Whole-genome sequencing reveals genetic architecture and selection signatures of Kazakh cattle
Niyazbekova Z. Xu Y. Qiu M. Wang H.-P. Primkul I. Nanaei H.A. Ussenbekov Y. Kassen K. Liu Y. Gao C.-Y. Akhmetsadykova S. Ruzikulov N. Jiang Y. Cai Y.-D.
18 March 2025Science Press
Zoological Research
2025#46Issue 2301 - 311 pp.
Local cattle breeds play a critical role in breeding programs due to their genetic adaptations to diverse environmental conditions. However, the genomic architecture of local cattle breeds in Kazakhstan remains largely unexplored. This study utilized whole-genome sequencing data from Kazakh cattle to elucidate their genetic composition, uncovering three primary ancestral components: European, Eurasian, and East Asian taurine. The East Asian taurine lineage likely represents the earliest genetic contribution to Kazakh cattle but was largely replaced by subsequent waves of cattle migrations across Eurasia, leaving only a minor genetic signature in the current cattle population. In contrast, Eurasian taurine ancestry predominated in the Alatau and Kazakh local breeds, while the European taurine component was most prevalent in Kazakh white-headed cattle, consistent with their documented breeding history. Kazakh cattle exhibited higher genetic diversity and lower inbreeding coefficients compared to European commercial breeds, reflecting reduced exposure to intense artificial selection. A strong selection signal was identified on chromosome 6 at a locus encompassing PDGFRA, KIT, and KDR, which may be associated with the white-headed pigmentation characteristic of Kazakh white-headed cattle. Additional genes under selection were linked to lipid metabolism (IRS1, PRKG1, and ADCY8), meat production traits (KCNMA1, PDGFRA, HIF1A, and ANTXR1), and dairy production (ATP2B1, DHX15, FUK, NEGR1, CCDC91, COG4, and PTK2B). This study represents the first comprehensive analysis of nuclear genome data from local Kazakh cattle. It highlights the impact of historical cattle migrations across Eurasia on their genetic landscape and identifies key genomic regions under selection. These findings advance our understanding of the evolutionary history of cattle and offer valuable genetic resources for future breeding strategies. Copyright
Alatau cattle , Genetic diversity , Kazakh white-headed cattle , Local breed , Selection signatures , Whole-genome sequencing
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College of Animal Science and Technology, Northwest A & F University, Shaanxi, Yangling, 712100, China
Faculty of Veterinary Medicine, Kazakh National Agrarian Research University, Almaty, 050000, Kazakhstan
College of Life Sciences, Northwest A & F University, Shaanxi, Yangling, 712100, China
College of Plant Protection, Northwest A & F University, Shaanxi, Yangling, 712100, China
Institute of Animal Husbandry and Veterinary Science, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
Research and Production Enterprise ANTIGEN Co. Ltd., Abai Village, Almaty, 050409, Kazakhstan
Samarkand State University of Veterinary Medicine, Animal Husbandry and Biotechnology, Samarkand, 140103, Uzbekistan
College of Animal Science and Technology
Faculty of Veterinary Medicine
College of Life Sciences
College of Plant Protection
Institute of Animal Husbandry and Veterinary Science
Research and Production Enterprise ANTIGEN Co. Ltd.
Samarkand State University of Veterinary Medicine
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