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Genes2026; 17(10); 1292; doi: 10.3390/genes17101292

The Western Ecotype of the Kazakh Horse: Current Status and Genomic Characterisation.

Abstract: The Kazakh horse comprises several locally adapted types and ecotypes of the Eurasian Steppe. The Adai is its western ecotype, kept year-round on desert pasture in Mangystau, Western Kazakhstan, and recognised as a separate breed in 2024 without genetic evaluation. We asked whether that label corresponds to a genetic unit and whether the population has remained closed. We genotyped 533 horses recorded as Adai, 500 traced to five farms in Mangystau, against 988 reference horses of 45 breeds on 36,193 shared autosomal SNPs. Structure was assessed by principal component analysis, pairwise with block-jackknife intervals, neighbour-joining trees and cross-validated individual assignment; introgression per animal by an statistic against an empirical null of 223 reference-steppe horses, with the ancestry scale calibrated on 1800 simulated crosses built from real genotypes; and eight body measurements were modelled within farms. The Adai was not separable from the Central Asian steppe complex as a population: pairwise was 0.004-0.008 against Tuva, Yili, Sanhe and Mongolian horses, and two Adai farms differed from each other as much as an Adai farm differed from a reference-steppe breed. Individual assignment was nonetheless accurate against those breeds (86-100% pairwise), but the same classifier separated two herds of Adai at 69-85%, so assignment accuracy on thousands of markers tracks marker number rather than breed identity. Against the empirical null, 15.6% of Adai exceeded the 95th percentile and twelve exceeded the maximum. The estimator carries a floor of 3.7 percentage points on an unadmixed Adai; on the calibrated scale, 9.6% of animals reached the ancestry expected from one Thoroughbred great-grandparent and 4.2% that expected from one grandparent (15.8% and 4.6% uncalibrated). Introgression was concentrated: one farm carried 42% of its horses at a great-grandparent equivalent or more against 0-9% at the other four, a difference that survived every analysis accounting for family structure. Ancestry showed no within-farm association with any of eight body measurements, with or without age in the model. The Adai is not a differentiated population but part of a continuous steppe complex, and carries undocumented ancestry of Thoroughbred affinity concentrated in particular holdings. As managed, it cannot be certified from a document or a phenotype. Genomic verification at registration is a plausible instrument, but the marker panel it would require was not developed or validated here.
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Publication Date: 2026-10-16 PubMed ID: 42938408PubMed Central: PMC13704455DOI: 10.3390/genes17101292Google 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 investigates whether the Adai, the western ecotype of the Kazakh horse, represents a genetically distinct breed and examines its genetic makeup and population structure.
  • The researchers used genomic data and physical measurements to evaluate the genetic differentiation, introgression, and distinctness of the Adai horse population in Western Kazakhstan.

Background and Objectives

  • The Kazakh horse has several ecotypes adapted to different regions of the Eurasian Steppe; the Adai is the western ecotype primarily found in Mangystau, Western Kazakhstan.
  • In 2024, the Adai was officially recognized as a separate breed, but this recognition had not yet been supported by genetic data.
  • The study aimed to determine:
    • If the Adai forms a genetically distinct population or breed.
    • Whether the population has remained genetically closed or if there has been introgression (gene flow) from other breeds, particularly Thoroughbreds.

Methods

  • Genotyping was performed on 533 Adai horses, of which 500 came from five farms in Mangystau.
  • Genotypes were compared with 988 horses from 45 other breeds, looking at 36,193 shared autosomal single nucleotide polymorphisms (SNPs).
  • Population structure was assessed using:
    • Principal component analysis (PCA) to visualize genetic similarity and differences.
    • Pairwise Fst values with block-jackknife intervals to estimate genetic differentiation.
    • Neighbour-joining trees to illustrate genetic relationships.
    • Cross-validated individual assignment methods to test how well horses could be classified into groups/breeds.
  • Introgression was estimated per individual using a statistic comparing the data to an empirical null distribution derived from 223 steppe horses.
  • Simulations of crosses were used to calibrate ancestry estimates against known pedigree scenarios (e.g., introgression equivalent to one Thoroughbred grandparent or great-grandparent).
  • Eight body measurements were taken for horses within farms and modeled to examine any associations with ancestry.

