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The main effects of an environmental factor will be included in the model as fixed effects and the GE interaction effects will be treated as random effects. NOTE: the design matrix of the overall mean in the model (which is a vector of all ones) is always a linear combination of the design matrix of a discrete environmental factor so that not all the main effects (fixed effects) are estimable.
GCTA will always constrain the main effect of the first level to be zero and the main effect of any other level represents its difference in effect compared to the first level. For example, if you fit sex as an environmental factor, GCTA will fit only one main effect in the model, i.
the mean difference between males and females.