Dissecting Genotype-Environment Interactions and Trait Correlations

Different genotypes show heterogeneous responses to environmental variation. Although such genotype-environment interactions influence performance of crop species and natural populations in the field, the genetic basis of these responses is poorly understood. We developed a broadly applicable method to investigate polygenic responses to local environments and to identify quantitative trait loci that control these environmental responses. Using this approach, we analyzed large, multi-environment experiments from rice, maize, and soybean. In most cases we find limited evidence that genetic tradeoffs control plant traits across diverse environments. Instead, yield tradeoffs arise when consistent effects on intermediate traits have opposite influences on crop yield in different environments.