Application of BovineSNP50 genotyping array in variability assessment in Pinzgau bulls

Absztrakt

The aim of this study was to evaluate the level of SNP polymorphisms and describe the basic characteristic of the analysed population genotyped using the BovineSNP50 genotyping array, which has lot of applications in cattle such as genome association studies, genetic prediction of breeding values, estimation of genetic diversity and population genetic parameters and investigation of genetic relationships among cattle breeds. In total 19 purebred Pinzgau bulls were successfully genotyped with Illumina BovineSNP50 BeadChip (98.96% of SNPs) with call rate 0.995. Genotyping results from 54,906 SNPs revealed that 43,120 SNPs (78.96%) were polymorphic with average minor allele frequency 0.273±0.133. Within 43,120 SNPs genotyped, 98.19% were autosomal, with 776 polymorphic SNP on chromosome X and only one on chromosome Y. The average values of observed and expected heterozygosity across polymorphic loci were 0.375±0.157 and 0.362±126, respectively. Sufficient proportion of heterozygotes indicated the value of FIS (0.037±0.031). Genomic data obtained for purebred Pinzgau bulls from the BovineSNP50 chip can be in further applied for evaluation of genetic diversity in Pinzgau breed as endangered population of cattle in Slovak republic.