i>AP1</i> ortholog). However, the regulatory contribution of these genes to <i>PIM</i> activation in legumes remains elusive. Here, we presented the theoretical and data-driven analyses of a feed-forward regulatory motif that includes a vernalization-responsive <i>FT</i> gene and several <i>SOC1</i> genes, which independently activate <i>PIM</i> and thereby mediate floral transition. Our theoretical model showed that the multiple regulatory branches in this regulatory motif facilitated the elimination of no-sense signals and amplified useful signals from the upstream regulator. We further developed and analyzed four data-driven models of <i>PIM</i> activation in <i>Medicago trancatula</i> in vernalized and non-vernalized conditions in wild-type and <i>fta1-1</i> mutants. The model with <i>FTa1</i> providing both direct activation and indirect activation via three intermediate activators, <i>SOC1a</i>, <i>SOC1b</i>, and <i>SOC1c</i>, resulted in the most relevant <i>PIM</i> dynamics. In this model, the difference between regulatory inputs of <i>SOC1</i> genes was nonessential. As a result, in the <i>M. trancatula</i> model, the cumulative action of <i>SOC1a</i>, <i>SOC1b</i>, and <i>SOC1c</i> was favored. Overall, in this study, we first presented the in silico analysis of vernalization-induced flowering in legumes. The considered vernalization network motif can be supplemented with additional regulatory branches as new experimental data become available.
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