Dynamics of the Inbreeding Coefficient and Homozygosity in Thoroughbred Horses in Russia

SIMPLE SUMMARY: The Thoroughbred horse breed provides a unique model for studying the theoretical bases and practical methods of selection in horse breeding. To assess the diversity in the modern population of Russian Thoroughbred horses, we used classic parameters, such as Wright’s inbreeding coefficient, the heterozygosity level, and population inbreeding level, over the period 1990–2018. The average inbreeding coefficient of the Thoroughbred horses was 0.83% and slowly increased over the past three decades. The individual observed heterozygosity levels of the tested horses varied within 23.1–100%, and the population’s parameters of observed heterozygosity tended to decrease. The relationship between the level of inbreeding and the rate of homozygosity was not significant (r = 0.022; p > 0.05). ABSTRACT: The Thoroughbred (TB) horse has hugely impacted the development of horse breeding around the world. This breed has unique genetic qualities due to having had a closed studbook for approximately 300 years. In Russia, TBs have been bred since the second half of the 18th century. Here, we analyzed the genetic diversity and the inbreeding level in TB horses (n = 9680) for the period from 1990 to 2018 using polymorphisms of 17 microsatellite loci. We found that the genetic structure of the TB breed in Russia is represented by 100 alleles of panel STR (short tandem repeat) loci and has been stable for the past three decades. The conducted monitoring revealed a slight increase in the Wright’s inbreeding coefficient in all age and sex groups of TB horses (stallions, broodmares, and foals) from 0.68% to 0.90%, which was followed by a decrease in the degree of heterozygosity, Ho, from 68.5% to 67.6%. The Spearman’s rank correlation coefficient between the level of inbreeding and the degree of homozygosity was estimated (r = 0.022; p > 0.05). The obtained data on the DNA genotypes of horses of different breeds provide a unique base for the evaluation of genetic variability and the control of genetic variability of horses in selection programs.