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

Abstract Unidirectional, cause-and-effect arrows are drawn from genotype (G), environment (E), and agronomic management (M) to the plant phenotype in crop stands. 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. From a computational viewpoint, the phenotype influences gene expression in a process of downward causation. The phenotype-to-environment arrow is captured in the process of niche construction, which spans from persistent and global ( e.g ., photosynthetic archaea and cyanobacteria that emerged ∼3.4 billion years ago created the oxygen-rich atmosphere that enabled the evolution of aerobic organisms and eukaryotes) to transient and local ( e.g. , lucerne tap root constructs soil biopores that influence the root phenotype of the following wheat crop). Research on crop rotations illustrates but is divorced of niche construction theory. The phenotype-to-management arrow involves, for example, a diseased crop that triggers fungicide treatments. Making explicit the bidirectionality of the arrows in the G × E × M model allows to connect crop improvement and agronomy with other, theoretically rich scientific fields. Highlight In the G × E × M model, the plant phenotype is not only influenced by but also influences G, E and M.