Abstract
Kazakh white-headed and Auliekol breeds are mostly spread through Kazakhstan and are animals with dual purpose productivity directions including meat and milk. Kazakh native cattle breeds are still largely unexplored based on the genetic markers and are of great interest in the country. In this study, we for the first time applied high-density SNP genotyping for two indigenous cattle breeds to study genetic diversity, population structure and relationships with the different foreign breeds. Using of GGP Bovine 150K SNP array the principal component analysis (PCA), populations estimates of the genetic structure (ADMIXTURE), genetic diversity and distances (Fst), and phylogenetic tree showed that the Kazakh white-headed and Auliekol breeds have certain separate genetic structure that differ from European and Russian cattle breeds The two of these Kazakh cattle breeds have their genetic background according to observed results as distinct breeds. The obtained results will be aided in the development breeding system and conservation programs of the Kazakh white-headed and Auliekol breeds of beef cattle in the Kazakhstan.