FRIMOUSS

Commercial fruit and wine productions are under significant pressure from environmental stresses, but also by changes in consumer demand for taste and nutritional value, resulting in a need constantly renewed for improved varieties that can meet this demand. One of the key goals of fruit biology is therefore to understand the factors that influence fruit growth and quality, ultimately with a view to manipulating these levels for improvement of fruit traits. The possibility to come up with unified strategies for improvement therefore represents a good opportunity for both major and minor fruit crops. Metabolism is an obvious target for crop improvement, especially in fruits, and understanding the mechanisms linking it to crop phenotypes will help to focus breeding strategies. The present project bets that comparing species for the programming and integration of primary metabolic pathways with growth and fruit quality will identify essential regulation points, especially regarding the trade-offs between fruit components. For this, three modelling approaches will be developed and combined in order to compare 10 contrasted fruit species (tomato, grapevine, peach, pepper, eggplant, apple, strawberry, clementine, kiwifruit and cucumber). An existing enzyme-based kinetic model, which consists in sets of ordinary differential equations for each step in sucrose metabolism, will be extended to enable the search for metabolic parameters exerting strong control over metabolic fluxes and concentrations. A stoichiometric model that has been developed to describe primary metabolism in tomato fruits will also be extended to a wider range of pathways to enable robust flux predictions throughout fruit development. A process-based simulation model will be built by adapting and integrating existing modules that describes the key processes of fruit development and ripening (cell division and expansion as well as resource allocation). All three models will be extended and optimised in tomato, and transferred to the other species. A standardisation effort will be undertaken by building a framework linking experimental data with model inputs and outputs. It will enable comparison and cross-validation of the model outputs on the one hand, and the integration of the models on the other hand. The latter challenge will be performed by running the kinetic model in a dynamic mode and by connecting it to the process-based model while key fluxes (redox and energy fluxes) calculated by the stoichiometric model will be used as constraints. Finally, the less influential enzymatic reactions will be removed and replaced by simplified rate equations, in order to keep only the parameters exerting the strongest influence on fruit biomass and composition. The parameterisation of all models will be made possible by a close interaction with experimental biologists. Thus, plants will be grown under optimal conditions, and fruits harvested throughout development and maturation. Ecophysiological, biochemical, and cytological data (biomass composition, concentrations of metabolic intermediates, enzyme capacities, and subcellular volumes) will be produced “à la carte” using state-of-the-art methodologies, thus enabling iterations between virtual and real experiments. This Systems Biology project is expected to produce a series of breakthroughs including a better understanding of the trade-offs that are behind the building of fruit biomass, the identification of parameters exerting a strong control over critical trade-offs, and ultimately a toolbox (a pre-parameterised SBML template to enable a range of predictions in fruits) for the manipulation of fruit quality that could be amenable to strategies involving reverse or forward genetics.