Population and genetic features, genomic inbriding and homozy-gosity level for black-and-white and holstein breeds by STR and SNP markers in Russia

Abstract

The object of the study was sires of the Black-and-White and Holstein breeds, which had STR profiles and passed the genotyping procedure for SNP markers. The subject of the study was the level of genomic inbreeding and homozygosity, as well as population-genetic characteristics based on them. With an increase in Fx based on pedigree data, an increase in the level of genomic inbreeding (FROH) calculated from SNP markers was also noted. The results for 9 STR markers record a wavelike increase in homozygosity from group I to group IV with a subsequent increase from group V to group VII inclusive. During the study of the average FROH values in accordance with the years of birth of sires, a significant difference was found between the last two groups (2009-2011; 2012-2014) from all the others in a pairwise comparison. The results of calculating the FROH and Ca9 of bulls from different countries of origin indicate a statistically significant differentiation of the group of animals from Russia (RF) from animals, born in German and Canadian. A significant difference was noted for the highest FROH level in the samples in the Holstein Black-and-White breed from the Red-and-White Holstein and Black-and-White breeds. The Fst values between the SNP and STR species of the animals had insignificant differentiation (0.008-0.027). Differences in STR calculation between the Black-and-White Holstein and Red-and-White Holstein breeds were insignificant, less than 20%, while the rest of the values differed many times. Fst between RF and Germany, RF and the Netherlands according to STR data is 0.006 and 0.008, according to SNP data 0.005 and 0.006, respectively. A mutual increase in the value of Fst and the year of birth of the sires was noted, emphasizing the greatest remoteness of the population of 1983-1997 from the populations of recent years, when new genotypes of bulls were obtained. The similarity of Fst values between genealogical lines is replaced by a significant scatter in the indicators when they are compared in pairs.