Genomic variability assess for breeding traits in holsteinizated Russian black-and-white cattle using GWAS analysis and ROH patterns

For using the pedigree information recorded in dairy herds rational, the creation of reference groups with a high reliability the estimated breeding value of animals is required. This is a necessary requirement not only for the genetic assessment procedure, but also for the introduction of genomic selection methods. However, without high-quality phenotyping cannot be this achieved. Therefore, it seems relevant to conduct model studies using the highly productive herd of Holsteinizated Russian Black-and-White cattle in the Urals as an example to study the genomic variability of phenotypic traits in animals’ different generations using data from genome-wide analysis (GWAS) and runs of homozygosity (ROH), as well as to replenish the Russian reference population. The novelty of the work is to assess the dynamics of genomic inbreeding variability (FROH) in animal generations (“dam of mother”-“mother”-“daughter”) and its comparison with direct genomic value (DGV), as well as the search for new mechanisms to confirm the scientific hypothesis of using a limited experimental dataset in GWAS. The object of this research was 76 cows and heifers of Holsteinizated Russian Black-and-White breed, as well as 9 Holstein sires genotyped for 139 thousand SNPs by the Bovine GGP HD platform (Illumina/Neogen, USA). To calculate the DGVs of studied animals the Russian reference bulls and cows group that include 591 individuals was used. GWAS and ROH analyzes were performed based on 110448 SNPs. The reliability (p-values) of genome-wide associations with direct cows’ phenotypes ranged from 2.31½10-5 to 1.08½10-7. Quantitative traits loci on autosomes BTA1, BTA2, BTA5, BTA7, BTA8, BTA10, BTA11, BTA12, BTA14, BTA16, BTA20, BTA21, and BTA26 were found. For milk yield a region on BTA14 (1.44-1.59 Mb) with the genes ZNF16 , ARHGAP39 , ZNF7 associated with an increased fat milk yield was detected. For the number of inseminations found SNPs included into the genes ( ARHGAP31 ) or located close to the genes ( SERPINA5 ) and associated with the growth intensity to a mature state, as well as ovarian function in animals. The characteristic of ROHs depending on the length of their fragments in the genome is given. Conservative homozygous regions on BTA12, BTA14, BTA26, and BTA29 and the most significant genes entering them were identified, which are potentially associated with selection pressure in the studied population mainly by milk production traits, reproduction, and udder type measurement parameters. The value of FROH significantly (р ROH = 0.135 were noted for bulls that were signed as fathers of cows (generation of “mother”) and heifers (generation of “daughter”). Each subsequent generation of individuals showed an average increase in DGV for milk yield by +94.2 kg, fat milk yield by +4.4 kg and protein milk yield by +3.0 kg, reflecting clear the strategy to improve milk production traits in the herd for obtaining new cattle genotypes. Thus, the possibilities for assessing the variability of direct cattle phenotypes, as a model for studying genomic variability in a single herd, based on the search for associations and loci in the genome under selection pressure are shown.