Genomic diversity of beef cattle in Slovakia

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.