On Hadamard and Kronecker products in covariance structures for genotype × environment interaction

When including genotype × environment interactions (G × E) in genomic prediction models, Hadamard or Kronecker products have been used to model the covariance structure of interactions. The relation between these two types of modeling has not been made clear in genomic prediction literature. Here, we demonstrate that a certain model based on a Hadamard formulation and another using the Kronecker product lead to exactly the same statistical model. Moreover, we illustrate how a multiplication of entries of covariance matrices is related to modeling locus × environmental-variable interactions explicitly. Finally, we use a wheat and a maize data set to illustrate that the environmental covariance E can be specified easily, also if no information on environmental variables – such as temperature or precipitation – is available. Given that lines have been tested in different environments, the corresponding environmental covariance can simply be estimated from the training set as phenotypic covariance between environments. To achieve a high level of increase in predictive ability, the environmental covariance has to be defined appropriately and records on the performance of the lines of the test set under different environmental conditions have to be included in the training set.