GENOMIC AND PEDIGREE-BASED INBREEDING IN SLOVAK SPOTTED CATTLE

Abstract

The objective of this study was to evaluate the level of inbreeding in population ofSlovak Spotted cattle and to compare its genomic and pedigree-based estimates.The genomic data have been obtained from in total of 37 AI sires and 50 sire damsgenotyped by using Illumina BovineSNP50v2 BeadChip and ICBF InternationalDairy and Beef v3, respectively. The genealogical information have been obtainedfrom the database of Breeding Services of the Slovak Republic, s. e. The pedigreefile consisted of 109,686 individuals (105,229 dams and 4,457 sires), while thereference population included only living animals, AI sires (129) and dams(36,949). The genomic inbreeding (FROH) was computed as the length of thegenome present in runs of homozygosity (ROH) divided by the total length of theautosomal genome covered by SNPs on the chip and the pedigree-based inbreeding(FPED) was calculated based on assumption that inbreeding of an individual reflectsthe probability that both alleles in one locus are derived from the same ancestor orare identical by descent. The ROH segments greater than 4 Mb (FROH > 4Mb) coveredin average 2.09 % of the genome, while the ROH segments greater than 16 Mb(FROH > 16Mb) achieved 0.43 % which indicated in analysed population recentinbreeding. Similarly, the increase of inbreeding across generation signalized theaverage ΔFPED computed from pedigree information (0.094%). However, thepedigree-based and genomic estimates of inbreeding differ from each other (inaverage FROH>4=0.02; FPED=0.004). In recent generation, the obtained values ofFROH indicated considerably higher degree of inbreeding.