The evaluation of genomic diversity and selection signals in the autochthonous Slovak Spotted cattle

Abstract

The aim of this study was to evaluate the effective population size based on linkage disequilibrium and the trend of inbreeding derived from runs of homozygosity (ROH) in the Slovak Spotted cattle. The ROH segments longer than 4 Mb were then analysed to identify selection signals. Eighty-five individuals were genotyped using the ICBF International Dairy and Beef chip (dams of sires) and Illumina BovineSNP50 BeadChip (sires). The ROH segments > 1 Mb occurred most often in the autosomal genome with an average number of 16.75 ± 7.23. The ROH segments > 16 Mb covering 0.41% of the genome pointed to the long-term effort of breeders to reduce inbreeding in the population of Slovak Spotted cattle. However, the average observed heterozygosity indicated a decrease in overall diversity in the current population. The decrease of heterozygosity per generation also confirmed the estimates of historical and recent effective population size (a decrease of 6.88 animals per generation). The predicted current effective population size was 58 animals. Twenty-one regions across 12 different autosomes were fixed due to the high selection pressure. Within these genomic regions were identified various genes associated with reproduction (SLC9C1, PTPN12), milk production (IGF1, ABCG2), beef production (IFRD1, PTPN4), developmental processes (FMNL2, GLI2), immune system (CD96, CSK) and coat colour (KIT). These selection signals detected in the genome of Slovak Spotted cattle confirm the constant effort of breeders to preserve the dual-purpose nature of this breed.