Computational modeling of horticultural crops under different light conditions

Light regulates many aspects of plant growth and developmental processes as well as disease resistance in plants. Computational models can be used to provide more detailed insights in how processes are regulated in plants and can contribute to investigating the mechanisms underlying these processes. The current study is performed to assess the influence of light conditions on several horticultural crops of commercial importance by developing systems biology models. Genome-scale modeling of the plant metabolic network in combination with flux balance analysis (FBA) could be suitable to model the influence of lighting conditions on horticultural crops. With FBA, the influence of light dependent enzymes on for instance biomass accumulation could be explored, without the need of hard-to-determine kinetic parameters of these enzymes. FBA was performed on a metabolic network reconstruction of Arabidopsis and generated some preliminary results. For instance, different effects and even opposite effects of catalase activity on biomass accumulation were found for catalase located in different compartments. Constrained-based reconstruction and analysis (COBRA) methods, including FBA, have often been applied for bacteria. COBRA methods are only able to model steady state reaction fluxes, therefore do not incorporate metabolite concentrations. Moreover, FBA performed on metabolic network reconstructions often leads to thermodynamically infeasible loops, resulting in unrealistic predictions. Despite the challenges revealed during this study, reaction fluxes predicted by FBA have often been reported to be quite accurate and efforts have already been made to overcome these limitations. For example, one of the solutions to overcome thermodynamically infeasible loops is by performing a loopless flux variability analysis (FVA), generating a set of boundary conditions that are thermodynamically feasible. It is expected that COBRA methods can be successfully applied for plant species, however, this has only scarcely been done to date and solely for the model plant Arabidopsis.