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.

Genetic diversity and production potential of animal food resources: Review article

“…In case of Slovak Pinzgau it is based on analyses of homozygous runs longer than 16 Mb, reflecting present inbreeding, which present 0.81% of the genome (Kukučková et al, 2017a, b;Kasarda et al, 2019b). Similar results were obtained in case of Slovak Spotted, whereas 0.43% of the genome was covered by homozygous segments (ROH) (Kasarda et al, 2018a, Kasarda et al, 2019c. Those observations clearly point a relatively large proportion of inbred animals in the present generation in case of both breeds.…”

State of conservation of animal genetic resources in Slovakia

“…Recently, several national research projects have been carried out to study the actual status of local breeds populations, and published papers showed different levels of inbreeding in several cattle and horse populations. While pedigree-based inbreeding under the acceptable level of 1% was estimated in Slovak Spotted and Slovak Pinzgau populations of cattle (Kukučková et al, 2017;Kasarda et al, 2019a), genomic analyses showed higher levels of inbreeding and thus increasing trends of inbreeding are expected in both populations. A low level of pedigree-based inbreeding (0.23%) and genomic inbreeding (0.11%) was observed in the relatively small population of Noric of Murany (Kasarda et al, 2019b).…”

Use of High-density SNP analyses to develop a long-term strategy for conventional populations to prevent loss of diversity - review

“…All the applied approaches confirmed, that intense selection act predominantly on specific regions of three chromosomes: BTA5 (59665562-68880383 bp), BTA6 (32489075-42866573 bp and 68546212-72969608 bp) and BTA7 (41321459-46354401 bp). Signals were detected directly in the sequences of genes involved in genetic control of milk production (ABCG2, SPP1, FAM13A), growth and feed conversion (FAM184B, PKD2, PACRGL), reproduction (GDF9) and coat colour (KIT, KDR) (Moravčíková et al, 2018b;Moravčíková et al, 2019f;Kasarda et al, 2019f ).…”