Context. Maize (Zea mays L.) is one of the most economically important plants of the cereal family; it has value as human food, livestock feed, and as a component of industrial products.

Aims. This study focused on genetic diversity and existence of genetic divergence among promising maize inbred lines in Iran.

Methods. A commercial maize 600K SNP (single-nucleotide polymorphism) array was used to inspect genetic variability among 93 maize inbred lines.

Key results. The rate of transition mutation was twice as high as transversion mutation, and the density of detected SNPs was greater close to telomere regions of maize chromosomes. Considering the fluctuation of observed, expected and total heterozygosity and fixation index values across maize chromosomes, as well as polymorphism information content values, there is a high level of genetic variability among the studied maize panel. In addition, discriminant analysis of the principal components revealed four subpopulations in which the subpopulation ‘Line’ was distinct from other subpopulations and had no genomic overlap with them. Selection signature analysis revealed 177 regions harbouring 75 genes that differentiate among subgroups. Detected genes had a role in the mitogen-activated protein kinase signalling pathway, spliceosome, protein processing in endoplasmic reticulum, and hormone signal transduction.

Conclusions. We conclude that remarkable genetic diversity and differentiation exists among the studied maize subpopulations. The most differentiated SNPs among the subpopulations were associated with important biological processing genes and pathways.

Implications. The findings provide valuable insights for future maize breeding programs through exploitation of heterosis, as well as marker-assisted selection.