Population Structure and Genetic Diversity Among Shagya Arabian Horse Genealogical Lineages in Bulgaria Based on Microsatellite Genotyping

The Shagya Arabian horse breed was created to address the need of Imperial Hussars (Hungarian light horsemen) for a horse with the intelligence, essential characteristics, and endurance of the Arabian breed, but also of a bigger size and having a better weight-carrying capacity and jumping ability. The present study aimed to explore the genetic variability and population structure of the uninvestigated Shagya Arabian horse population in Bulgaria based on genotyping at 15 equine microsatellite markers. A total of 140 horses belonging to six genealogical lines (Dahoman, Gazal, Ibrahim, Kuhailan Zaid, O’Bajan, and Shagya) were included in the survey. Genetic distances, analysis of molecular variance, principal coordinates analysis, and a Bayesian method were applied. The mean number of alleles in the individual subpopulations ranged from 3.67 in the Shagya to 5.13 in the Ibrahim sire line. The FIS index was negative or close to 0 for the entire population and was −0.202. The overall FST was 0.014, indicating a low level of genetic differentiation between the subpopulations. The results of the principal components and the STRUCTURE analysis showed some level of admixture among the subpopulations in almost all genealogical lines. However, structural analysis also indicated a genetic similarity between the Ibrahim, Kuhailan Zaid, and Shagya lineages, while it showed a completely different genetic profile regarding the other three sire lines. Due to the higher admixture and the discovery of more distinct genetic clusters, it can be assumed that there is a higher gene flow from one lineage to another in the Shagya Arabian horse population in Bulgaria and that there is sufficient genetic variability and diversity to suggest adequate measures for preserving this rare breed. In addition, this study may highlight the risk of the loss of gene diversity in this population and help to implement suitable breeding programs to preserve genetic diversity.