Abstract
Understanding the genetic diversity and population structure of farm animals is key to developing effective breeding strategies and conserving genetic resources. The aim of this study was to assess the genetic diversity and population structure of the Auliekol cattle breed based on genotyping using the BovineSNP50 BeadChip. This study included 1440 animals from eight farms. Genetic diversity indices (observed and expected heterozygosity), the inbreeding coefficient (FIS), and allelic richness were calculated, and population structure was analyzed using PCA, ADMIXTURE, fineSTRUCTURE, and genomic relationship matrix (GRM) methods. The results showed comparable levels of observed and expected heterozygosity across populations (Ho = 0.3478–0.3537; He = 0.3445–0.3492) and negative FIS values ranging from −0.0211 to −0.0025, suggesting no strong population-level signal of inbreeding. Low FST (0.007–0.028) and GRM values indicate weak genetic differentiation between populations. PCA and fineSTRUCTURE analyses showed no clear clustering, while ADMIXTURE identified three main genetic components shared across all populations. TreeMix analysis further suggested genetic connectivity among farms, with the Moskalyevskoe population occupying a central position in the inferred network of genetic relationships and migration events. In general, the Auliekol breed is characterized by a high level of genetic coherence and preserved genetic diversity, which creates favorable conditions for its further selective improvement and the preservation of genetic resources.