The results of a study of the genetic diversity of the Transbaikal horse breed based on the polymorphism of whey proteins TF, Es, and ALB in four herds of the Transbaikal region are presented. The Transbaikal horse belongs to the ancient aboriginal breeds and is most adapted to the local climatic conditions of dry, hot summers and frosty winters with little snow. It is unpretentious, hardy, and has a strong constitution. Research is aimed at preserving the breed’s genetic diversity by studying polymorphic variants of whey proteins, which are reliable genetic markers due to their codominant inheritance and comprehensive polymorphism. In the albumin locus, two alleles and three genotypes were identified. In the esterase locus, there are six alleles and 13 genotypes. In the transferrin locus - 7 alleles and 18 genotypes occur with different frequencies in the studied herds, which makes it possible to characterise their genotypic characteristics. Rarely encountered genotypes of the transferrin locus (less than 10 %) include eight genotypes: TFDD, TFDH, TFDI, TFDR, TFFI, TFFM, TFOR, TFR; esterase locus – 6 genotypes: EsGI, EsHH, EsHI, EsHO, EsII, EsGI. Based on the frequency of genotypes and alleles, homozygosity was calculated for each whey protein system and for the entire sample from the herd, the level of which ranges from 7.87 to 12.25 %. The overall homozygosity rate varies from 34.35 to 43.36 %, and the number of effective alleles (Na) in all herds is almost the same (2.30–2.91). Genetic variability ranges from 56.96–63.74 %. The index of gene similarity between herds is at the level of 0.8439–0.9058. The analysed herds form two subclusters: the first includes horses from the APC (Agricultural Production Cooperative) Livestock Breeding Farm named after. Kalinin and SPK “Rassvet”. In the second - animals from APC (Agricultural Production Cooperative) “Livestock Breeding Farm “Rodina” and AC (Agricultural Cooperative) “Taptanay”.
