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.