The Genetic Structure of Slovak Spotted Cattle Based on Genome-wide Analysis

Abstract

The objective of the study was to determine the membership probability and level of admixture among Slovak Spotted cattle and historically related breeds (Ayshire, Holstein, Swiss Simmental and Slovak Pinzgau). The analysis was based on the panel of 35 934 SNPs that were used for genotyping of 423 individuals. The optimal number of clusters was estimated in two ways; by analysis of Bayesian information criterion and Bayesian clustering algorithm. The optimal number of clusters ranged from 3 to 5, depending on the applied approach. Subsequently, the population structure was tested by discriminant analysis of principal components (DAPC) and unsupervised Bayesian analysis based on the correlated allele frequencies model. The first discriminant function revealed three genetic clusters in population resulting from the production type and origin of analysed breeds. The unsupervised Bayesian analysis showed similar results, where the highest level of admixture was found between Slovak Pinzgau and Slovak Spotted cattle (0.6%). Despite that, the results of this study clearly showed that the Slovak Spotted cattle is genetically separated from other breeds that were involved in its grading-up process.

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

“…Different methods for determination of admixture level of populations were used based on Bayesian approach and discriminant analysis of principal components (DAPC) (Moravčíková et al, 2017b, c;Lehocká et al, 2020) evaluation of genetic differentiation of populations based on linkage disequilibrium (LD) with simultaneous identification of genomic regions showing selection signatures linked on their genetic differentiation (Kukučková et al, 2016a,b), determination of the level of genetic differentiation of populations based on Wright´s F ST index and determination of genomic regions characteristic for particular breeds and local populations, respectively (Lehocká et al, 2019a). As part of the methodology for evaluation of the effect of selection on genome structure and identification of genomic regions significantly affected by the specific selection type, were evaluated parameters as extended haplotype homozygosity (EHH) integrated haplotype score (iHS) (Kasarda et al, 2015), Wright´s F ST on the whole genome level (Moravčíková et al, 2018c), level of autozygosity based on the distribution of homozygous segments (ROH) (Kasarda et al, 2018a;Moravčíková et al, 2018d;Moravčíková et al, 2019a) and the variability of linkage disequilibrium (Kasarda et al, 2016c;).…”