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Animals : an open access journal from MDPI2025; 15(18); 2690; doi: 10.3390/ani15182690

Analysis of Genetic Diversity and Race Genetic Structure of Major Horse Breeds in Xinjiang, China.

Abstract: The study of horse genetic diversity is imperative for informing conservation strategies, safeguarding ancestral lineages, and enhancing breed adaptability to environmental and disease pressures. This study employed 13 microsatellite markers with fluorescent-labeled capillary electrophoresis to analyze the genetic diversity of the Kyrgyz horse ( = 30) and Barkol horse ( = 30) for the first time, comparing them with three other indigenous horse breeds ( = 30 per breed) from Xinjiang, China. A total of 208 alleles were detected. The Polymorphic Information Content (PIC) results from GenAlEx 6.5115 show that all loci, except for the HTG06 locus in the Yanqi horse races, were highly polymorphic (PIC > 0.5), indicating a high level of genetic diversity across the five races. Among the five races, the Kyrgyz horse exhibited the lowest mean values for the effective number of alleles (Ne), observed heterozygosity (Ho), and expected heterozygosity (He), which were 6.025, 0.737, and 0.810, respectively. In contrast, the Barkol horse showed the highest mean number of alleles (Na), Ne, and He values, at 11.308, 6.330, and 0.816, respectively. Principal Coordinate Analysis (PCoA), performed using GenAlEx 6.5115, revealed the smallest genetic distance between the Kyrgyz and Yanqi horse breeds. Combined with phylogenetic tree and clustering analysis results, this supports the hypothesis that the two breeds share a common origin. This study offers valuable scientific insights for conserving and utilizing the genetic resources of indigenous Xinjiang horse breeds, specifically the Kyrgyz and Barkol horses.
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Publication Date: 2025-09-14 PubMed ID: 41007935PubMed Central: PMC12466770DOI: 10.3390/ani15182690Google 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 research analyzed the genetic diversity and population structure of five major indigenous horse breeds in Xinjiang, China, focusing on the Kyrgyz and Barkol horses for the first time.
  • The study used microsatellite markers to measure genetic variation, providing insights to support conservation and breed management efforts.

Introduction and Purpose

  • Genetic diversity in horses is crucial for effective conservation strategies, preserving ancestral lineages, and improving their adaptability to environmental changes and disease.
  • The study aimed to assess the genetic diversity of the Kyrgyz and Barkol horse breeds, along with three other indigenous breeds in Xinjiang, expanding knowledge on their genetic makeup.

Methods

  • A total of five horse breeds were studied: Kyrgyz horse, Barkol horse, and three other indigenous breeds (each sampled with 30 individuals).
  • Thirteen microsatellite markers were used for genotyping, utilizing fluorescently labeled capillary electrophoresis to detect genetic variation.
  • GenAlEx 6.5115 software was employed for analyzing genetic diversity parameters and performing Principal Coordinate Analysis (PCoA).

Genetic Diversity Findings

  • A total of 208 alleles were detected across the 13 loci, indicating considerable genetic variation among the studied horse breeds.
  • Polymorphic Information Content (PIC) values were greater than 0.5 for almost all loci, revealing highly polymorphic markers indicative of rich genetic diversity.
  • Exception: The HTG06 locus in the Yanqi horse showed lower polymorphism but did not significantly affect overall diversity conclusions.

Breed-Specific Diversity Measures

  • The Kyrgyz horse exhibited the lowest genetic diversity among the breeds with:
    • Effective number of alleles (Ne) = 6.025
    • Observed heterozygosity (Ho) = 0.737
    • Expected heterozygosity (He) = 0.810
  • The Barkol horse showed the highest genetic diversity with:
    • Mean number of alleles (Na) = 11.308
    • Effective number of alleles (Ne) = 6.330
    • Expected heterozygosity (He) = 0.816

Population Structure and Genetic Relationship

  • Principal Coordinate Analysis (PCoA) demonstrated the smallest genetic distance between the Kyrgyz and Yanqi horse breeds.
  • Phylogenetic tree and clustering analyses further supported the close genetic relationship and likely common origin of these two breeds.

Implications and Conclusions

  • The study provides essential baseline data for conserving genetic resources of Xinjiang’s indigenous horses, which is vital for sustainable breed management.
  • Understanding genetic diversity differences, such as between the Kyrgyz and Barkol horses, helps target conservation priorities effectively.
  • Identifying shared origins among breeds can inform breeding programs to maintain genetic integrity and promote healthy breed populations.

Cite This Article

APA
Hou L, Sulayman A, Zeng Y, Zhou L, Aimaier A, Kader A, Shi L. (2025). Analysis of Genetic Diversity and Race Genetic Structure of Major Horse Breeds in Xinjiang, China. Animals (Basel), 15(18), 2690. https://doi.org/10.3390/ani15182690

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 18
PII: 2690

Researcher Affiliations

Hou, Linlang
  • Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organism, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China.
Sulayman, Ablat
  • Institute of Animal Husbandry, Xinjiang Academy of Animal Science, Urumqi 830011, China.
Zeng, Yaqi
  • Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, College of Animal Sciences, Xinjiang Agricultural University, Urumqi 830052, China.
Zhou, Lu
  • Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organism, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China.
Aimaier, Ainiwan
  • Pratacultural Research Institute, Xinjiang Academy of Animal Science, Urumqi 830011, China.
Kader, Adiljan
  • Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organism, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China.
Shi, Lei
  • Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organism, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China.

Grant Funding

  • 2022D01A168 / Natural Science Foundation of Xinjiang Uygur Autonomous Region
  • 3226040101 / National Natural Science Foundation of China

Conflict of Interest Statement

The authors declare no conflicts of interest.

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