The causal arrows from genotype, environment, and management to plant phenotype are double headed

Cause-and-effect arrows are drawn from genotype (G), environment (E), and agronomic management (M) to the plant phenotype in crop stands in a useful but incomplete framework that informs research questions, experimental design, statistical analysis, data interpretation, modelling, and breeding and agronomic applications. Here we focus on the overlooked bidirectionality of these arrows. The phenotype-to-genotype arrow includes increased mutation rates in stressed phenotypes, relative to basal rates. From a developmental viewpoint, the phenotype modulates gene expression, returning multiple cellular phenotypes with a common genome. The phenotype-to-environment arrow is captured in the process of niche construction, which spans from persistent and global to transient and local. Research on crop rotations recognizes the influence of the phenotype on the environment but is divorced from niche construction theory. The phenotype-to-management arrow involves, for example, a diseased crop that may trigger fungicide treatment. Making explicit the bidirectionality of the arrows in the G×E×M framework contributes to narrowing the gap between data-driven technologies and integrative theory, and is an invitation to think cautiously of the internal teleonomy of plants in contrast to the view of the phenotype as the passive end of the arrows in the current framework.