GENOMIC AND PEDIGREE-BASED INBREEDING IN SLOVAK SPOTTED CATTLE

Abstract

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