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The aim of this study was to investigate the genetic diversity and structurein three Iranian native goat breeds (Markhoz, Mahabadi and Lori) and the Beetalimported breed using inter-simple sequence repeat (ISSR) markers and also to investigate ISSRmarkers' potential in order to genetically separate single (S) and twin-birth (T)subpopulations. Blood samples were collected from 210 animals for thispurpose. In total, 16 primers were used, and finally 5 primers were selectedbased on the number of clear bands and the level of polymorphisms. The result of thisstudy showed that 76 of 86 observed fragments were polymorphic.Genetic diversity for each breed ranged from 0.23 in the Beetal breed to 0.26in the Markhoz breed; this represents a relatively similar genetic diversity in thesebreeds. An unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on the Nei's standard genetic distancebetween the breeds studied showed that three Iranian goat breeds (Mahabadi, Lori and Markhoz) were clustered closer together, while the Beetalbreed formed a separate cluster. In the constructed dendrogram of the subpopulations, the S and T subpopulations of each breed were clusteredtogether. The constructed dendrogram of the Beetal breed and the S and Tsubpopulations of all breeds studied showed a separate cluster for the Beetal breedas an imported breed and another cluster for the S and T subpopulations asIranian native breeds. The current study showed that the ISSR markers studied hadno potential to genetically separate S and T subpopulations. On the otherhand, these ISSR markers can be used for the clustering of distinct populations

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Genetic diversity and distance of Iranian goat breeds (Markhoz, Mahabadi and Lori) compared to the Beetal breed using inter-simple sequence repeat (ISSR) markers