First-time description of MHC diversity in Straight Egyptian Arabian horses using immune-linked microsatellite markers

Understanding the immunogenetic structure of the major histocompatibility complex (MHC) in Arabian horses helps to clarify the population health structure-related phenotypes of this historically influential breed. Straight Egyptian (SE) Arabian horses, which fall under Equus ferus caballus , are of global value but are limited in number, raising concerns about their distribution and the genetic diversity associated with immunity. In this study, we examined 57 Egyptian Arabian horses from two breeding programs: one in Germany (AR-DE) and the other in Qatar (AR-QA). Sixteen polymorphic intra-MHC microsatellite markers were used to cover classes I, II, and III. Population genetic calculations were then performed to determine allelic richness, heterozygosity, fixation indices, and departures from the Hardy–Weinberg equilibrium (HWE) after the fragment length analysis. Despite the small population size, the diversity and allelic richness were remarkable. The range of alleles per locus was 4–12, with a mean of 7.88 in all horses. Observed heterozygosity (Ho) was between 0.070 and 0.860, while the expected heterozygosity (He) was between 0.542 and 0.877, suggestive of heterozygote deficiency at several loci, based on a mean fixation index ( F ) of 0.226. Polymorphism information content (PIC) was from average to highly informative, with a mean of 0.672. When the population was divided into two groups, AR-DE and AR-QA, both showed overlapping genetic patterns. However, in the AR-DE group, a higher mean was observed in Ho (0.604) and a lower mean in F (0.061). In the AR-QA group, there were more genetic loci diverging from HWE, and the shortage was also more evident in the mean F values (0.142). Strong heterozygote deficits in loci such as TKY3324 and CZM004 in both populations likely reflect locus-specific selection or population structure. Overall, the results present statistical evidence of MHC-associated genetic diversity in SE horses that equals or exceeds levels observed in other Arabian horse breeds or in geographically isolated populations. The Ho pattern and HWE deviations indicate possible selection within the MHC and demographic history. This study could provide a firm foundation for the genetic immunology of Egyptian horses and support the wider use of microsatellites to assess histocompatibility diversity in equine populations.