Dynamical Modeling of the Core Gene Network Controlling Transition to Flowering in Pisum sativum

Abstract

Transition to flowering is an important stage of plant development. Many regulatory modules that control floral transition are conservative across plants. This process is best studied for the model plant Arabidopsis thaliana. The homologues of Arabidopsis genes responsible for the flowering initiation in legumes have been identified, and available data on their expression provide a good basis for gene network modeling. In this study, we developed several dynamical models of a gene network controlling transition to flowering in pea (Pisum sativum) using two different approaches. We used differential equations for modeling a previously proposed gene regulation scheme of floral initiation in pea and tested possible alternative hypothesis about some regulations. As the second approach, we applied neural networks to infer interactions between genes in the network directly from gene expression data. All models were verified on previously published experimental data on the dynamic expression of the main genes in the wild type and in three mutant genotypes. Based on modeling results, we made conclusions about the functionality of the previously proposed interactions in the gene network and about the influence of different growing conditions on the network architecture. It was shown that regulation of the PIM, FTa1, and FTc genes in pea does not correspond to the previously proposed hypotheses. The modeling suggests that short- and long-day growing conditions are characterized by different gene network architectures. Overall, the results obtained can be used to plan new experiments and create more accurate models to study the flowering initiation in pea and, in a broader context, in legumes.