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Registro Completo |
Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Gado de Leite; Embrapa Recursos Genéticos e Biotecnologia. |
Data corrente: |
19/05/2017 |
Data da última atualização: |
30/12/2020 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
STAFUZZA, N. B.; ZERLOTINI NETO, A.; LOBO, F. P.; YAMAGISHI, M. E. B.; CHUD, T. C. S.; CAETANO, A. R.; MUNARI, D. P.; GARRICK, D. J.; MACHADO, M. A.; MARTINS, M. F.; CARVALHO, M. R.; COLE, J. B.; SILVA, M. V. G. B. |
Afiliação: |
NEDENIA BONVINO STAFUZZA, FCAV/Unesp; ADHEMAR ZERLOTINI NETO, CNPTIA; FRANCISCO PEREIRA LOBO, CNPTIA; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA; TATIANE CRISTINA SELEGUIM CHUD, FCAV/Unesp; ALEXANDRE RODRIGUES CAETANO, Cenargen; DANÍSIO PRADO MUNARI, FCAV/Unesp; DORIAN J. GARRICK, Iowa State University; MARCO ANTONIO MACHADO, CNPGL; MARTA FONSECA MARTINS, CNPGL; MARIA RAQUEL CARVALHO, UFMG; JOHN BRUCE COLE, Agricultural Research Service; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL. |
Título: |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. |
Ano de publicação: |
2017 |
Fonte/Imprenta: |
Plos One, v. 12, n. 3, p. 1-15, 2017. |
DOI: |
https://doi.org/10.1371/journal.pone.0173954 |
Idioma: |
Inglês |
Notas: |
Artigo e0173954. Na publicação: Adhemar Zerlotini, Marcos Vinicius Gualberto Barbosa da Silva. |
Conteúdo: |
Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs. MenosWhole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated... Mostrar Tudo |
Palavras-Chave: |
Genetic variants; Genomic markers; Important traits; Molecular mechanisms; Polimorfismo de nucleotídeo único; Potential genomic markers; Raças bovinas; Single nucleotide variations. |
Thesagro: |
Gado; Variação genética. |
Thesaurus Nal: |
Cattle breeds; Genome; Single nucleotide polymorphism; Sires. |
Categoria do assunto: |
-- G Melhoramento Genético |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/171980/1/AP-Single-nucleotide-Stafuzza-etal.pdf
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/161515/1/Cnpgl-2017-PlosOne-Stafuzza-Single.pdf
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/180929/1/journal.pone.0173954.pdf
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Marc: |
LEADER 03086naa a2200457 a 4500 001 2086824 005 2020-12-30 008 2017 bl uuuu u00u1 u #d 024 7 $ahttps://doi.org/10.1371/journal.pone.0173954$2DOI 100 1 $aSTAFUZZA, N. B. 245 $aSingle nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds.$h[electronic resource] 260 $c2017 500 $aArtigo e0173954. Na publicação: Adhemar Zerlotini, Marcos Vinicius Gualberto Barbosa da Silva. 520 $aWhole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs. 650 $aCattle breeds 650 $aGenome 650 $aSingle nucleotide polymorphism 650 $aSires 650 $aGado 650 $aVariação genética 653 $aGenetic variants 653 $aGenomic markers 653 $aImportant traits 653 $aMolecular mechanisms 653 $aPolimorfismo de nucleotídeo único 653 $aPotential genomic markers 653 $aRaças bovinas 653 $aSingle nucleotide variations 700 1 $aZERLOTINI NETO, A. 700 1 $aLOBO, F. P. 700 1 $aYAMAGISHI, M. E. B. 700 1 $aCHUD, T. C. S. 700 1 $aCAETANO, A. R. 700 1 $aMUNARI, D. P. 700 1 $aGARRICK, D. J. 700 1 $aMACHADO, M. A. 700 1 $aMARTINS, M. F. 700 1 $aCARVALHO, M. R. 700 1 $aCOLE, J. B. 700 1 $aSILVA, M. V. G. B. 773 $tPlos One$gv. 12, n. 3, p. 1-15, 2017.
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Embrapa Agricultura Digital (CNPTIA) |
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Registro Completo
Biblioteca(s): |
Embrapa Hortaliças. |
Data corrente: |
10/10/2005 |
Data da última atualização: |
06/07/2009 |
Autoria: |
BAPTISTA, M. J.; SOUZA, R. B. de; LOPES, C. A.; FURUMOTO, O. |
Afiliação: |
Embrapa Hortaliças, Brasília, DF. |
Título: |
Efeito da solarização e biofumigação, em área livre de doenças do solo, sobre a cultura da batata. |
Ano de publicação: |
2005 |
Fonte/Imprenta: |
Horticultura Brasileira, Brasília, DF, v. 23, n. 2, ago. 2005. Suplemento 2. CD-ROM. |
Idioma: |
Português |
Notas: |
Trabalho apresentado no 45. Congresso Brasileiro de Olericultura, Fortaleza, 2005. Publicado também como resumo em: Horticultura Brasileira, Brasília, DF, v. 23, n. 2, p. 357, ago. 2005. Suplemento 1. |
Palavras-Chave: |
Biofumigação; Controle; Doença do solo; Solarização. |
Thesagro: |
Batata; Solanum Tuberosum. |
Categoria do assunto: |
-- |
Marc: |
LEADER 00882naa a2200229 a 4500 001 1778488 005 2009-07-06 008 2005 bl uuuu u00u1 u #d 100 1 $aBAPTISTA, M. J. 245 $aEfeito da solarização e biofumigação, em área livre de doenças do solo, sobre a cultura da batata. 260 $c2005 500 $aTrabalho apresentado no 45. Congresso Brasileiro de Olericultura, Fortaleza, 2005. Publicado também como resumo em: Horticultura Brasileira, Brasília, DF, v. 23, n. 2, p. 357, ago. 2005. Suplemento 1. 650 $aBatata 650 $aSolanum Tuberosum 653 $aBiofumigação 653 $aControle 653 $aDoença do solo 653 $aSolarização 700 1 $aSOUZA, R. B. de 700 1 $aLOPES, C. A. 700 1 $aFURUMOTO, O. 773 $tHorticultura Brasileira, Brasília, DF$gv. 23, n. 2, ago. 2005. Suplemento 2. CD-ROM.
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