Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland Tomasz Szmatoła n , Artur Gurgul, Katarzyna Ropka-Molik, Igor Jasielczuk, Tomasz Ząbek, Monika Bugno-Poniewierska National Research Institute of Animal Production, Department of Genomics and Animal Molecular Biology, Krakowska 1, 32-083 Balice, Poland article info Article history: Received 6 November 2015 Received in revised form 31 March 2016 Accepted 8 April 2016 Keywords: Runs of homozygosity Autozygosity Selection signatures 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 se- lection. 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 F ROH , 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 de- tected. & 2016 Elsevier B.V. All rights reserved. 1. Introduction Runs of homozygosity (ROH) are contiguous homozygous seg- ments of the genome where the two haplotypes inherited from the parents are identical. These haplotypes are most likely iden- tical because the parents inherited them from a common ancestor (Purfield et al., 2012; Curik et al., 2014; Gurgul et al., 2014). Bro- man and Weber (1999) originally described long homozygous segments of the genome in human populations using micro- satellite markers. These analyses have shown that ROH are not only common, but that they may also have an effect on gene mapping and health. Currently, homozygous segments of the genome can be easily identified using information obtained from high-density SNP (single nucleotide polymorphism) arrays en- compassing genome-wide marker panels. In humans, a deep re- search about runs of homozygosity has been conducted and now ROH are considered as a valuable method of identifying suscept- ibility of an individual to recessive diseases (Gibson et al., 2006; Lencz et al., 2007; McQuillan et al., 2008; Hildebrandt et al., 2009; Kirin et al., 2010). In animal genetics, runs of homozygosity may be utilized as a measure of inbreeding by estimating the level of au- tozygosity of the genome (Ferenčaković et al., 2013b; Curik et al., 2014) and to identify regions having an unfavourable effect on a phenotype when being homozygous (Pryce et al., 2014; Saura et al., 2015). It has been shown that the length and frequency of ROH may help to describe the history of the population in which an in- dividual occurs and the history of that individual's ancestors (Kirin et al., 2010; Purfield et al., 2012; Curik et al., 2014). It has also been shown, that long ROH can be used to identify consanguinity (Kirin et al., 2010). In particular, recent inbreeding resulting from the mating of closely-related ancestors leads to a high occurrence of long ROH. On the other hand, very long ROH sometimes occur in outbred populations (Gibson et al., 2006). Shorter ROH appear because chromosomal segments are broken up by repeated meiosis and have older origins (Kirin et al., 2010). The fact that ROH are mainly autozygous, makes them a useful tool to estimate inbreeding, by the estimation of genome portion covered by ROH (F ROH )(Broman and Weber, 1999; McQuillan et al., 2008). The homozygous segments of the genome, with reduced variability within a population, may also arise as a result of strong artificial selection which leads to the fixation of favourable alleles in the population in a sort of “hitchhiking” process (Ron et al., 1996; McQuillan et al., 2008; Hildebrandt et al., 2009). The Contents lists available at ScienceDirect journal homepage: www.elsevier.com/locate/livsci Livestock Science http://dx.doi.org/10.1016/j.livsci.2016.04.006 1871-1413/& 2016 Elsevier B.V. All rights reserved. n Corresponding author. E-mail address: tomasz.szmatola@izoo.krakow.pl (T. Szmatoła). Livestock Science 188 (2016) 72–80