Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods
Autor(a) principal: | |
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Data de Publicação: | 2013 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1371/journal.pone.0064280 http://hdl.handle.net/11449/75408 |
Resumo: | As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10-7) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10-12), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection. |
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Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methodscalpaincalpastatingangliosideallelebeef cattlebiogenesisbiological activityCNIH3 genecontrolled studydairy cattledairy productdata analysisDNA footprintinggenegene frequencygene identificationgene locusgenetic associationgenetic databasegenetic selectiongenetic transcriptiongenetic variabilitygluconeogenesisglycolysishaplotypeheterozygosityhomozygosityluteinizing hormone releasemeatnonhumanpopulation geneticsribosomesignal detectionsingle nucleotide polymorphismAs the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10-7) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10-12), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.Departamento de Medicina Veterinária Preventiva e Reprodução Animal Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP), Jaboticabal, São PauloDivision of Livestock Sciences Department of Sustainable Agricultural Systems BOKU - University of Natural Resources and Life Sciences, ViennaDepartamento de Apoio, Saúde e Produção Animal Faculdade de Medicina Veterinária de Araçatuba Universidade Estadual Paulista (UNESP), Araçatuba, São PauloBovine Functional Genomics Laboratory ARS-USDA - Agricultural Research Service - United States Department of Agriculture, Beltsville, MDDepartamento de Medicina Veterinária Preventiva e Reprodução Animal Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP), Jaboticabal, São PauloDepartamento de Apoio, Saúde e Produção Animal Faculdade de Medicina Veterinária de Araçatuba Universidade Estadual Paulista (UNESP), Araçatuba, São PauloUniversidade Estadual Paulista (Unesp)BOKU - University of Natural Resources and Life SciencesARS-USDA - Agricultural Research Service - United States Department of AgricultureUtsunomiya, Yuri Tani [UNESP]Pérez O'Brien, Ana MariaSonstegard, Tad StewartVan Tassell, Curtis Pauldo Carmo, Adriana Santana [UNESP]Mészáros, GáborSölkner, JohannGarcia, José Fernando [UNESP]2014-05-27T11:29:30Z2014-05-27T11:29:30Z2013-05-16info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.1371/journal.pone.0064280PLoS ONE, v. 8, n. 5, 2013.1932-6203http://hdl.handle.net/11449/7540810.1371/journal.pone.0064280WOS:0003190819000772-s2.0-848778346962-s2.0-84877834696.pdf9991374083045897Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPLOS ONE2.7661,164info:eu-repo/semantics/openAccess2024-06-06T18:09:20Zoai:repositorio.unesp.br:11449/75408Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-06-06T18:09:20Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods |
title |
Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods |
spellingShingle |
Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods Utsunomiya, Yuri Tani [UNESP] calpain calpastatin ganglioside allele beef cattle biogenesis biological activity CNIH3 gene controlled study dairy cattle dairy product data analysis DNA footprinting gene gene frequency gene identification gene locus genetic association genetic database genetic selection genetic transcription genetic variability gluconeogenesis glycolysis haplotype heterozygosity homozygosity luteinizing hormone release meat nonhuman population genetics ribosome signal detection single nucleotide polymorphism |
title_short |
Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods |
title_full |
Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods |
title_fullStr |
Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods |
title_full_unstemmed |
Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods |
title_sort |
Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods |
author |
Utsunomiya, Yuri Tani [UNESP] |
author_facet |
Utsunomiya, Yuri Tani [UNESP] Pérez O'Brien, Ana Maria Sonstegard, Tad Stewart Van Tassell, Curtis Paul do Carmo, Adriana Santana [UNESP] Mészáros, Gábor Sölkner, Johann Garcia, José Fernando [UNESP] |
author_role |
author |
author2 |
Pérez O'Brien, Ana Maria Sonstegard, Tad Stewart Van Tassell, Curtis Paul do Carmo, Adriana Santana [UNESP] Mészáros, Gábor Sölkner, Johann Garcia, José Fernando [UNESP] |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) BOKU - University of Natural Resources and Life Sciences ARS-USDA - Agricultural Research Service - United States Department of Agriculture |
dc.contributor.author.fl_str_mv |
Utsunomiya, Yuri Tani [UNESP] Pérez O'Brien, Ana Maria Sonstegard, Tad Stewart Van Tassell, Curtis Paul do Carmo, Adriana Santana [UNESP] Mészáros, Gábor Sölkner, Johann Garcia, José Fernando [UNESP] |
dc.subject.por.fl_str_mv |
calpain calpastatin ganglioside allele beef cattle biogenesis biological activity CNIH3 gene controlled study dairy cattle dairy product data analysis DNA footprinting gene gene frequency gene identification gene locus genetic association genetic database genetic selection genetic transcription genetic variability gluconeogenesis glycolysis haplotype heterozygosity homozygosity luteinizing hormone release meat nonhuman population genetics ribosome signal detection single nucleotide polymorphism |
topic |
calpain calpastatin ganglioside allele beef cattle biogenesis biological activity CNIH3 gene controlled study dairy cattle dairy product data analysis DNA footprinting gene gene frequency gene identification gene locus genetic association genetic database genetic selection genetic transcription genetic variability gluconeogenesis glycolysis haplotype heterozygosity homozygosity luteinizing hormone release meat nonhuman population genetics ribosome signal detection single nucleotide polymorphism |
description |
As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10-7) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10-12), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection. |
publishDate |
2013 |
dc.date.none.fl_str_mv |
2013-05-16 2014-05-27T11:29:30Z 2014-05-27T11:29:30Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1371/journal.pone.0064280 PLoS ONE, v. 8, n. 5, 2013. 1932-6203 http://hdl.handle.net/11449/75408 10.1371/journal.pone.0064280 WOS:000319081900077 2-s2.0-84877834696 2-s2.0-84877834696.pdf 9991374083045897 |
url |
http://dx.doi.org/10.1371/journal.pone.0064280 http://hdl.handle.net/11449/75408 |
identifier_str_mv |
PLoS ONE, v. 8, n. 5, 2013. 1932-6203 10.1371/journal.pone.0064280 WOS:000319081900077 2-s2.0-84877834696 2-s2.0-84877834696.pdf 9991374083045897 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
PLOS ONE 2.766 1,164 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1803045264809787392 |