Genetic diversity in Iranian indigenous sheep vis‐à‐vis selected exogenous sheep breeds and wild mouflon

Summary The heterogeneity of climate and different agro‐ecological conditions in Iran have resulted in development of 27 indigenous sheep breeds. Wild Asiatic mouflon ( Ovis orientalis ) is believed to be the ancestor of Iranian sheep. Evaluation of genetic diversity and population structure within and among domestic breeds has important implications for animal breeding programs and genetic resources management. Based on 50K SNP genotype data, we studied the genetic diversity of five indigenous Iranian sheep breeds: Afshari ( n = 37), Moghani ( n = 34), Qezel ( n = 35), Zel ( n = 46) and Lori‐Bakhtiari ( n = 46), and Asiatic mouflon ( n = 8) sampled from Iran. Furthermore, genetic diversity and the breed admixture of Iranian sheep were assessed on a larger geographic scale using a reference panel comprising: three indigenous Afghan breeds – Arabi ( n = 15), Balouchi ( n = 15) and Gadik ( n = 15); three indigenous breeds from Turkey and Cyprus – Cyprus Fat Tail ( n = 30), Karakas ( n = 18) and Norduz ( n = 20); and three commercial European breeds – Suffolk ( n = 19), Comisana ( n = 24) and Engadine Red Sheep ( n = 24). The results revealed that the investigated breeds are divided into five genetically distinct clusters according to their geographic origin. Afshari was closest to the local mouflon population and showed signs of mouflon admixture. Qezel was identified as a hybrid sheep breed. Much evidence supported the Afghan breeds being identical. Inbreeding values, which were estimated based on ROHs, were highest for Suffolk ( F ROH = 0.0544 ) and lowest for Balouchi ( F ROH = 0.0078 ). In conclusion, analysis of selected breeds from neighboring countries along with Asiatic mouflon gave a deeper insight into the evolutionary history and origin of Iranian sheep with important implications for future breed management.