REGULAR ARTICLES Genetic structure of Iranian indigenous sheep breeds: insights for conservation Otsanda Ruiz-Larrañaga 1 & Hojjat Asadollahpour Nanaei 2 & Iratxe Montes 1 & Ahmad Ayatollahi Mehrgardi 2 & Alireza Abdolmohammadi 3 & Hamed Kharrati-Koopaee 4 & Saeed S. Sohrabi 2 & Fernando Rendo 5 & Carmen Manzano 1 & Andone Estonba 1 & Mikel Iriondo 1 & Ali Esmailizadeh 2 Received: 12 August 2019 /Accepted: 27 February 2020 # Springer Nature B.V. 2020 Abstract Genetic structure and genetic diversity levels of indigenous Iranian sheep breeds are not clear, despite the interest this region has in itself as an important center for domestication of livestock. Early population genetic studies have reported high levels of diversity among Iranian sheep breeds until recently, when high admixture levels and genetic homogeneity have been detected. The rapid reduction of diversity observed in Iranian breeds might be due to an increasing trend of intensive crossbreeding practices or even total replacement of native breeds by highly specialized and productive ones. From a conservative perspective, this situation is highly concerning; thus, it might be wise to consider a conservation program in Iran to preserve the original genetic diversity in native sheep breeds. In this study, a total of 1065 animals with the purest morphological features representing 24 Iranian indigenous sheep breeds were sampled, corresponding to ancestral breed diversity. These samples were genotyped for 17 microsatellite loci in order to (1) determine the native ancestral diversity of Iranian breeds, (2) define the degree of genetic relationship among studied breeds, and (3) assess conservation priorities among defined groups. Our results showed no recent loss of diversity, but high genetic diversity levels for indigenous sheep breeds in Iran. Indeed, the analysis of conservation priorities pointed out the importance of 8 breeds for maintaining Iranian sheep breeds’ maximum genetic diversity. Thus, under a genetic perspective, these 8 breeds should be the ones included into conservation programs for restocking endangered areas. Keywords Iranian sheep . Breeding . Genetic structure . Conservation . Genetic diversity Introduction Domestication of sheep (Ovis aries) was likely initiated 11,000 years ago in the Fertile Crescent, between the northern Zagros in Iran and southeastern Anatolia in Turkey (Zeder 2008). Since domestication, sheep widely extended their distribution range, due to their adaptability to poor nutrition diets, tolerance to extreme climatic con- ditions, and manageable size (Kijas et al. 2009). Such extension in the distribution range led to partial reproduc- tive isolation started due to geographical isolation and followed by breeders’ selective process. As a consequence of this isolation and selection, native breeds evolved in- dependently and their genetic differentiation started, giv- ing rise to the huge variety of sheep breeds we can find nowadays. Consequently, indigenous breeds have specific adaptive traits (e.g., heat tolerance) as a result of evolu- tionary history under local environmental pressures (Soma et al. 2012). Otsanda Ruiz-Larrañaga and Hojjat Asadollahpour Nanaei contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11250-020-02252-3) contains supplementary material, which is available to authorized users. * Ali Esmailizadeh aliesmaili@uk.ac.ir 1 Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), c/Barrio Sarriena s/n, E-48940 Leioa, Biscay, Spain 2 Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman PB 76169-133, Iran 3 Department of Animal Science, Campus of Agriculture and Natural Resources, Razi University, Kermanshah, Iran 4 Institute of Biotechnology, Shiraz University, Shiraz, Iran 5 Sequencing and Genotyping Unit, Genomics and Proteomics Facilities of Advanced Research Facilities (SGIker), Faculty of Science and Technology, University of the Basque Country (UPV/ EHU), c/Barrio Sarriena s/n, E-48940 Leioa, Biscay, Spain Tropical Animal Health and Production https://doi.org/10.1007/s11250-020-02252-3