Predicting genotype-to-phenotype relationships under contrasting environments is a great challenge for plant biology and breeding. Classical crop models have been developed to predict crop yield or product quality under fluctuating environments but they are usually calibrated for a single genotype, restricting the validity range of the model itself. To overcome this limitation, genetic control has to be integrated into crop models and genotype × environment interactions have to be made explicit. The aim of this chapter is to provide an overview of a panel of approaches that have been developed to integrate genetic control in plant and crop models. The fundamentals of quantitative genetics of complex traits are first introduced, with special attention to methods for quantitative trait loci (QTL) cartography and QTL genetic modelling. The integration of genetic control within ecophysiological models is then discussed. Several methods are reviewed, ranging from classical statistical approaches, relying on specific model parameters reflecting gene or QTL effects, to recent multi-scale models, explicitly integrating molecular networks. This chapter proposes a review of a few techniques from systems biology that can be used to describe the behaviour of cellular networks, in a simplified way. Coupling different organizational scales is finally discussed and a few examples of multi-scale plant models are presented