Genotype × environment interaction QTL mapping in plants: lessons from Arabidopsis

•Different genetic models can account for genotype × environment (G×E) interactions.•Considering the genetic basis of G×E interactions improves QTL analysis.•Local adaptations due to G×E can cause antagonistic pleiotropy and contrasting fitness.•Multi-environment QTL analysis is more powerful than single-environment analysis.

Plant growth and development are influenced by the genetic composition of the plant (G), the environment (E), and the interaction between them (G × E). To produce suitable genotypes for multiple environments, G × E should be accounted for and assessed in plant-breeding programs. Here, we review the genetic basis of G × E and its consequence for quantitative trait loci (QTL) mapping in biparental and genome-wide association (GWA) mapping populations. We also consider the implications of G × E for understanding plant fitness trade-offs and evolutionary ecology.