Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle

The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH...

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Main Authors:	Kim, Eui-Soo, Cole, John B., Huson, Heather, Wiggans, George R., Van Tassell, Curtis P., Crooker, Brian A., Liu, George, Da, Yang, Sonstegard, Tad S.
Format:	Online
Language:	English
Published:	Public Library of Science 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858116/

id	pubmed-3858116
recordtype	oai_dc
spelling	pubmed-38581162013-12-12 Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle Kim, Eui-Soo Cole, John B. Huson, Heather Wiggans, George R. Van Tassell, Curtis P. Crooker, Brian A. Liu, George Da, Yang Sonstegard, Tad S. Research Article The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH) occasionally spanning millions of continuous base pairs at a specific locus. In this study, genome signatures of artificial selection in NA Holsteins born between 1953 and 2008 were identified by comparing changes in ROH between three distinct groups under different selective pressure for milk production. The ROH regions were also used to estimate the inbreeding coefficients. The comparisons of genomic autozygosity between groups selected or unselected since 1964 for milk production revealed significant differences with respect to overall ROH frequency and distribution. These results indicate selection has increased overall autozygosity across the genome, whereas the autozygosity in an unselected line has not changed significantly across most of the chromosomes. In addition, ROH distribution was more variable across the genomes of selected animals in comparison to a more even ROH distribution for unselected animals. Further analysis of genome-wide autozygosity changes and the association between traits and haplotypes identified more than 40 genomic regions under selection on several chromosomes (Chr) including Chr 2, 7, 16 and 20. Many of these selection signatures corresponded to quantitative trait loci for milk, fat, and protein yield previously found in contemporary Holsteins. Public Library of Science 2013-11-14 /pmc/articles/PMC3858116/ /pubmed/24348915 http://dx.doi.org/10.1371/journal.pone.0080813 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Kim, Eui-Soo Cole, John B. Huson, Heather Wiggans, George R. Van Tassell, Curtis P. Crooker, Brian A. Liu, George Da, Yang Sonstegard, Tad S.
spellingShingle	Kim, Eui-Soo Cole, John B. Huson, Heather Wiggans, George R. Van Tassell, Curtis P. Crooker, Brian A. Liu, George Da, Yang Sonstegard, Tad S. Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle
author_facet	Kim, Eui-Soo Cole, John B. Huson, Heather Wiggans, George R. Van Tassell, Curtis P. Crooker, Brian A. Liu, George Da, Yang Sonstegard, Tad S.
author_sort	Kim, Eui-Soo
title	Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle
title_short	Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle
title_full	Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle
title_fullStr	Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle
title_full_unstemmed	Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle
title_sort	effect of artificial selection on runs of homozygosity in u.s. holstein cattle
description	The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH) occasionally spanning millions of continuous base pairs at a specific locus. In this study, genome signatures of artificial selection in NA Holsteins born between 1953 and 2008 were identified by comparing changes in ROH between three distinct groups under different selective pressure for milk production. The ROH regions were also used to estimate the inbreeding coefficients. The comparisons of genomic autozygosity between groups selected or unselected since 1964 for milk production revealed significant differences with respect to overall ROH frequency and distribution. These results indicate selection has increased overall autozygosity across the genome, whereas the autozygosity in an unselected line has not changed significantly across most of the chromosomes. In addition, ROH distribution was more variable across the genomes of selected animals in comparison to a more even ROH distribution for unselected animals. Further analysis of genome-wide autozygosity changes and the association between traits and haplotypes identified more than 40 genomic regions under selection on several chromosomes (Chr) including Chr 2, 7, 16 and 20. Many of these selection signatures corresponded to quantitative trait loci for milk, fat, and protein yield previously found in contemporary Holsteins.
publisher	Public Library of Science
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858116/
_version_	1612036979751387136

Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle

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