Genome-Wide Detection of Selective Signature in Chinese Holstein

Selective signatures in whole genome can help us understand the mechanisms of selection and target causal variants for breeding program. In present study, we performed Extended Haplotype Homozygosity (EHH) tests to identify significant core regions harboring such signals in Chinese Holstein, and the...

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Main Authors:	Pan, Dunfei, Zhang, Shengli, Jiang, Jicai, Jiang, Li, Zhang, Qin, Liu, JianFeng
Format:	Online
Language:	English
Published:	Public Library of Science 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610670/

id	pubmed-3610670
recordtype	oai_dc
spelling	pubmed-36106702013-04-03 Genome-Wide Detection of Selective Signature in Chinese Holstein Pan, Dunfei Zhang, Shengli Jiang, Jicai Jiang, Li Zhang, Qin Liu, JianFeng Research Article Selective signatures in whole genome can help us understand the mechanisms of selection and target causal variants for breeding program. In present study, we performed Extended Haplotype Homozygosity (EHH) tests to identify significant core regions harboring such signals in Chinese Holstein, and then verified the biological significance of these identified regions based on commonly-used bioinformatics analyses. Results showed a total of 125 significant regions in entire genome containing some of important functional genes such as LEP, ABCG2, CSN1S1, CSN3 and TNF based on the Gene Ontology database. Some of these annotated genes involved in the core regions overlapped with those identified in our previous GWAS as well as those involved in a recently constructed candidate gene database for cattle, further indicating these genes under positive selection maybe underlie milk production traits and other important traits in Chinese Holstein. Furthermore, in the enrichment analyses for the second level GO terms and pathways, we observed some significant terms over represented in these identified regions as compared to the entire bovine genome. This indicates that some functional genes associated with milk production traits, as reflected by GO terms, could be clustered in core regions, which provided promising evidence for the exploitability of the core regions identified by EHH tests. Findings in our study could help detect functional candidate genes under positive selection for further genetic and breeding research in Chinese Holstein. Public Library of Science 2013-03-28 /pmc/articles/PMC3610670/ /pubmed/23555972 http://dx.doi.org/10.1371/journal.pone.0060440 Text en © 2013 Pan et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
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	Pan, Dunfei Zhang, Shengli Jiang, Jicai Jiang, Li Zhang, Qin Liu, JianFeng
spellingShingle	Pan, Dunfei Zhang, Shengli Jiang, Jicai Jiang, Li Zhang, Qin Liu, JianFeng Genome-Wide Detection of Selective Signature in Chinese Holstein
author_facet	Pan, Dunfei Zhang, Shengli Jiang, Jicai Jiang, Li Zhang, Qin Liu, JianFeng
author_sort	Pan, Dunfei
title	Genome-Wide Detection of Selective Signature in Chinese Holstein
title_short	Genome-Wide Detection of Selective Signature in Chinese Holstein
title_full	Genome-Wide Detection of Selective Signature in Chinese Holstein
title_fullStr	Genome-Wide Detection of Selective Signature in Chinese Holstein
title_full_unstemmed	Genome-Wide Detection of Selective Signature in Chinese Holstein
title_sort	genome-wide detection of selective signature in chinese holstein
description	Selective signatures in whole genome can help us understand the mechanisms of selection and target causal variants for breeding program. In present study, we performed Extended Haplotype Homozygosity (EHH) tests to identify significant core regions harboring such signals in Chinese Holstein, and then verified the biological significance of these identified regions based on commonly-used bioinformatics analyses. Results showed a total of 125 significant regions in entire genome containing some of important functional genes such as LEP, ABCG2, CSN1S1, CSN3 and TNF based on the Gene Ontology database. Some of these annotated genes involved in the core regions overlapped with those identified in our previous GWAS as well as those involved in a recently constructed candidate gene database for cattle, further indicating these genes under positive selection maybe underlie milk production traits and other important traits in Chinese Holstein. Furthermore, in the enrichment analyses for the second level GO terms and pathways, we observed some significant terms over represented in these identified regions as compared to the entire bovine genome. This indicates that some functional genes associated with milk production traits, as reflected by GO terms, could be clustered in core regions, which provided promising evidence for the exploitability of the core regions identified by EHH tests. Findings in our study could help detect functional candidate genes under positive selection for further genetic and breeding research in Chinese Holstein.
publisher	Public Library of Science
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610670/
_version_	1611966042820575232

Genome-Wide Detection of Selective Signature in Chinese Holstein

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