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International Journal of Genomics
Volume 2016 (2016), Article ID 2152847, 8 pages
http://dx.doi.org/10.1155/2016/2152847
Research Article

Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

1Department of Chemistry and Bioscience, Aalborg University, Section of Biology and Environmental Engineering, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
2Aalborg Zoo, Mølleparkvej 63, 9000 Aalborg, Denmark
3Mammal Research Institute Polish Academy of Sciences, Ul. Waszkiewicza 1, 17-230 Białowieża, Poland
4Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, C/Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
5Department of Animal Genetics, University of Warmia and Mazury in Olsztyn, 10-718 Olsztyn, Poland
6Animal & Biosciences Department, Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, County Cork, Ireland

Received 14 December 2015; Accepted 28 September 2016

Academic Editor: Graziano Pesole

Copyright © 2016 Laura Iacolina et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.