Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)

Detalhes bibliográficos
Autor(a) principal: Iamartino, Daniela
Data de Publicação: 2017
Outros Autores: 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.
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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spelling 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)
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