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 | Acesso ao texto completo restrito à biblioteca da Embrapa Pecuária Sul. Para informações adicionais entre em contato com cppsul.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Pecuária Sul. |
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Data corrente: |
15/07/2019 |
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Data da última atualização: |
23/10/2019 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
SOLLERO, B. P.; HOWARD, J. T.; SPANGLER, M. L. |
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Afiliação: |
BRUNA PENA SOLLERO, CPPSUL; Jeremy T Howard; Matthew L Spangler. |
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Título: |
The impact of reducing the frequency of animals genotyped at higher density on imputation and prediction accuracies using ssGBLUP. |
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Ano de publicação: |
2019 |
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Fonte/Imprenta: |
Journal of Animal Science, v. 97, n. 7, p. 2780-2792, July 2019. |
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DOI: |
doi-org.ez103.periodicos.capes.gov.br/10.1093/jas/skz147 |
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Idioma: |
Inglês |
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Conteúdo: |
The largest gains in accuracy in a genomic selection program come from genotyping young selection candidates who have not yet produced progeny and who might, or might not, have a phenotypic record recorded. To reduce genotyping costs and to allow for an increased amount of genomic data to be available in a population, young selection candidates may be genotyped with low-density (LD) panels and imputed to a higher density. However, to ensure that a reasonable imputation accuracy persists overtime, some parent animals originally genotyped at LD must be re-genotyped at a higher density. This study investigated the long-term impact of selectively re-genotyping parents with a medium-density (MD) SNP panel on the accuracy of imputation and on the genetic predictions using ssGBLUP in a simulated beef cattle population. Assuming a moderately heritable trait (0.25) and a population undergoing selection, the simulation generated sequence data for a founder population (100 male and 500 female individuals) and 9,000 neutral markers, considered as the MD panel. All selection candidates from generation 8 to 15 were genotyped with LD panels corresponding to a density of 0.5% (LD_0.5), 2% (LD_2), and 5% (LD_5) of the MD. Re-genotyping scenarios chose parents at random or based on EBV and ranged from 10% of male parents to re-genotyping all male and female parents with MD. Ranges in average imputation accuracy at generation 15 were 0.567 to 0.936, 0.795 to 0.985, and 0.931 to 0.995 for the LD_0.5, LD_2, and LD_5, respectively, and the average EBV accuracies ranged from 0.453 to 0.735, 0.631 to 0.784, and 0.748 to 0.807 for LD_0.5, LD_2, and LD_5, respectively. Re-genotyping parents based on their EBV resulted in higher imputation and EBV accuracies compared to selecting parents at random and these values increased with the size of LD panels. Differences between re-genotyping scenarios decreased when the density of the LD panel increased, suggesting fewer animals needed to be re-genotyped to achieve higher accuracies. In general, imputation and EBV accuracies were greater when more parents were re-genotyped, independent of the proportion of males and females. In practice, the relationship between the density of the LD panel used and the target panel must be considered to determine the number (proportion) of animals that would need to be re-genotyped to enable sufficient imputation accuracy. MenosThe largest gains in accuracy in a genomic selection program come from genotyping young selection candidates who have not yet produced progeny and who might, or might not, have a phenotypic record recorded. To reduce genotyping costs and to allow for an increased amount of genomic data to be available in a population, young selection candidates may be genotyped with low-density (LD) panels and imputed to a higher density. However, to ensure that a reasonable imputation accuracy persists overtime, some parent animals originally genotyped at LD must be re-genotyped at a higher density. This study investigated the long-term impact of selectively re-genotyping parents with a medium-density (MD) SNP panel on the accuracy of imputation and on the genetic predictions using ssGBLUP in a simulated beef cattle population. Assuming a moderately heritable trait (0.25) and a population undergoing selection, the simulation generated sequence data for a founder population (100 male and 500 female individuals) and 9,000 neutral markers, considered as the MD panel. All selection candidates from generation 8 to 15 were genotyped with LD panels corresponding to a density of 0.5% (LD_0.5), 2% (LD_2), and 5% (LD_5) of the MD. Re-genotyping scenarios chose parents at random or based on EBV and ranged from 10% of male parents to re-genotyping all male and female parents with MD. Ranges in average imputation accuracy at generation 15 were 0.567 to 0.936, 0.795 to 0.985, and 0.931 to 0.995 for the L... Mostrar Tudo |
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Palavras-Chave: |
Coeficiente de parentesco; Habilidade preditiva; Herdabilidade; Validação cruzada. |
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Thesagro: |
Melhoramento Genético Animal; Seleção Genótipa. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 03224naa a2200229 a 4500
001 2110612
005 2019-10-23
008 2019 bl uuuu u00u1 u #d
024 7 $adoi-org.ez103.periodicos.capes.gov.br/10.1093/jas/skz147$2DOI
100 1 $aSOLLERO, B. P.
