Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland

Abstract

Runs of homozygosity (ROH) are defined as contiguous homozygous regions of the genome where the two haplotypes inherited from the parents are identical. It has been shown that the length and frequency of ROH may describe the history of the population in which an individual occurs; they may also reveal the level of inbreeding within populations, recent population bottlenecks or signatures of positive selection. In this study, BovineSNP50 whole-genome genotyping assay was used to analyse the lengths and distributions of the ROH found in the genomes of four cattle breeds maintained in Poland (Holstein, Polish Red, Limousin and Simmental) to assess both the level of autozygosity of each breed and to identify the genomic regions most commonly associated with ROH that may reflect directional selection pressure. Visible differences in the length and distribution of homozygous regions across the genome between selected breeds were observed. The breeds also varied in the level of autozygosity (inbreeding) estimated by FROH, which was lower for unselected cattle. Moreover, within the regions of the genome most commonly associated with ROH that may reveal signatures of recent selection a number of genes potentially connected with different production features characteristic for individual breeds were detected.