A first generation whole genome RH map of the river buffalo with comparison to domestic cattle
Autor(a) principal: | |
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Data de Publicação: | 2008 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/1471-2164-9-631 http://hdl.handle.net/11449/21645 |
Resumo: | Background: The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH(5000)) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species.Results: A total of 3990 markers were typed on the BBURH(5000) panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >= 8. The estimated total length of the WG-RH map is 36,933 cR(5000). Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0).Conclusion: We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome. |
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A first generation whole genome RH map of the river buffalo with comparison to domestic cattleBackground: The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH(5000)) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species.Results: A total of 3990 markers were typed on the BBURH(5000) panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >= 8. The estimated total length of the WG-RH map is 36,933 cR(5000). Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0).Conclusion: We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)NSF-USAConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)ARCDepartment of Biotechnology, Government of India, New DelhiAlberta Livestock Industry DevelopmentUNESP São Paulo State Univ, Dept Biol, IBILCE, Sao Jose do Rio Preto, SP, BrazilUNESP São Paulo State Univ, Dept Anim Sci, FCAV, Jaboticabal, SP, BrazilUniv Alberta, Dept Agr Food & Nutr Sci, Edmonton, AB, CanadaTexas A&M Univ, Dept Anim Sci, College Stn, TX 77843 USATexas A&M Univ, Dept Vet Pathobiol, College Stn, TX 77843 USAUniv Alberta, Dept Comp Sci, Edmonton, AB, CanadaNatl Bur Anim Genet Resources, Karnal, Haryana, IndiaForschungsinst Biol Landwirtschaftlicher Nutztier, Forsch Bereich Mol Biol, Dummerstorf, GermanyCtr Cellular & Mol Biol, Hyderabad 500007, Andhra Pradesh, IndiaUniv Brasilia, Programa Pos Grad Ciencias Animais, Brasilia, DF, BrazilEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Recursos Genet & Biotecnol, Brasilia, DF, BrazilPolo Univ, Lodi, ItalyUNESP São Paulo State Univ, Dept Biol, IBILCE, Sao Jose do Rio Preto, SP, BrazilUNESP São Paulo State Univ, Dept Anim Sci, FCAV, Jaboticabal, SP, BrazilFAPESP: 02/10150-5NSF-USA: OISE-0405743CNPq: 210280/2006-9ARC: 472359/07-0Biomed Central Ltd.Universidade Estadual Paulista (Unesp)University of AlbertaTexas A&M UniversityNational Bureau of Animal Genetic ResourcesForschungsinstitut für die Biologie landwirtschaftlicher NutztiereUniversidade de Brasília (UnB)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Amaral, M. Elisabete J. [UNESP]Grant, Jason R.Riggs, Penny K.Stafuzza, Nedenia B. [UNESP]Rodrigues Filho, Edson A. [UNESP]Goldammer, TomWeikard, RosemarieBrunner, Ronald M.Kochan, Kelli J.Greco, Anthony J.Jeong, JoohaCai, ZhipengLin, GuohuiPrasad, AparnaKumar, SatishSaradhi, G. PardhaMathew, BobyKumar, M. AravindMiziara, Melissa N.Mariani, PaolaCaetano, Alexandre R.Galvao, Stephan R.Tantia, Madhu S.Vijh, Ramesh K.Mishra, BinaKumar, S. T. BharaniPelai, Vanderlei A. [UNESP]Santana, Andre M. [UNESP]Fornitano, Larissa C. [UNESP]Jones, Brittany C.Tonhati, Humberto [UNESP]Moore, StephenStothard, PaulWomack, James E.2014-05-20T14:01:15Z2014-05-20T14:01:15Z2008-12-24info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article11application/pdfhttp://dx.doi.org/10.1186/1471-2164-9-631Bmc Genomics. London: Biomed Central Ltd., v. 9, p. 11, 2008.1471-2164http://hdl.handle.net/11449/2164510.1186/1471-2164-9-631WOS:000263110300001WOS000263110300001.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Genomics3.7302,110info:eu-repo/semantics/openAccess2024-01-11T06:25:15Zoai:repositorio.unesp.br:11449/21645Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-01-11T06:25:15Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle |
title |
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle |
spellingShingle |
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle Amaral, M. Elisabete J. [UNESP] |
