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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
22/06/2016 |
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Data da última atualização: |
22/06/2016 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
SILVA, J. M. da; GIACHETTO, P. F.; SILVA, L. O. da; CINTRA, L. C.; PAIVA, S. R.; YAMAGISHI, M. E. B.; CAETANO, A. R. |
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Afiliação: |
JOAQUIM MANOEL DA SILVA, Unemat, IB/Unicamp; POLIANA FERNANDA GIACHETTO, CNPTIA; LUIZ OTAVIO CAMPOS DA SILVA, CNPGC; LEANDRO CARRIJO CINTRA, CNPTIA; SAMUEL REZENDE PAIVA, SRI; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA; ALEXANDRE RODRIGUES CAETANO, Cenargen. |
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Título: |
Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits. |
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Ano de publicação: |
2016 |
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Fonte/Imprenta: |
BMC Genomics, London, v. 17, p. 1-14, 2016. |
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DOI: |
10.1186/s12864-016-2752-9 |
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Idioma: |
Inglês |
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Conteúdo: |
Background: Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. Results: Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively. Conclusions: Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits. MenosBackground: Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. Results: Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed... Mostrar Tudo |
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Palavras-Chave: |
Bioinformática; Copy number variations; Genotipagem; Polimorfismo de nucleotídeo único; SNP genotyping. |
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Thesagro: |
Gado de corte. |
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Thesaurus Nal: |
Beef cattle; Bioinformatics; Genotyping; High-throughput nucleotide sequencing; Single nucleotide polymorphism. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/144667/1/AP-Genome-Silva-et-al.pdf
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Marc: |
LEADER 02983naa a2200337 a 4500
001 2047683
005 2016-06-22
008 2016 bl uuuu u00u1 u #d
024 7 $a10.1186/s12864-016-2752-9$2DOI
100 1 $aSILVA, J. M. da
245 $aGenome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.$h[electronic resource]
260 $c2016
520 $aBackground: Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. Results: Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively. Conclusions: Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits.
650 $aBeef cattle
650 $aBioinformatics
650 $aGenotyping
650 $aHigh-throughput nucleotide sequencing
650 $aSingle nucleotide polymorphism
650 $aGado de corte
653 $aBioinformática
653 $aCopy number variations
653 $aGenotipagem
653 $aPolimorfismo de nucleotídeo único
653 $aSNP genotyping
700 1 $aGIACHETTO, P. F.
700 1 $aSILVA, L. O. da
700 1 $aCINTRA, L. C.
700 1 $aPAIVA, S. R.
700 1 $aYAMAGISHI, M. E. B.
700 1 $aCAETANO, A. R.
773 $tBMC Genomics, London$gv. 17, p. 1-14, 2016.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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 | Acesso ao texto completo restrito à biblioteca da Embrapa Florestas. Para informações adicionais entre em contato com cnpf.biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Florestas. |
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Data corrente: |
25/11/2004 |
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Data da última atualização: |
11/07/2014 |
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Autoria: |
SOUTO, R. L.; OLIVEIRA, G. B. de; CARDOSO, I. M.; SOUZA, H. N. de; BONFIM, V. R.; GJORUP, D. F.; CARVALHO, A. F. de. |
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Título: |
Metodologia de sistematização da experimentação participativa comsistemas agroflorestais na Zona da Mata de Minas Gerais. |
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Ano de publicação: |
2004 |
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Fonte/Imprenta: |
In: CONGRESSO BRASILEIRO DE SISTEMAS AGROFLORESTAIS, 5., 2004, Curitiba. SAFs: desenvolvimento com proteção ambiental: anais. Colombo: Embrapa Florestas, 2004. p. 55-57. |
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Série: |
(Embrapa Florestas. Documentos, 98). |
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ISSN: |
1517-536X |
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Idioma: |
Português |
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Palavras-Chave: |
Experimentação; Metodologia; SAF; Sistema agroflorestal. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 00893naa a2200253 a 4500
001 1309839
005 2014-07-11
008 2004 bl uuuu u00u1 u #d
022 $a1517-536X
100 1 $aSOUTO, R. L.
245 $aMetodologia de sistematização da experimentação participativa comsistemas agroflorestais na Zona da Mata de Minas Gerais.
260 $c2004
490 $a(Embrapa Florestas. Documentos, 98).
653 $aExperimentação
653 $aMetodologia
653 $aSAF
653 $aSistema agroflorestal
700 1 $aOLIVEIRA, G. B. de
700 1 $aCARDOSO, I. M.
700 1 $aSOUZA, H. N. de
700 1 $aBONFIM, V. R.
700 1 $aGJORUP, D. F.
700 1 $aCARVALHO, A. F. de
773 $tIn: CONGRESSO BRASILEIRO DE SISTEMAS AGROFLORESTAIS, 5., 2004, Curitiba. SAFs: desenvolvimento com proteção ambiental: anais. Colombo: Embrapa Florestas, 2004. p. 55-57.
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