AUTOZYGOSITY ISLAND RESULTING FROM ARTIFICIAL SELECTION IN SLOVAK SPOTTED CATTLE

Abstract

The aim of this study was to identify the runs of homozygosity (ROH) segments within genome and to identify regions significantly affected by artificial selection in Slovak Spotted cattle. In total of 85 animals representing the nucleus of Slovak Spotted cattle were included in present study. The sampled population consisted of 37 AI sires and 48 dams of sires that were genotyped by using two platforms, Illumina BovineSNP50v2 BeadChip and ICBF International Dairy and Beef v3. The consensus map file, constructed to identify common SNPs within these platforms, consisted of overall 40,033 markers. Subsequently, all of loci with call rate lower than 90% and minor allele frequency lower than 0.01% were removed. The final database included genotyping information for 37,833 SNPs. The ROH segments were defined as genomic regions with 15 or more consecutive homozygous calls at density of one SNPs on every 100 kb and maximum gap between consecutive SNPs of 1 Mb. One heterozygous call was allowed for length >16 Mb. In addition, one missing call was allowed for length >4 Mb, 2 for >8 Mb and 4 for >16 Mb. The subsequent analyses of genome-wide selection signatures were based on the assumption that the most frequent homozygous regions in population (minimum ROHs with length 4 Mb) reflected the recent selection characteristic for Slovak Spotted breed. As expected due to the dual-purpose character of this breed the strongest signals of artificial selection was found direct or very close to genes associated with milk production and beef quality.