Whole-genome sequencing reveals genetic architecture and selection signatures of Kazakh cattle

Local cattle breeds are vital for breeding programs due to their genetic adaptations to diverse environments. Despite their importance, the genomic architecture of local cattle breeds in Kazakhstan remains largely unexplored. In this study, we analyzed whole-genome sequencing data from Kazakh cattle, uncovering three primary ancestral components: European, Eurasian, and East Asian taurine. The East Asian taurine component likely represents the earliest lineage of Kazakh cattle. However, it was largely replaced by subsequent cattle migrations across Eurasia, leaving only a small proportion in the current cattle population. In contrast, the Eurasian taurine constitutes the predominant ancestry in Alatau and Kazakh local breeds, while the European taurine component is most prevalent in Kazakh white-headed cattle, aligning with their breeding history. Compared to European commercial breeds, Kazakh cattle exhibit higher genetic diversity and lower inbreeding coefficients, reflecting less intense artificial selection. A strong selection signal was identified on a locus of chromosome 6 (PDGFRA, KIT, and KDR), could related to white-headed pigmentation in Kazakh white-headed cattle. Additional selected genes are 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 cattle in Kazakhstan. It uncovers the influence of cattle migrations across Eurasia on their genetic composition and identifies genomic selection features. These findings provide valuable insights into the evolutionary history of cattle and provide resources for breeding improvements.