Genomic diversity of beef cattle in Slovakia

Kristína Lehocká, Radovan Kasarda, Barbora Olšanská, Nina Moravčíková


Received: 2020-10-22 Accepted: 2021-02-08 Available online: 2021-02-28

The aim of the study was to determine the state of genetic diversity in Charolais and Limousine populations. The analysis was
based on the panel of 49 629 SNPs that were used for genotyping of 85 individuals. For the assessment of the genetic diversity,
the genomic inbreeding coefficient resulting from runs of homozygosity distribution in the genome and linkage disequilibrium
based effective population size (Ne) were calculated. The results reflected a decrease in recent inbreeding (FROH >16 Mb under 1%)
compared to historical (FROH >1 Mb in average 6%). The current effective population size was estimated based on the linear regression
using Ne estimates for 50 generations ago. The effective population size across all analysed animals was 33.05 for Charolais breed
(decrease of 4.51 animals per generation) and 7.02 for Limousine breed (decrease of 2.81 animals per generation). The estimation
of current Ne indicated the endangered status of assessment populations and referred the need for continuous monitoring to
increase population size but without reducing genetic diversity as a result of inbreeding.

Keywords: effective populations size, homozygosity, Charolais, inbreeding, Limousine

AL-MAMUN, H.A. et al. (2015). Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian
domestic sheep. Genetics Selection Evolution, 47(90). DOI: 10.1186/s12711-015-0169-6.
BARBATO, M. et al. (2015). SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide
SNP data. Front Genetics, 6, 109. DOI:10.3389/fgene.2015.00109.
BOUQUET, A. et al. (2011). Genetic structure of the European Charolais and Limousin cattle metapopulations using pedigree
analyses. Journal of Animal Science, 89(6), 1719–1730.
CHANG, CH. C. et al. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience, 4, 7.
CURIK, I., FERENČÁKOVIĆ, M. and SÖLKNER, J. (2014). Inbreeding and runs of homozygosity: A possible solution to an old
problem. Livestock Science, 166, 26–34.
FERENČAKOVIĆ, M., SÖLKNER, J. and CURIK, I. (2013). Estimating autozygosity from high-throughput information: effects of
SNP density and genotyping errors. Genetics Selection Evolution, 45, 42.
FLURY, C. et al. (2010). Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium.
Journal of Animal Breeding and Genetics, 127(5), 339-347. DOI: 10.1111/j.1439-0388.2010.00862.x.
FORUTAN, M. et al. (2018). Inbreeding and runs of homozygosity before and after genomic selection in North American
Holstein cattle. BMC Genomics, 19, 98.
KADLEČÍK, O. et al. (2016). Inbreeding and genetic diversity loss of four cattle beef breeds in Slovakia. Acta fytotechn zootechn,
19(2), 59–63.
KASARDA, R., KUKUČKOVÁ, V. and MORAVČÍKOVÁ, N. (2017). The most important sires in Pinzgau population. Acta fytotechn
zootechn, 20(2), 28–30.
KELLER, M. C., VISSCHER, P. M. and GODDARD, M. E. (2011). Quantification of inbreeding due to distant ancestors and its
detection using dense single nucleotide polymorphism data. Genetics.
LEE, S. H. et al. (2011). Linkage disequilibrium and effective population size in Hanwoo Korean cattle. Asian-Australas. Journal
of Animal Science, 34, 1660–1665.
LENSTRA, J. A. et al. (2012). Molecular tools and analytical approaches for the characterization of farm animal genetic diversity.
Anim Genet., 43, 483–502.
LU, D. et al. (2012). Linkage disequilibrium in Angus, Charolais and Crossbred beef cattle. Front. Genet.
MÉSZÁROS, G. et al. (2015). Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey
cattle. Front Genet., 6, 173.
METZGER, J. et al. (2015). Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and nonbreed
horses. BMC Genomics, 16(764). DOI: 10.1186/s12864-015-1977-3.
MORAVČÍKOVÁ, N. et al. (2018) Autozygosity island resulting from artificial selection in slovak spotted cattle. Agriculture &
Forestry, 64(4), 21–28.
MORAVČÍKOVÁ, N. et al. (2017). Effective Population Size and Genomic Inbreeding in Slovak Pinzgau Cattle. Agriculturae
Conspectus Scientifi cus., 82(2), 97–100.
PERIPOLLI, E. et al. (2018). Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus)
dairy cattle. BMC Genomics, 19, 34. DOI: 10.1186/s12864-017-4365-3.
ŠIDLOVÁ, V. et al. (2015). Genomic variability among cattle populations based on runs of homozygosity. Poljoprivreda, 21(1),
SZMATOŁA, T. et al. (2019). A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different
Production Types. Animals, 9, 1024. DOI:10.3390/ani9121024.
WRIGHT, S. (1938). Size of population and breeding structure in relation to evolution. Science, 87, 430–431.

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