Single-step genome-wide association study and candidate genes networks affecting reproductive traits in Iranian Holstein cattle

•De-regressed proofs were used as pseudo phenotypes in ssGWAS analysis. A bull's published estimated breeding value is a weighted mean of his daughter's deviations and his parental average.•We identified a total of 196 genes which were located within or nearby 33 SNPs significantly associated with reproductive traits in Holstein cattle.•In total, 47 biological process terms showed significant associations with reproductive traits (FDR < 0.05).•The network analysis using K-means clustering algorithm divided the genes in three clusters.•Population stratification was observed which could be due to the existence of different genotypes from different companies and systematic differences in allelic frequencies between subpopulations and non-random mating within populations.