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 | Acesso ao texto completo restrito à biblioteca da Embrapa Gado de Leite. Para informações adicionais entre em contato com cnpgl.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
28/11/2014 |
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Data da última atualização: |
05/02/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
O'BRIEN, A. M. P.; MÉSZÁROS, G.; UTSUNOMIYA, Y. T.; SONSTEGARD, T. S.; GARCIA, J. F.; TASSEL, C. P. V.; CARVALHEIRO, R.; SILVA, M. V. G. B.; SÖLKNER, J. |
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Afiliação: |
ANA M. PÉREZ O'BRIEN, University of Natural Resources and Life Sciences, Vienna; GÁBOR MÉSZÁROS, University of Natural Resources and Life Sciences, Vienna; YURI T. UTSUNOMIYA, UNESP; TAD S. SONSTEGARD, ARS-USDA, USA; JOSÉ F. GARCIA, UNESP; CURTIS P. VAN TASSEL, ARS-USDA, USA; ROBERTO CARVALHEIRO, GenSys Consultores Associados; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL; JOHANN SÖLKNER, University of Natural Resources and Life Sciences, Vienna. |
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Título: |
Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions. |
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Ano de publicação: |
2014 |
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Fonte/Imprenta: |
Livestock Science, v. 166, p. 121-132, 2014. |
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Idioma: |
Inglês |
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Conteúdo: |
Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD. This study analyzes levels of LD assessed through the r2 measurement in seven breeds of cattle from both indicine (Bos indicus) and taurine (Bos taurus) (sub)species, genotyped with a high density panel (HD) of over 777,000 single nucleotide polymorphism (SNP) markers. Average levels of LD were assessed for inter-marker distances from 0 kb up to 10 Mb. Two more SNP panels were built in silico from the original genotypes to represent a lower density SNP chip including approximately 50,000 SNPs (50K) and a panel of 249,000 SNPs chosen to comply with specific minor allele frequency (MAF) distributions. The results show higher levels of LD than previously reported, especially at short inter-marker distances of less than 20 kb, assessed through the use of the higher density panel. Negligible impact of MAF changes in the estimation of r2 was observed, supporting the use of the HD panel for LD-based methodologies even when ascertainment bias in the choice of SNPs is suspected. The 50K SNP panel indicated lower levels of LD in the first 100 kb and highly unreliable LD estimates for distances shorter than 50 kb. Overall, lower levels of LD were observed for all indicine breeds as compared to taurine breeds, with larger differences assessed in the first 100 kb, suggesting the need for use of higher SNP densities in this (sub)species when applying LD-dependent methods, as compared to most taurine breeds. MenosLinkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD. This study analyzes levels of LD assessed through the r2 measurement in seven breeds of cattle from both indicine (Bos indicus) and taurine (Bos taurus) (sub)species, genotyped with a high density panel (HD) of over 777,000 single nucleotide polymorphism (SNP) markers. Average levels of LD were assessed for inter-marker distances from 0 kb up to 10 Mb. Two more SNP panels were built in silico from the original genotypes to represent a lower density SNP chip including approximately 50,000 SNPs (50K) and a panel of 249,000 SNPs chosen to comply with specific minor allele frequency (MAF) distributions. The results show higher levels of LD than previously reported, especially at short inter-marker distances of less than 20 kb, assessed through the use of the higher density panel. Negligible impact of MAF changes in the estimation of r2 was observed, supporting the use of the HD panel for LD-based methodologies even when ascertainment bias in the choice of SNPs is suspected. The 50K SNP panel indicated lower levels of LD in the first 100 kb and highly unreliable LD estimates for distances shorter than 50 kb. Overall, lower levels of LD... Mostrar Tudo |
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Palavras-Chave: |
Indicine; Minor allele frequency. |
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Thesaurus Nal: |
cattle; linkage disequilibrium; taurine. |
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Categoria do assunto: |
L Ciência Animal e Produtos de Origem Animal |
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Marc: |
LEADER 02632naa a2200277 a 4500
001 2001105
005 2024-02-05
008 2014 bl uuuu u00u1 u #d
100 1 $aO'BRIEN, A. M. P.
245 $aLinkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions.$h[electronic resource]
260 $c2014
520 $aLinkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD. This study analyzes levels of LD assessed through the r2 measurement in seven breeds of cattle from both indicine (Bos indicus) and taurine (Bos taurus) (sub)species, genotyped with a high density panel (HD) of over 777,000 single nucleotide polymorphism (SNP) markers. Average levels of LD were assessed for inter-marker distances from 0 kb up to 10 Mb. Two more SNP panels were built in silico from the original genotypes to represent a lower density SNP chip including approximately 50,000 SNPs (50K) and a panel of 249,000 SNPs chosen to comply with specific minor allele frequency (MAF) distributions. The results show higher levels of LD than previously reported, especially at short inter-marker distances of less than 20 kb, assessed through the use of the higher density panel. Negligible impact of MAF changes in the estimation of r2 was observed, supporting the use of the HD panel for LD-based methodologies even when ascertainment bias in the choice of SNPs is suspected. The 50K SNP panel indicated lower levels of LD in the first 100 kb and highly unreliable LD estimates for distances shorter than 50 kb. Overall, lower levels of LD were observed for all indicine breeds as compared to taurine breeds, with larger differences assessed in the first 100 kb, suggesting the need for use of higher SNP densities in this (sub)species when applying LD-dependent methods, as compared to most taurine breeds.
