Inbreeding and homozygosity in Orlov trotter breed

Evaluation of animals for the pedigree does not track the actual similarity of probands with ancestors, including that when inbreeding is used. The total number of marker genes defined in horses already reached several hundred and enables to control a significant part of the genome of animals and use genetic information in practical breeding. Previously, we showed that Thoroughbred horse degree of homozygosity on microsatellite loci is not directly based on the degree of inbreeding, and the largest scale variability of this indicator is observed in the group of inbred horses. In the present work we investigated the effects of inbreeding in Orlov Trotter breed on an individual level. The analysis was carried out of the relationship between the degree of homozygosity of 16 microsatellite loci (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, VHL20) and an indicator of inbreeding in 1194 individuals from 14 leading horse-breeding studs and farms in Russia, including 19 stallions, 688 mares and 316 foals. Data on he LEX loci 3, localized in X-chromosome, were not taken into account to obtain comparable results on the degree of homo-/heterozygosity in horses of different sex. It has been determined that the degree of homozygosity in Orlov Trotters varies within a wide range (from 0 up to 75.00 %) and has a normal distribution with a positive coefficient of asymmetry As = 0.186 and a small negative excess Ex = -0.039. The most wide variability on homozygosity was indicated in the horses of mild inbreeding (F x = 0.1-1.0 %). The homozygosity in outbred horses also varied significantly, from 0 (100 % heterozygosity) to 56.30 %, being much more and less than an average index for the population. Previously, we showed the similar trend in the Thoroughbred horses. The average level of inbreeding of the tested horses amounted to 1.61 % by Wright`s inbreeding coefficient (F x) in 5 generations in pedigrees and in fact remained unchanged over the past four decades. The average inbreeding coefficient in sires and mares reached 1.65 % and 1.67 %, respectively, while in young stock was 1.45 % only. Dynamics of changes in homozygosity with increase of inbreeding coefficient in all sex and age groups of compared horses had unidirectional trend of slowly increasing. A significant rise of the homozygosity degree was noted only at inbreeding coefficient of 6.10 % and more, on the margin of inbred depression for economically valuable traits. The coefficient of correlation between the degree of homozygosity of microsatellite loci and the level of inbreeding was 0.079 with the regression coefficient of 0.546. In all groups, it has been found an evident decline in the degree of homozygosity in Orlov Trotter horses when the inbreeding coefficient reached 5.1-6.0 % due to complex inbreeding, with two or more ancestors used.