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Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds
Iacolina, Laura Stronen, Astrid V. Pertoldi, Cino Tokarska, Małgorzata Norgaard, Louise S. Munoz, Joaquin Kjaersgaard, Anders Ruiz-Gonzalez, Aritz Kaminski, Stanislaw Purfield, Deirdre C
Iacolina, Laura
Stronen, Astrid V.
Pertoldi, Cino
Tokarska, Małgorzata
Norgaard, Louise S.
Munoz, Joaquin
Kjaersgaard, Anders
Ruiz-Gonzalez, Aritz
Kaminski, Stanislaw
Purfield, Deirdre C
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2016
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IJG2016-2152847.pdf
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Laura Iacolina, Astrid V. Stronen, Cino Pertoldi, et al., Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds, International Journal of Genomics, vol. 2016, Article ID 2152847, 8 pages, 2016. doi:10.1155/2016/2152847
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.