Intrabreed Differentiation of Native Kostroma Cattle Breed Based on SNP Markers of Meat Productivity

— A study of the intrabreed variability of four single nucleotide polymorphisms in the RORC , GHR , Lep , and LepR genes associated with meat productivity was carried out for the first time in five samples of the Kostroma breed of dairy and beef cattle. A comparison was also made with known data for two related beef breeds (Aberdeen Angus and Russian Polled). The same alleles of loci of the studied genes prevailed in frequency both in all samples of the Kostroma breed and in the two additional breeds involved for the joint analysis. The distribution of genotype frequencies in all Kostroma breed samples did not deviate from the Hardy–Weinberg distribution. According to a complex of studied markers, a differentiation of the Kostroma breed samples from each other and from the Aberdeen Angus and Russian Polled breeds was detected by a multidimensional scaling method based on pairwise F ST values and using a G test. The analysis of the Kostroma breed samples with two other breeds by Bayesian clustering method identified four latent genetic structures. All types of clusters were found in the Kostroma breed, while only a few were found in the Aberdeen Angus and Russian Polled breeds. A different contribution of the studied loci in intra- and interbreed differentiation was established. Thus, the Lep and LepR genes showed themselves at the intrabreed level, and the RORC gene, at the interbreed level. At the same time, the GHR gene locus was characterized by the greatest variability. In general, according to the loci of the studied genes, the intrabreed variability of the Kostroma breed was comparable to the interbreed variability. The results are discussed with regard to the involvement of these loci in population processes in the studied cattle breeds and justify the need for a more detailed study of intrabreed variability by SNP markers associated with breeding valuable traits for the whole spectrum of breeds, regardless of their productive orientation: beef or dairy.