This dataset corresponds to the data and code associated to the study: "Improving genomic predictions with inbreeding and non-additive effects in two admixed maize hybrid populations in single and multi-environment contexts" by Roth et al. submitted in 2021. The data includes raw genotypic and phenotypic information for two panels called heterosis#2 (Het2) and iF2 constituted of respectively 291 and 265 maize admixed hybrids generated by mating dent and flint lines. Grain yield, flowering time, plant height and grain moisture were measured in 3 to 5 environments. The R code used to run variance decompositions and genomic predictions presented in the results was also included to this dataset. The file number for these .R files gives the order in which the data were loaded and the analyses were performed.