Genetic diversity of Greek sheep breeds and transhumant populations utilizing microsatellite markers

•We study the genetic variation in 13 local sheep breeds and three transhumant populations in Greece.•The genetic differentiation of the native breeds is low indicating admixture.•However, there is evidence for isolation of some breeds.•The differentiation of the transhumant populations is very low due to uncontrolled crossbreeding between them and with native breeds as well.•Utilization of many different local breeds for breeding purposes of the transhumant populations.

Genetic variation in 13 local sheep breeds, raised in different regions of Greece, was assessed using 10 polymorphic microsatellite markers and was compared with that of three transhumant populations from the Greek Prefectures of Epirus, Sterea Ellada and Thessaly. The total number of alleles per marker ranged from 8 to 32 alleles, and transhumant samples exhibited higher values for allelic number, observed/expected heterozygosity and allelic richness than the local ones. Estimates of inbreeding coefficient (FIS) were significant only in the transhumant population of Epirus (*P < 0.05). The genetic differentiation of the native breeds was low (FST = 4.9%), indicating admixture, though all analyses provided clear evidence for the isolation of Thraki and Sarakatsaniko breeds. Differentiation of the three transhumant populations was much lower (FST = 0.2%), indicating a high rate of gene flow between them. The admixture analysis, using Bayesian methods, suggested that many different local breeds have been used for breeding purposes in each of the three transhumant populations. Among the breeds with high proportion of membership to transhumant farming was Karagouniko which, as already known from literature, is used for the upgrading of numerous sheep populations in Greece.