Key Findings

  • Genetic differentiation:
    • The Adai horses were genetically very similar to the broader Central Asian steppe horse complex, specifically breeds like Tuva, Yili, Sanhe, and Mongolian horses.
    • Pairwise Fst ranged from 0.004 to 0.008, indicating very low genetic differentiation.
    • Differences between two Adai farms were as large as differences between an Adai farm and an unrelated steppe breed, suggesting internal genetic variability within the Adai population.
  • Population assignment:
    • Individual horses could be assigned accurately to the Adai versus other breeds (86-100% accuracy), but distinguishing between herds within the Adai population was more challenging (69-85% accuracy).
    • This indicates that the accuracy of classification depends more on the number of genetic markers than on true genetic breed identity.
  • Introgression results:
    • About 15.6% of Adai horses showed evidence of introgression exceeding the 95th percentile among steppe horses; twelve individuals had values higher than any in the reference group.
    • Introgression was attributed to Thoroughbred ancestry and estimated on a calibrated scale to reflect ancestry equivalents of one great-grandparent (around 9.6% of animals) or one grandparent (4.2%).
    • Introgression was not evenly spread: one farm had 42% of horses with substantial introgressed ancestry, while the other four farms had only 0-9%.
  • Phenotypic associations:
    • There was no significant association between Thoroughbred introgression levels and any of the eight body measurements, regardless of accounting for age.

Conclusions and Implications

  • The Adai does not constitute a genetically differentiated or isolated population but forms part of a continuous steppe horse gene pool across Central Asia.
  • The recognition of Adai as a separate breed is not supported by clear genetic boundaries, as gene flow and similarity to other steppe horses remain high.
  • The population contains undocumented Thoroughbred genetic introgression, mainly concentrated on specific farms.
  • Due to overlapping genetic identity and lack of distinct phenotype markers, official breed certification for Adai cannot rely solely on physical traits or pedigree documentation.
  • Genomic testing could potentially be used for breed verification and management to ensure population integrity.
  • However, a specific marker panel optimized for Adai breed verification was not developed or validated in this study, indicating the need for further genomic tool development.

Cite This Article

APA
Yanin K, Kanat R, Zhambakin K, Ulyanova T, Beishova I, Kovalchuk A, Shamshidin A, Shamekova M. (2026). The Western Ecotype of the Kazakh Horse: Current Status and Genomic Characterisation. Genes (Basel), 17(10), 1292. https://doi.org/10.3390/genes17101292

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 17
Issue: 10
PII: 1292

Researcher Affiliations

Yanin, Kirill
  • Tanir Research Laboratory, Almaty 050010, Kazakhstan.
  • Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan.
Kanat, Rakhim
  • Tanir Research Laboratory, Almaty 050010, Kazakhstan.
  • Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan.
Zhambakin, Kabyl
  • Tanir Research Laboratory, Almaty 050010, Kazakhstan.
  • Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan.
Ulyanova, Tatyana
  • Zhangir Khan West Kazakhstan Agrarian Technical University, Oral 090009, Kazakhstan.
Beishova, Indira
  • Zhangir Khan West Kazakhstan Agrarian Technical University, Oral 090009, Kazakhstan.
Kovalchuk, Alexandr
  • Zhangir Khan West Kazakhstan Agrarian Technical University, Oral 090009, Kazakhstan.
Shamshidin, Alzhan
  • Zhangir Khan West Kazakhstan Agrarian Technical University, Oral 090009, Kazakhstan.
Shamekova, Malika
  • Tanir Research Laboratory, Almaty 050010, Kazakhstan.
  • Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan.

MeSH Terms

  • Animals
  • Horses / genetics
  • Horses / classification
  • Polymorphism, Single Nucleotide
  • Ecotype
  • Genotype
  • Breeding
  • Genomics / methods
  • Kazakhstan
  • Genome

Grant Funding

  • BR22887106 / the Ministry of Agriculture of the Republic of Kazakhstan
  • AP22782840 / the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan

Conflict of Interest Statement

The authors declare no conflicts of interest.

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