Kassymbekova Shinara N, Bimenova Zhanat Z, Iskhan Kairat Z, Sobiech Przemyslaw, Jastrzebski Jan P, Brym Pawel, Babis Wiktor, Kalykova Assem S, Otebayev Zhassulan M, Kabylbekova Dinara I, Baneh Hasan, Romanov Michael N
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.
Animals (Basel). 2025 Sep 11;15(18):2667. doi: 10.3390/ani15182667.
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.
穆加尔扎尔马是哈萨克斯坦一个相对年轻的本土品种，因其肉奶产量和适应性而备受珍视。本研究旨在利用全基因组序列数据调查该品种的遗传多样性，并确定与选择印记相关的基因组区域。变异检测共产生了21,722,393个高质量变异，包括19,495,163个单核苷酸多态性（SNP）和2,227,230个插入缺失。大多数变异位于内含子和基因间区域，而外显子变异仅占1.94%。遗传多样性估计值中等，预期杂合度、观察到的杂合度和核苷酸多样性分别为0.2325、0.2402和0.0021。我们鉴定出九个适应性候选基因（、、、、、、、和），这些基因在纯合状态下携带对替代等位基因有高影响的外显子变异。在该群体中未发现与孟德尔性状相关的有害分离变异，而在低频杂合状态下检测到七个与毛色和步态相关的变异。我们的研究结果表明，在祖先品种形成和适应过程中，某些基因组区域受到了古代选择印记的影响。本研究结果为未来基于基因组的策略、该品种的更广泛利用以及其他马品种的基因组研究提供了参考依据。
