A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types

Tomasz Szmatoła; Artur Gurgul; Igor Jasielczuk; Tomasz Ząbek; Katarzyna Ropka-Molik; Zygmunt Litwińczuk; Monika Bugno-Poniewierska

doi:10.3390/ani9121024

A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types

Animals (Basel). 2019 Nov 25;9(12):1024. doi: 10.3390/ani9121024.

Authors

Tomasz Szmatoła^{1

2}, Artur Gurgul^{1

2}, Igor Jasielczuk^{1

2}, Tomasz Ząbek², Katarzyna Ropka-Molik², Zygmunt Litwińczuk³, Monika Bugno-Poniewierska⁴

Affiliations

¹ University Centre of Veterinary Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland.
² Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
³ Sub-Department of Cattle Breeding and Genetic Resources Conservation, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland.
⁴ Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059 Kraków, Poland.

Abstract

In the presented research, BovineSNP50 microarrays (Illumina) were applied to determine runs of homozygosity in the genomes of 11 cattle breeds maintained in Poland. These cattle breeds represent three basic utility types: milk, meat and dual purpose. Analysis of runs of homozygosity allowed the evaluation of the level of autozygosity within each breed in order to calculate the genomic inbreeding coefficient (F_ROH), as well as to identify regions of the genome with a high frequency of ROH occurrence, which may reflect traces of directional selectin left in their genomes. Visible differences in the length and distribution of runs of homozygosity in the genomes of the analyzed cattle breeds have been observed. The highest mean number and mean sums of lengths of runs of homozygosity were characteristic for Hereford cattle and intermediate for the Holstein-Friesian Black-and-White variety, Holstein-Friesian Red-and-White variety, Simmental, Limousin, Montbeliarde and Charolais breeds. However, lower values were observed for cattle of conserved breeds. Moreover, the selected livestock differed in the level of inbreeding estimated using the F_ROH coefficient. In regions of the genome with a high frequency of ROH occurrence, which may reflect the impact of directional selection, a number of genes were observed that can be potentially related to the production traits which are under selection pressure for specific production types. The most important detected genes were GHR, MSTN, DGAT1, FABP4, and TRH, with a known influence on the milk and meat traits of the studied cattle breeds.

Keywords: autozygosity; cattle; microarray; runs of homozygosity.