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Frontiers in immunology2026; 17; 1859977; doi: 10.3389/fimmu.2026.1859977

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

Abstract: 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 , 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 () 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 (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 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.
Copyright © 2026 Alkhamees, Cavalleri and Hammer.
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Publication Date: 2026-08-17 PubMed ID: 42676859PubMed Central: PMC13527931DOI: 10.3389/fimmu.2026.1859977Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This study analyzed the genetic diversity of the major histocompatibility complex (MHC), which is important for immune function, in Straight Egyptian Arabian horses using polymorphic microsatellite markers.
  • The research assessed immunogenetic variation in two populations of these horses from Germany and Qatar and found notable allelic richness and heterozygosity, suggesting healthy genetic diversity despite small population sizes.

Background and Importance

  • The major histocompatibility complex (MHC) is a crucial set of genes involved in immune response regulation.
  • Studying MHC diversity helps understand the immune-related genetic health and disease resistance of populations.
  • Straight Egyptian (SE) Arabian horses are a historically significant yet numerically limited breed, making genetic diversity studies important for their conservation and breeding management.
  • Evaluating MHC diversity in these horses provides insights into their immunogenetic structure and population health.

Methods

  • Samples were collected from 57 SE Arabian horses from two breeding populations: one in Germany (AR-DE) and one in Qatar (AR-QA).
  • A total of sixteen microsatellite markers located within the MHC region, covering classes I, II, and III, were analyzed.
  • Fragment length analysis was used to identify allele variants at each microsatellite locus.
  • Population genetic parameters calculated included:
    • Allelic richness (number of alleles per locus)
    • Observed heterozygosity (Ho) – actual frequency of heterozygotes
    • Expected heterozygosity (He) – predicted heterozygosity under Hardy-Weinberg equilibrium
    • Fixation index (F) – indicates heterozygote deficiency or excess
    • Tests for deviations from Hardy-Weinberg Equilibrium (HWE)
    • Polymorphism information content (PIC) – measures marker informativeness

Key Findings

  • Despite the relatively small sample size, there was remarkable genetic diversity in MHC markers among SE Arabian horses.
  • The number of alleles per microsatellite locus ranged from 4 to 12, averaging 7.88.
  • Observed heterozygosity (Ho) varied widely (0.070 to 0.860), while expected heterozygosity (He) was consistently higher (0.542 to 0.877), indicating heterozygote deficiency at some loci.
  • Mean fixation index (F) of 0.226 suggests an overall deficit of heterozygotes in the population.
  • Polymorphism information content had a high average value (0.672), implying the microsatellites used were informative for genetic studies.
  • Both subpopulations (AR-DE and AR-QA) showed overlapping genetic patterns, but:
    • The German group (AR-DE) had higher observed heterozygosity (mean Ho = 0.604) and lower fixation index (mean F = 0.061), indicating less heterozygote deficiency.
    • The Qatar group (AR-QA) showed more loci deviating from HWE and higher mean fixation index (mean F = 0.142), suggesting greater heterozygote deficiency and possible population structure or selection effects.
  • Two loci, TKY3324 and CZM004, showed strong heterozygote deficits in both populations, possibly due to locus-specific natural selection or demographic effects.
  • Overall, MHC diversity in SE Arabian horses matches or exceeds that observed in other Arabian horse breeds or isolated equine populations.

Interpretation and Implications

  • High allelic richness and heterozygosity are indicators of good genetic health and immune competence within the SE Arabian breed despite population limitations.
  • Heterozygote deficiencies and deviations from Hardy-Weinberg equilibrium suggest the influence of natural selection, breeding practices, or population bottlenecks on genetic variation.
  • The patterns observed could reflect past demographic events and ongoing selection pressures acting on the immune gene complex.
  • This study provides the first comprehensive genetic immunology baseline for this Egyptian breed’s MHC diversity.
  • The findings support the utility of immune-linked microsatellite markers in equine population genetics and can guide conservation or breeding programs aimed at maintaining immune diversity.
  • Future research could expand sample sizes or include additional markers to refine understanding of selection and demographic history impacting MHC diversity.

Conclusion

  • The research successfully documented and quantified MHC-linked genetic diversity in Straight Egyptian Arabian horses for the first time.
  • The two geographically separated breeding populations show substantial immune-related genetic variation with some signs of selection or population structure.
  • These insights are critical for genetic management and conservation efforts to maintain the health and resilience of this valuable horse breed.

Cite This Article

APA
Alkhamees ASA, Cavalleri JV, Hammer SE. (2026). First-time description of MHC diversity in Straight Egyptian Arabian horses using immune-linked microsatellite markers. Front Immunol, 17, 1859977. https://doi.org/10.3389/fimmu.2026.1859977

Publication

Frontiers in immunology
ISSN: 1664-3224
NlmUniqueID: 101560960
Country: Switzerland
Language: English
Volume: 17
Pages: 1859977
PII: 1859977

Researcher Affiliations

Alkhamees, Abdullah Saleh A
  • Immunology Unit, Centre of Pathobiology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria.
Cavalleri, Jessika-M V
  • Equine Internal Medicine, Clinical Centre for Equine Health and Research, Clinical Department of Small Animals and Horses, University of Veterinary Medicine Vienna, Vienna, Austria.
Hammer, Sabine E
  • Immunology Unit, Centre of Pathobiology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria.

MeSH Terms

  • Animals
  • Microsatellite Repeats / genetics
  • Horses / genetics
  • Horses / immunology
  • Major Histocompatibility Complex / genetics
  • Genetic Variation
  • Alleles
  • Gene Frequency
  • Heterozygote
  • Breeding
  • Egypt
  • Polymorphism, Genetic

Conflict of Interest Statement

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author SEH declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

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