650 $acattle
650 $alinkage disequilibrium
650 $ataurine
653 $aIndicine
653 $aMinor allele frequency
700 1 $aMÉSZÁROS, G.
700 1 $aUTSUNOMIYA, Y. T.
700 1 $aSONSTEGARD, T. S.
700 1 $aGARCIA, J. F.
700 1 $aTASSEL, C. P. V.
700 1 $aCARVALHEIRO, R.
700 1 $aSILVA, M. V. G. B.
700 1 $aSÖLKNER, J.
773 $tLivestock Science$gv. 166, p. 121-132, 2014.
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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Registro Completo
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Biblioteca(s): |
Embrapa Milho e Sorgo. |
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Data corrente: |
25/06/2004 |
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Data da última atualização: |
05/06/2018 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
BRITO, A. R.; GONCALVES, L. C.; RODRIGUES, J. A. S.; ROCHA JUNIOR, V. R.; RODRIGUEZ, N. M.; BORGES, I. |
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Afiliação: |
JOSE AVELINO SANTOS RODRIGUES, CNPMS. |
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Título: |
Avaliação da silagem de sete genótipos de sorgo {(Sorghum bicolor (L.) Moench)}. II. Padrão de fermentação. |
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Ano de publicação: |
2000 |
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Fonte/Imprenta: |
Arquivo Brasileiro de Medicina Veterinaria e Zootecnia, Belo Horizonte, v. 52, n. 5, p. 491-497, out. 2000. |
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Idioma: |
Português |
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Conteúdo: |
Foram utilizados quatro genótipos de sorgo de porte alto, colmo suculento e com açúcar e três de porte baixo, colmo seco e sem açúcar com o objetivo de determinar as percentagens de matéria seca (MS), proteína bruta (PB), nitrogênio amoniacal em relação ao nitrogênio total (N-NH3/NT), pH e carboidratos solúveis em álcool (CHOS). O sorgo CMSXS156, de porte baixo, apresentou, o maior teor de MS (33,6%) aos 28 dias de ensilagem. Os genótipos de porte baixo tiveram em média 8,8% de PB e os de porte alto 5
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Thesagro: |
Sorgo. |
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Categoria do assunto: |
F Plantas e Produtos de Origem Vegetal |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/30989/1/Avaliacao-silagem-II.pdf
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Marc: |
LEADER 01651naa a2200193 a 4500
001 1487697
005 2018-06-05
008 2000 bl uuuu u00u1 u #d
100 1 $aBRITO, A. R.
245 $aAvaliação da silagem de sete genótipos de sorgo {(Sorghum bicolor (L.) Moench)}. II. Padrão de fermentação.$h[electronic resource]
260 $c2000
520 $aForam utilizados quatro genótipos de sorgo de porte alto, colmo suculento e com açúcar e três de porte baixo, colmo seco e sem açúcar com o objetivo de determinar as percentagens de matéria seca (MS), proteína bruta (PB), nitrogênio amoniacal em relação ao nitrogênio total (N-NH3/NT), pH e carboidratos solúveis em álcool (CHOS). O sorgo CMSXS156, de porte baixo, apresentou, o maior teor de MS (33,6%) aos 28 dias de ensilagem. Os genótipos de porte baixo tiveram em média 8,8% de PB e os de porte alto 5<X diferença provavelmente devida à maior proporção de folhas e panícula nos de porte baixo. O pH médio d silagens aos 56 dias de fermentação foi de 3,6 e variou de 3,5 a 3,8, e o teor médio de N-NH/NT nesse mesmo período foi de 5,3%, mostrando que as silagens apresentaram um adequado processo fermentativo O teor médio de CHOS no material original foi de 9,7% e a variação de 13,2 a 16,5% e de 2,2 a 4,0% nos genótipos de porte alto e baixo, respectivamente.
650 $aSorgo
700 1 $aGONCALVES, L. C.
700 1 $aRODRIGUES, J. A. S.
700 1 $aROCHA JUNIOR, V. R.
700 1 $aRODRIGUEZ, N. M.
700 1 $aBORGES, I.
773 $tArquivo Brasileiro de Medicina Veterinaria e Zootecnia, Belo Horizonte$gv. 52, n. 5, p. 491-497, out. 2000.
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Embrapa Milho e Sorgo (CNPMS) |
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