Microsatellite-based genetic diversity and population structure of local goat breeds in Cyprus

This study investigated the genetic diversity of three economically important goat breeds, Damascus, Pisuri, and Mahari, from Cyprus, utilizing 20 heterologous microsatellite loci. A total of 200 alleles were detected, averaging 10 alleles per locus. Damascus showed the highest genetic diversity (Na = 8.5), followed by Pisuri and Mahari (Na = 8.3). The effective number of alleles ranged from 2.589 (INRA005) to 8.891 (HSC), and Polymorphic Information Content (PIC) values (0.55-0.86) confirmed high polymorphism across loci. Observed (H_O) and expected (H_E) heterozygosities ranged from 0.4118 to 0.9574 and 0.4890 to 0.9016, respectively, with Pisuri displaying the highest genetic diversity. The mean inbreeding coefficient (F_IS = 0.061) indicated moderate inbreeding. Genetic differentiation was low to moderate (F_ST = 0.0068-0.1298), with Damascus being the most distinct population. STRUCTURE and factorial analyses supported the presence of three genetic clusters, clearly separating Damascus from Pisuri and Mahari. Despite minor deviations from Hardy-Weinberg equilibrium, the overall results revealed limited differentiation and high genetic diversity, particularly in Damascus. These findings provide valuable insights into the genetic composition of Cyprus goat breeds and highlight their importance for conservation and selective breeding strategies.