Accumulating evidence for trade-offs involving metabolic traits has demonstrated their importance in evolution of organisms. Metabolic models with different level of complexity have already been considered when investigating mechanisms that explain various metabolic trade-offs. Here we provide a systematic review of modelling approaches that have been used to study and explain trade-offs between: (i) kinetic properties of individual enzymes, (ii) rates of metabolic reactions, (iii) rate and yield of metabolic pathways and networks, (iv) different metabolic objectives in single organisms and in metabolic communities, and (v) metabolic concentrations. In providing insights into mechanisms underlying these five types of metabolic trade-offs obtained from constraint-based metabolic modelling, we emphasize the relation of metabolic trade-offs to the classical black box Y-model that provides conceptual explanation for resource acquisition-allocation trade-offs. In addition, we identify several pressing concerns and offer a perspective for future research in the identification and manipulation of metabolic trade-offs by relying on the toolbox provided by constraint-based metabolic modelling for single organisms and microbial communities.

Trade-offs between traits arise and reflect constraints imposed by the environment and physicochemical laws. Trade-off situations are expected to be highly relevant for sessile plants, which have to respond to changes in the environment to ensure survival. Despite increasing interest in determining the genetic and molecular basis of plant trade-offs, there are still gaps and differences with respect to how trade-offs are defined, how they are measured, and how their genetic architecture is dissected. The first step to fill these gaps is to establish what is meant by trade-offs. In this review we provide a classification of the existing definitions of trade-offs according to: (1) the measures used for their quantification, (2) the dependence of trade-offs on environment, and (3) whether data based on which they are inferred are from a single individual across different environments or a population of individuals in single or multiple environments. We then compare the approaches for quantification of trade-offs based on phenotypic, between-individual, and genetic correlations, and stress the need for developing further quantification indices particularly for trade-offs between multiple traits. Lastly, we highlight the genetic mechanisms underpinning trade-offs and experimental designs that facilitate their discovery in plants, with focus on usage of natural variability. This review also offers a perspective for future research aimed at identification of plant trade-offs, dissection of their genetic architecture, and development of strategies to overcome trade-offs, with applications in crop breeding.