Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)
Autor(a) principal: | |
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Data de Publicação: | 2017 |
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.0185220 http://hdl.handle.net/11449/170247 |
Resumo: | Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods: The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results: This 90K “SNP-Chip” was tested in several river buffalo populations and found to have *70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised. |
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Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods: The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results: This 90K “SNP-Chip” was tested in several river buffalo populations and found to have *70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.Ministero dell’Istruzione, dell’Università e della RicercaAIA-LGS Associazione Italiana Allevatori–Laboratorio Genetica e ServiziFondazione Parco Tecnologico PadanoBioinformatics core Parco Tecnologico PadanoAnimal Genomics and Improvement Laboratory BARC USDA-ARSDepartment of Animal Science Iowa State UniversityInstitute of Zootechnics Università Cattolica del S. CuoreANASB-Associazione Nazionale Allevatori Specie BufalinaUniversidade Estadual Paulista (UNESP) Câmpus de AraçatubaCOMSATS Institute of Information TechnologyDipartimento di Scienze Zootecniche ed Ispezione degli Alimenti Facoltà di Agraria Università degli Studi di Napoli Federico IIUniversidade Federal De Minas Gerais (UFMG)Affymetrix UK LtdDavies Research Centre School of Animal and Veterinary Sciences University of AdelaideDepartment of Animal Science University of ArkansasRecombinetics Inc.Council on Dairy Cattle Breeding, 4201 Northview Dr. One Town CentreUniversidade Estadual Paulista (UNESP) Câmpus de AraçatubaAIA-LGS Associazione Italiana Allevatori–Laboratorio Genetica e ServiziFondazione Parco Tecnologico PadanoParco Tecnologico PadanoUSDA-ARSIowa State UniversityUniversità Cattolica del S. CuoreANASB-Associazione Nazionale Allevatori Specie BufalinaUniversidade Estadual Paulista (Unesp)COMSATS Institute of Information TechnologyUniversità degli Studi di Napoli Federico IIUniversidade Federal de Minas Gerais (UFMG)Affymetrix UK LtdUniversity of AdelaideUniversity of ArkansasRecombinetics Inc.Council on Dairy Cattle BreedingIamartino, DanielaNicolazzi, Ezequiel L.Van Tassell, Curtis P.Reecy, James M.Fritz-Waters, Eric R.Koltes, James E.Biffani, StefanoSonstegard, Tad S.Schroeder, Steven G.Ajmone-Marsan, PaoloNegrini, RiccardoPasquariello, RolandoRamelli, PaolaColetta, AngeloGarcia, José F. [UNESP]Ali, AhmadRamunno, LuigiCosenza, GianfrancoDe Oliveira, Denise A. A.Drummond, Marcela G.Bastianetto, EduardoDavassi, AlessandroPirani, AliBrew, FionaWilliams, John L.2018-12-11T16:49:56Z2018-12-11T16:49:56Z2017-10-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.1371/journal.pone.0185220PLoS ONE, v. 12, n. 10, 2017.1932-6203http://hdl.handle.net/11449/17024710.1371/journal.pone.01852202-s2.0-850307510022-s2.0-85030751002.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPLoS ONE1,164info:eu-repo/semantics/openAccess2023-10-22T06:06:12Zoai:repositorio.unesp.br:11449/170247Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T15:35:21.257300Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis) |
title |
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis) |
spellingShingle |
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis) Iamartino, Daniela |
title_short |
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis) |
title_full |
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis) |
title_fullStr |
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis) |
title_full_unstemmed |
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis) |
title_sort |
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis) |
author |
Iamartino, Daniela |
author_facet |
Iamartino, Daniela Nicolazzi, Ezequiel L. Van Tassell, Curtis P. Reecy, James M. Fritz-Waters, Eric R. Koltes, James E. Biffani, Stefano Sonstegard, Tad S. Schroeder, Steven G. Ajmone-Marsan, Paolo Negrini, Riccardo Pasquariello, Rolando Ramelli, Paola Coletta, Angelo Garcia, José F. [UNESP] Ali, Ahmad Ramunno, Luigi Cosenza, Gianfranco De Oliveira, Denise A. A. Drummond, Marcela G. Bastianetto, Eduardo Davassi, Alessandro Pirani, Ali Brew, Fiona Williams, John L. |
author_role |
author |
author2 |
Nicolazzi, Ezequiel L. Van Tassell, Curtis P. Reecy, James M. Fritz-Waters, Eric R. Koltes, James E. Biffani, Stefano Sonstegard, Tad S. Schroeder, Steven G. Ajmone-Marsan, Paolo Negrini, Riccardo Pasquariello, Rolando Ramelli, Paola Coletta, Angelo Garcia, José F. [UNESP] Ali, Ahmad Ramunno, Luigi Cosenza, Gianfranco De Oliveira, Denise A. A. Drummond, Marcela G. Bastianetto, Eduardo Davassi, Alessandro Pirani, Ali Brew, Fiona Williams, John L. |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
AIA-LGS Associazione Italiana Allevatori–Laboratorio Genetica e Servizi Fondazione Parco Tecnologico Padano Parco Tecnologico Padano USDA-ARS Iowa State University Università Cattolica del S. Cuore ANASB-Associazione Nazionale Allevatori Specie Bufalina Universidade Estadual Paulista (Unesp) COMSATS Institute of Information Technology Università degli Studi di Napoli Federico II Universidade Federal de Minas Gerais (UFMG) Affymetrix UK Ltd University of Adelaide University of Arkansas Recombinetics Inc. Council on Dairy Cattle Breeding |
dc.contributor.author.fl_str_mv |
Iamartino, Daniela Nicolazzi, Ezequiel L. Van Tassell, Curtis P. Reecy, James M. Fritz-Waters, Eric R. Koltes, James E. Biffani, Stefano Sonstegard, Tad S. Schroeder, Steven G. Ajmone-Marsan, Paolo Negrini, Riccardo Pasquariello, Rolando Ramelli, Paola Coletta, Angelo Garcia, José F. [UNESP] Ali, Ahmad Ramunno, Luigi Cosenza, Gianfranco De Oliveira, Denise A. A. Drummond, Marcela G. Bastianetto, Eduardo Davassi, Alessandro Pirani, Ali Brew, Fiona Williams, John L. |
description |
Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods: The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results: This 90K “SNP-Chip” was tested in several river buffalo populations and found to have *70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-10-01 2018-12-11T16:49:56Z 2018-12-11T16:49:56Z |
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.0185220 PLoS ONE, v. 12, n. 10, 2017. 1932-6203 http://hdl.handle.net/11449/170247 10.1371/journal.pone.0185220 2-s2.0-85030751002 2-s2.0-85030751002.pdf |
url |
http://dx.doi.org/10.1371/journal.pone.0185220 http://hdl.handle.net/11449/170247 |
identifier_str_mv |
PLoS ONE, v. 12, n. 10, 2017. 1932-6203 10.1371/journal.pone.0185220 2-s2.0-85030751002 2-s2.0-85030751002.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
PLoS ONE 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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1808128537393102848 |