17 E. Kovács K. Tempfli A. Shannon P. Zenke Á. Maróti-Agóts L. Sáfár Á. Bali Papp A. Gáspárdy Journal of Animal and Plant Sciences JAPS 20192019/02/01 29 1 41-47 1018-7081 N/A <p>The population structure of the endangered Cikta sheep breed was evaluated by means of nine microsatellite polymorphisms. Seventy-two individuals from three flocks were sampled to determine genetic indices in the Hungarian population. Overall, average observed and effective allele numbers were 5.63 and 3.76, respectively. Discriminant analysis based on genotype frequencies revealed moderate genetic diversity among Cikta flocks, since only three loci (<em>OarCP49</em>,&nbsp;<em>CSSM47</em>&nbsp;and&nbsp;<em>OarHH41</em>) contributed significantly (P&lt;0.05) to differences between subpopulations. Low squared Mahalanobis distances from group centroids also confirmed that the breed is almost equally represented by the three flocks. Moderate level of diversity between flocks was attributed to the long-term effects of a population bottleneck dating back to the 1970s. Negative average FIS value (-0.18) indicated heterozygote excess. Chi-squared tests identified significant (P&lt;0.05) deviation from HWE in the case of&nbsp;<em>BM8125</em>,&nbsp;<em>CSSM47</em>, and<em>&nbsp;MAF214</em>&nbsp;markers<em>.</em> Continuous microsatellite information is required for the preservation of rare alleles and diversity in Cikta sheep.</p> Cikta sheep; microsatellite; indigenous; population structure Pakistan Agricultural Scientists Forum https://thejaps.org.pk/AbstractView.aspx?mid=AS-17-0211