In present study, genetic diversity of domestic and wild Iranian sheep and goats were evaluated using inbreeding coefficients (FGRM, FHOM and FROH), linkage disequilibrium (LD), and effective population size (Ne). Genomic data of Iranian sheep and goat species were obtained from the NEXTGEN project. Animals consisted of 20 domestic sheep (Ovis aries), 14 wild sheep (Ovis orientalis), 20 domestic goats (Capra hircus) and 18 wild goats (Capra aegagrus). Mutations equivalent to the IlluminaSNPchip50K were extracted to study mutations for each animal. Based on FGRM, FHOM and FROH, higher rates of inbreeding were observed in wild species than domestic species. Wild sheep had the highest rate of inbreeding among studied populations. Our results showed a decreasing in LD with increasing in distance between pairs of SNPs so that the average LD in short distance was in the range of 0.11-0.12, and in long distance was in the range of 0.091-0.093. The analysis of LD also demonstrated higher genetic diversity in domestic sheep and goat than wild species and wild sheep had the lowest genetic diversity among studied populations. The results indicated that Ne in 13 generations ago was higher in domestic species compared to wild species. In general, present results revealed that wild species had lower genetic diversity compared to the domestic species in Iran. Meanwhile, wild sheep population is in critical conditions from genetic diversity point of view and required more attention. Designing appropriate breeding programs to improve genetic diversity in wild species, especially in wild sheep in Iran is necessary to protect them from extinction.

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