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Background  Sheep were among the first animals to be domesticated. They are raised all over the world and produce a major scale of animal-based protein for human consumption and play an important role in agricultural economy. Iran is one of the important locations for sheep genetic resources in the world. Here, we compared the Illumina Ovine SNP50 BeadChip data of three Iranian local breeds (Moghani, Afshari and Gezel), as a population that does not undergone artificial breeding programs as yet, and five other sheep breeds namely East Friesian white, East Friesian brown, Lacaune, DorsetHorn and Texel to detect genetic mechanisms underlying economical traits and daptation to harsh environments in sheep.    Results  To identify genomic regions that have been targeted by positive selection, we used fixation index (Fst) and nucleotide diversity (Pi) statistics. Further analysis indicated candidate genes involved in different important traits such as; wool production included crimp of wool ( PTPN3, NBEA  and  KRTAP20–2  genes), fiber diameter ( PIK3R4  gene), hair follicle development ( LHX2  gene), the growth and development of fiber ( COL17A1  gene)), adaptation to hot arid environments ( CORIN  gene), adaptive in deficit water status ( CPQ  gene), heat stress ( PLCB4, FAM107B, NBEA, PIK3C2B  and  USP43  genes) in sheep.    Conclusions  We detected several candidate genes related to wool production traits and adaptation to hot arid environments in sheep that can be applicable for inbreeding goals. Our findings not only include the results of previous researches, but also identify a number of novel candidate genes related to studied traits. However, more works will be essential to acknowledge phenotype- genotype relationships of the identified genes in our study.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12917-021-03077-4.

Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds