Linkage disequilibrium decay in the dairy cattle population of the Sverdlovsk region

Over the past two decades, the dairy cattle population in the Sverdlovsk region has undergone a transition from Black Pied to Holstein breeds, raising questions about its consequences for the genome structure. Analysis of linkage disequilibrium is a key tool for evaluating genetic structure, efficiency of genomic selection, and preservation of genetic diversity. A comparison of two generations of female stock in the Sverdlovsk region revealed that younger animals have 20–35 % higher values of linkage disequilibrium compared to older ones. The average values of determination coefficient (R²) across the genome were 0.10 and 0.08, while normalized coefficients (D’) were 0.59 and 0.50 for younger and older generations, respectively. Despite differences in mean values, the overall pattern of distribution of linkage disequilibrium along chromosomes remains consistent (Spearman correlation coefficient >0.94). Linkage disequilibrium peaks are observed on chromosomes BTA14, BTA16, and BTA20, where loci associated with milk productivity and health are located. The rate of decay of linkage disequilibrium is higher in the older generation compared to young individuals. These findings indicate an increase in selection intensity and greater homogeneity of the genome in modern populations, which is important for optimizing regional programs of genomic selection.