Uncovering Genetic Diversity and Adaptive Candidate Genes in the Mugalzhar Horse Breed Using Whole-Genome Sequencing Data
Kassymbekova S.N. Bimenova Z.Z. Iskhan K.Z. Sobiech P. Jastrzebski J.P. Brym P. Babis W. Kalykova A.S. Otebayev Z.M. Kabylbekova D.I. Baneh H. Romanov M.N.
September 2025Multidisciplinary Digital Publishing Institute (MDPI)
Animals
2025#15Issue 18
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 (SCAPER, FHAD1, MMP15, ADGRE1, CMKLR1, MRPL15, ZNF667, CCDC66, and LOC100055310), 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.
adaptation , inbreeding , Mugalzhar horse , single nucleotide polymorphisms (SNPs) , whole-genome sequencing (WGS)
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Department of Clinical Disciplines, Faculty of Veterinary and Zooengineering, Kazakh National Agrarian Research University, Almaty, 050010, Kazakhstan
Department of Animal Biology Named after N.U. Bazanova, Faculty of Veterinary and Zooengineering, Kazakh National Agrarian Research University, Almaty, 050010, Kazakhstan
Department and Clinic of Internal Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, 10-719, Poland
Department of Plant Physiology Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, 10-719, Poland
Department of Animal Genetics, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, Olsztyn, 10-719, Poland
Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, 90520, Finland
Department of Fundamental Medicine, al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
Project Center for Agro Technologies, Skolkovo Institute of Science and Technology (Skoltech), Moscow, 121205, Russian Federation
Animal Science Research Department, Kurdistan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj, 6616936311, Iran
School of Natural Sciences, University of Kent, Canterbury, CT2 7NJ, United Kingdom
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, Russian Federation
Department of Clinical Disciplines
Department of Animal Biology Named after N.U. Bazanova
Department and Clinic of Internal Diseases
Department of Plant Physiology Genetics and Biotechnology
Department of Animal Genetics
Ecology and Genetics
Department of Fundamental Medicine
Project Center for Agro Technologies
Animal Science Research Department
School of Natural Sciences
Animal Genomics and Bioresource Research Unit (AGB Research Unit)
L. K. Ernst Federal Research Center for Animal Husbandry
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