Identification of gene interactions in fungal-plant symbiosis through discrete dynamical system modelling

Fungal-plant root associations involve nutrient exchanges, between the partners and the soil, particularly phosphate, that benefit both organisms. Discrete dynamical system (DDS) models are reconstructed to capture gene regulation in the arbuscular mycorrhizae Glomus versiforme-Medicago trunculata root symbiosis. Previously published time-course gene expression data derived from various days post-inoculation were clustered to identify genes co-regulated in mycorrhizal roots. Uncolonised roots grown with high phosphate provide a key nutritional control condition. First-order linear DDS models were created using a data-driven method to fit to the observed gene expression data. The result of the modelling constitutes active gene interactions in the regulatory network of the plant root at 8, 15, 22, 31 and 36 days post-inoculation. These genes are involved in basic metabolism, development, oxidative stress and defense pathways, and show consistent dynamic behaviours in the model. The functions of previously unannotated genes were further elucidated from the developed system maps.