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Animals : an open access journal from MDPI2025; 15(18); 2667; doi: 10.3390/ani15182667

Uncovering Genetic Diversity and Adaptive Candidate Genes in the Mugalzhar Horse Breed Using Whole-Genome Sequencing Data.

Abstract: Mugalzhar horses are a relatively young native breed of Kazakhstan, prized for meat and milk production and adaptation. This study was conducted to investigate genetic diversity and pinpoint genomic regions associated with selection signatures in this breed using whole-genome sequence data. Variant calling yielded a total of 21,722,393 high-quality variants, including 19,495,163 SNPs and 2,227,230 indels. Most variants were located in introns and intergenic regions, while only 1.94% were exonic. Estimates of genetic diversity were moderate, with expected and observed heterozygosity and nucleotide diversity of 0.2325, 0.2402, and 0.0021, respectively. We identified nine adaptive candidate genes (, , , , , , , , and ), harboring high-impact exonic variants in the homozygote state for an alternative allele. No deleterious segregating variants associated with Mendelian traits were found in this population, while seven variants linked to coat color and gaitedness were detected in a low frequency heterozygous state. Our findings suggest that there are certain genomic regions subjected to ancient selection footprints during the ancestor breed formation and adaptation. The outcome of this study serves as a foundation for future genomic-driven strategies, a broader utilization of this breed, and a reference for genomic studies on other horse breeds.
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Publication Date: 2025-09-11 PubMed ID: 41007912PubMed Central: PMC12466398DOI: 10.3390/ani15182667Google 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 and identified key adaptive genes in the Mugalzhar horse breed from Kazakhstan using whole-genome sequencing data.
  • The research highlighted specific genomic regions influenced by historical selection and provided insights that support future breeding and genomic research efforts.

Background and Objective

  • The Mugalzhar horse is a relatively new native breed from Kazakhstan, valued for meat, milk production, and environmental adaptation.
  • The study aimed to examine the genetic diversity of this breed and discover genomic regions under selection that are linked to its adaptation traits.
  • Whole-genome sequencing was used as the primary method to comprehensively survey genetic variations.

Methods

  • Whole-genome sequencing data was collected and variant calling performed to identify genomic variants.
  • A total of approximately 21.7 million high-quality variants were detected, including:
    • ~19.5 million single nucleotide polymorphisms (SNPs)
    • ~2.2 million insertions and deletions (indels)
  • Variants were categorized based on their location within the genome (introns, intergenic, exonic).
  • Estimates of genetic diversity were calculated using metrics such as expected heterozygosity, observed heterozygosity, and nucleotide diversity.
  • Adaptive candidate genes were identified based on the presence of high-impact exonic variants that were homozygous for the alternative allele.
  • Variants linked to Mendelian traits, coat color, and gaitedness were also investigated.

Key Findings

  • Genetic variant distribution:
    • The majority of variants were located in non-coding regions: introns and intergenic sequences.
    • Only 1.94% of variants were found in exonic (protein-coding) regions.
  • Genetic diversity metrics indicated moderate heterozygosity and nucleotide diversity:
    • Expected heterozygosity: 0.2325
    • Observed heterozygosity: 0.2402
    • Nucleotide diversity: 0.0021
  • Identification of nine adaptive candidate genes containing high-impact homozygous exonic variants suggestive of functional importance related to adaptation.
  • No variants with deleterious effects or associated with Mendelian inherited disorders were found in the population.
  • Seven low-frequency heterozygous variants related to coat color and gait (movement patterns in horses) were detected.
  • Some genomic regions appear to carry ancient selection footprints from ancestor breeds, supporting the breed’s formation and adaptive traits.

Implications and Applications

  • The study establishes a genomic resource base for the Mugalzhar horse breed, facilitating future research and breeding programs.
  • Understanding genetic diversity and adaptation genes can inform selective breeding to enhance desirable traits such as environmental resilience or production qualities.
  • The findings serve as a reference for comparative genomic studies in other horse breeds worldwide.
  • These insights could eventually contribute to the conservation and sustainable utilization of the Mugalzhar breed.

Conclusion

  • This research provides a comprehensive analysis of genetic variation in the Mugalzhar horse breed using whole-genome sequencing.
  • The identification of adaptive genes and selection signatures helps explain how the breed has evolved and adapted over time.
  • The data generated lays the groundwork for genetics-informed breeding strategies and deeper studies on equine genetics and adaptation.

Cite This Article

APA
Kassymbekova SN, Bimenova ZZ, Iskhan KZ, Sobiech P, Jastrzebski JP, Brym P, Babis W, Kalykova AS, Otebayev ZM, Kabylbekova DI, Baneh H, Romanov MN. (2025). Uncovering Genetic Diversity and Adaptive Candidate Genes in the Mugalzhar Horse Breed Using Whole-Genome Sequencing Data. Animals (Basel), 15(18), 2667. https://doi.org/10.3390/ani15182667

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 18
PII: 2667

Researcher Affiliations

Kassymbekova, Shinara N
  • Department of Clinical Disciplines, Faculty of Veterinary and Zooengineering, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan.
Bimenova, Zhanat Z
  • Department of Clinical Disciplines, Faculty of Veterinary and Zooengineering, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan.
Iskhan, Kairat Z
  • Department of Animal Biology Named after N.U. Bazanova, Faculty of Veterinary and Zooengineering, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan.
Sobiech, Przemyslaw
  • Department and Clinic of Internal Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland.
Jastrzebski, Jan P
  • Department of Plant Physiology Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland.
Brym, Pawel
  • Department of Animal Genetics, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland.
Babis, Wiktor
  • Ecology and Genetics, Faculty of Science, University of Oulu, 90520 Oulu, Finland.
Kalykova, Assem S
  • Department of Clinical Disciplines, Faculty of Veterinary and Zooengineering, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan.
  • Department of Fundamental Medicine, al-Farabi Kazakh National University, Almaty 050040, Kazakhstan.
Otebayev, Zhassulan M
  • Department of Animal Biology Named after N.U. Bazanova, Faculty of Veterinary and Zooengineering, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan.
Kabylbekova, Dinara I
  • Department of Clinical Disciplines, Faculty of Veterinary and Zooengineering, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan.
Baneh, Hasan
  • Project Center for Agro Technologies, Skolkovo Institute of Science and Technology (Skoltech), Moscow 121205, Russia.
  • Animal Science Research Department, Kurdistan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj 6616936311, Iran.
Romanov, Michael N
  • School of Natural Sciences, University of Kent, Canterbury CT2 7NJ, UK.
  • Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
  • L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Russia.

Grant Funding

  • AP19677892 / Ministry Education and Science of the Republic of Kazakhstan

Conflict of Interest Statement

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

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