Genome-Wide SNP Analysis Reveals the Unique Genetic Diversity Represented by Fat-Tailed Coarse-Wooled Sheep Breeds of Kazakhstan
Dossybayev K. Amandykova M. Ualiyeva D. Kapassuly T. Kozhakhmet A. Ciani E. Bekmanov B. Amzeyev R.
November 2025Multidisciplinary Digital Publishing Institute (MDPI)
Biology
2025#14Issue 11
Background: The fat-tailed coarse-wooled sheep breeds exhibit excellent reproductive performance, exceptional adaptability to pasture conditions, and high precocity, contributing to enhanced meat, fat, and wool productivity in sheep breeding. Despite the significant role of these sheep breeds in Kazakhstan’s livestock production, their genetics remain poorly studied. This raises concerns about the potential loss of unique, breed-specific traits that could be important for the future development and resilience of Kazakh stan’s sheep farming sector. This study aimed to analyze genome-wide genotyping SNP data of local fat-tailed coarse-wooled sheep breeds (Kazakh fat-tailed coarse-wooled, Edilbay, and Gissar) to reveal their genetic diversity, breed characteristics, and phylogenetic relationships with worldwide domestic sheep breeds and wild sheep. Methods: The OvineSNP50 Genotyping BeadChip was used to obtain genome-wide SNP genotyping data from 160 fat-tailed coarse-wooled sheep from Kazakhstan. Population structure analysis, principal component analysis, phylogenetic and the maximum likelihood tree analysis were performed in comparison with foreign domestic sheep breeds and wild sheep populations. Results: Kazakh breeds exhibited high genetic diversity, with Edilbay showing the greatest allelic richness. PCA and Admixture revealed clear differentiation among the three breeds: Edilbay and Gissar formed homogeneous clusters, while Kazakh fat-tailed coarse-wooled sheep displayed admixture and substructure. Evidence of gene flow from Edilbay into other Kazakh populations supports its role as a genetic source for regional breeds. Phylogenetic analysis placed Kazakhstani sheep close to other Central Asian breeds, while clearly distinct from East Asian and European populations. Wild sheep (Argali and Urial) formed separate clades, with Kerman wild sheep clustering closer to Urial. Conclusions: Our results highlight the value of genotyping data for studying genetic diversity and population structure. Developing genetic resources for Kazakhstan’s native sheep breeds will help preserve their unique diversity and ensure it remains available for future use in breeding and adaptation efforts.
Edilbay sheep breed , genetic diversity , genetic structure , genome-wide SNP genotyping , Gissar sheep breed , Kazakh fat-tailed coarse-wooled sheep breed , Ovis aries , phylogenetics
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Laboratory of Animal Genetics and Cytogenetics, RSE Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, 93 Al-Farabi Avenue, Almaty, 050060, Kazakhstan
Laboratory of Molecular Genetic Examination, LLP «Kazakh Research Institute of Animal Husbandry and Fodder Production», 51 Zhandosov Street, Almaty, 050071, Kazakhstan
Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, 71 Al-Farabi Avenue, Almaty, 050040, Kazakhstan
Laboratory of Ornithology and Herpetology, Institute of Zoology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, 93 Al-Farabi Avenue, Almaty, 050060, Kazakhstan
Chengdu Institute of Biology, Chinese Academy of Sciences, 23 Qunxian South Street, Chengdu, 610041, China
Department of Biosciences, Biotechnologies and Environment, University of Bari, 1 Piazza Umberto I, Bari, 70121, Italy
Faculty of Natural Sciences and Geography, Abai Kazakh National Pedagogical University, 13 Dostyk Avenue, Almaty, 050010, Kazakhstan
Laboratory of Animal Genetics and Cytogenetics
Laboratory of Molecular Genetic Examination
Faculty of Biology and Biotechnology
Laboratory of Ornithology and Herpetology
Chengdu Institute of Biology
Department of Biosciences
Faculty of Natural Sciences and Geography
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