title_short |
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle |
title_full |
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle |
title_fullStr |
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle |
title_full_unstemmed |
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle |
title_sort |
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle |
author |
Amaral, M. Elisabete J. [UNESP] |
author_facet |
Amaral, M. Elisabete J. [UNESP] Grant, Jason R. Riggs, Penny K. Stafuzza, Nedenia B. [UNESP] Rodrigues Filho, Edson A. [UNESP] Goldammer, Tom Weikard, Rosemarie Brunner, Ronald M. Kochan, Kelli J. Greco, Anthony J. Jeong, Jooha Cai, Zhipeng Lin, Guohui Prasad, Aparna Kumar, Satish Saradhi, G. Pardha Mathew, Boby Kumar, M. Aravind Miziara, Melissa N. Mariani, Paola Caetano, Alexandre R. Galvao, Stephan R. Tantia, Madhu S. Vijh, Ramesh K. Mishra, Bina Kumar, S. T. Bharani Pelai, Vanderlei A. [UNESP] Santana, Andre M. [UNESP] Fornitano, Larissa C. [UNESP] Jones, Brittany C. Tonhati, Humberto [UNESP] Moore, Stephen Stothard, Paul Womack, James E. |
author_role |
author |
author2 |
Grant, Jason R. Riggs, Penny K. Stafuzza, Nedenia B. [UNESP] Rodrigues Filho, Edson A. [UNESP] Goldammer, Tom Weikard, Rosemarie Brunner, Ronald M. Kochan, Kelli J. Greco, Anthony J. Jeong, Jooha Cai, Zhipeng Lin, Guohui Prasad, Aparna Kumar, Satish Saradhi, G. Pardha Mathew, Boby Kumar, M. Aravind Miziara, Melissa N. Mariani, Paola Caetano, Alexandre R. Galvao, Stephan R. Tantia, Madhu S. Vijh, Ramesh K. Mishra, Bina Kumar, S. T. Bharani Pelai, Vanderlei A. [UNESP] Santana, Andre M. [UNESP] Fornitano, Larissa C. [UNESP] Jones, Brittany C. Tonhati, Humberto [UNESP] Moore, Stephen Stothard, Paul Womack, James E. |
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 author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) University of Alberta Texas A&M University National Bureau of Animal Genetic Resources Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere Universidade de Brasília (UnB) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) |
dc.contributor.author.fl_str_mv |
Amaral, M. Elisabete J. [UNESP] Grant, Jason R. Riggs, Penny K. Stafuzza, Nedenia B. [UNESP] Rodrigues Filho, Edson A. [UNESP] Goldammer, Tom Weikard, Rosemarie Brunner, Ronald M. Kochan, Kelli J. Greco, Anthony J. Jeong, Jooha Cai, Zhipeng Lin, Guohui Prasad, Aparna Kumar, Satish Saradhi, G. Pardha Mathew, Boby Kumar, M. Aravind Miziara, Melissa N. Mariani, Paola Caetano, Alexandre R. Galvao, Stephan R. Tantia, Madhu S. Vijh, Ramesh K. Mishra, Bina Kumar, S. T. Bharani Pelai, Vanderlei A. [UNESP] Santana, Andre M. [UNESP] Fornitano, Larissa C. [UNESP] Jones, Brittany C. Tonhati, Humberto [UNESP] Moore, Stephen Stothard, Paul Womack, James E. |
description |
Background: The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH(5000)) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species.Results: A total of 3990 markers were typed on the BBURH(5000) panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >= 8. The estimated total length of the WG-RH map is 36,933 cR(5000). Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0).Conclusion: We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome. |
publishDate |
2008 |
dc.date.none.fl_str_mv |
2008-12-24 2014-05-20T14:01:15Z 2014-05-20T14:01:15Z |
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/10.1186/1471-2164-9-631 Bmc Genomics. London: Biomed Central Ltd., v. 9, p. 11, 2008. 1471-2164 http://hdl.handle.net/11449/21645 10.1186/1471-2164-9-631 WOS:000263110300001 WOS000263110300001.pdf |
url |
http://dx.doi.org/10.1186/1471-2164-9-631 http://hdl.handle.net/11449/21645 |
identifier_str_mv |
Bmc Genomics. London: Biomed Central Ltd., v. 9, p. 11, 2008. 1471-2164 10.1186/1471-2164-9-631 WOS:000263110300001 WOS000263110300001.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
BMC Genomics 3.730 2,110 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
11 application/pdf |
dc.publisher.none.fl_str_mv |
Biomed Central Ltd. |
publisher.none.fl_str_mv |
Biomed Central Ltd. |
dc.source.none.fl_str_mv |
Web of Science 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 |
|
_version_ |
1799965582836105216 |