245 $aThe impact of reducing the frequency of animals genotyped at higher density on imputation and prediction accuracies using ssGBLUP.$h[electronic resource]
260 $c2019
520 $aThe largest gains in accuracy in a genomic selection program come from genotyping young selection candidates who have not yet produced progeny and who might, or might not, have a phenotypic record recorded. To reduce genotyping costs and to allow for an increased amount of genomic data to be available in a population, young selection candidates may be genotyped with low-density (LD) panels and imputed to a higher density. However, to ensure that a reasonable imputation accuracy persists overtime, some parent animals originally genotyped at LD must be re-genotyped at a higher density. This study investigated the long-term impact of selectively re-genotyping parents with a medium-density (MD) SNP panel on the accuracy of imputation and on the genetic predictions using ssGBLUP in a simulated beef cattle population. Assuming a moderately heritable trait (0.25) and a population undergoing selection, the simulation generated sequence data for a founder population (100 male and 500 female individuals) and 9,000 neutral markers, considered as the MD panel. All selection candidates from generation 8 to 15 were genotyped with LD panels corresponding to a density of 0.5% (LD_0.5), 2% (LD_2), and 5% (LD_5) of the MD. Re-genotyping scenarios chose parents at random or based on EBV and ranged from 10% of male parents to re-genotyping all male and female parents with MD. Ranges in average imputation accuracy at generation 15 were 0.567 to 0.936, 0.795 to 0.985, and 0.931 to 0.995 for the LD_0.5, LD_2, and LD_5, respectively, and the average EBV accuracies ranged from 0.453 to 0.735, 0.631 to 0.784, and 0.748 to 0.807 for LD_0.5, LD_2, and LD_5, respectively. Re-genotyping parents based on their EBV resulted in higher imputation and EBV accuracies compared to selecting parents at random and these values increased with the size of LD panels. Differences between re-genotyping scenarios decreased when the density of the LD panel increased, suggesting fewer animals needed to be re-genotyped to achieve higher accuracies. In general, imputation and EBV accuracies were greater when more parents were re-genotyped, independent of the proportion of males and females. In practice, the relationship between the density of the LD panel used and the target panel must be considered to determine the number (proportion) of animals that would need to be re-genotyped to enable sufficient imputation accuracy.
650 $aMelhoramento Genético Animal
650 $aSeleção Genótipa
653 $aCoeficiente de parentesco
653 $aHabilidade preditiva
653 $aHerdabilidade
653 $aValidação cruzada
700 1 $aHOWARD, J. T.
700 1 $aSPANGLER, M. L.
773 $tJournal of Animal Science$gv. 97, n. 7, p. 2780-2792, July 2019.
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Embrapa Pecuária Sul (CPPSUL) |
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| 10. |  | REIS, V. M.; OLIVEIRA, R. P.; SCHULTZ, N.; ARAÚJO, A. P.; URQUIAGA, S. Análise de crescimento e acúmulo de nutrientes pela variedade RB92579 de cana-de-açúcar plantada em um argissolo com e sem inoculação e aplicação de N-fertilizante. IBEMPA CONFERENCE, 2.; NATIONAL MEETING OF THE SPANISH SOCIETY OF NITROGEN FIXATION (SEFIN), 14; LATIN AMERICAN MEETING ON RHIZOBIOLOGY (ALAR), 26.; SPANISH-PORTUGUESE CONGRESS ON NITROGEN FIXATION, 3., 2013, Sevilla. Microorganisms for future agriculture: [works and papers...]. Sevilla: Universidad Sevilla, 2013.| Tipo: Artigo em Anais de Congresso |
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| 17. | | MONTEIRO, R. C.; MACHADO, D. O.; SOUSA, J. S; SCHULTZ, N.; REIS, V. M. Desenvolvimento de cana-de-açúcar em função de diferentes métodos de aplicação do inoculante com bactérias diazotróficas In: SEMANA CIENTÍFICA JOHANNA DÖBEREINER, 13., 2013, Seropédica Ciência, saúde e esporte: caderno de resumos... Seropédica: Embrapa Agrobiologia, 2013.| Tipo: Resumo em Anais de Congresso |
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| 19. | | SILVA, J. A.; SCHULTZ, N.; ALVES, B. J. R.; BODDEY, R. M.; URQUIAGA, S. Potencial produtivo de cana-de-açúcar sem adubação nitrogenada em estudo de longo prazo. In: CONGRESSO BRASILEIRO DE CIÊNCIA DO SOLO, 33., 2011, Uberlândia. Solos nos biomas brasileiros: sustentabilidade e mudanças climáticas: anais. [Uberlândia]: SBCS: UFU, ICIAG, 2011.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agrobiologia. |
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| 20. | | SILVA, J. A.; SCHULTZ, N.; URQUIAGA, S.; ALVES, B. J. R.; BODDEY, R. M. Potencial produtivo de cana-de-açúcar sem adubação nitrogenada em estudo de longo prazo. In: CONGRESSO BRASILEIRO DE CIÊNCIA DO SOLO, 33., 2011, Uberlândia. Solos nos biomas brasileiros: sustentabilidade e mudanças climáticas: anais. [Uberlândia]: SBCS: UFU, ICIAG, 2011.| Tipo: Resumo em Anais de Congresso |
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