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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
15/02/2016 |
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Data da última atualização: |
06/02/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
BOISON, S. A.; SANTOS, D. J. A.; UTSONOMIYA, A. H. T.; CARVALHEIRO, R.; NEVES, H. H. R.; O'BRIEN, A. M. P.; GARCIA, J. F.; SÖLKNER, J.; SILVA, M. V. G. B. |
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Afiliação: |
S. A. Boison, University of Natural Resources and Life Sciences, Vienna, Austria; D. J. A. Santos, UNESP; A. H. T. Utsunomiya, UNESP; R. Carvalheiro, UNESP; H. H. R. Neves, UNESP; A. M. Perez O'Brien, University of Natural Resources and Life Sciences, Vienna, Aústria; J. F. Garcia, UNESP; J. Sölkner, University of Natural Resources and Life Sciences, Vienna, Aústria; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL. |
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Título: |
Strategies for single nucleotide polymorphism (SNP) genotyping to enhance genotype imputation in Gyr (Bos indicus) dairy cattle: Comparison of commercially available SNP chips. |
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Ano de publicação: |
2015 |
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Fonte/Imprenta: |
Journal of Dairy Science, v. 98, n. 7, p. 4969-4989, 2015. |
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Idioma: |
Português |
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Conteúdo: |
Genotype imputation is widely used as a cost-effective strategy in genomic evaluation of cattle. Key determinants of imputation accuracies, such as linkage disequilibrium patterns, marker densities, and ascertainment bias, differ between Bos indicus and Bos taurus breeds. Consequently, there is a need to investigate effectiveness of genotype imputation in indicine breeds. Thus, the objective of the study was to investigate strategies and factors affecting the accuracy of genotype imputation in Gyr (Bos indicus) dairy cattle. Four imputation scenarios were studied using 471 sires and 1,644 dams genotyped on Illumina BovineHD (HD-777K; San Diego, CA) and BovineSNP50 (50K) chips, respectively. Scenarios were based on which reference high-density single nucleotide polymorphism (SNP) panel (HDP) should be adopted [HD-777K, 50K, and GeneSeek GGP-75Ki (Lincoln, NE)]. Depending on the scenario, validation animals had their genotypes masked for one of the lower-density panels: Illumina (3K, 7K, and 50K) and GeneSeek (SGGP-20Ki and GGP-75Ki). We randomly selected 171 sires as reference and 300 as validation for all the scenarios. Additionally, all sires were used as reference and the 1,644 dams were imputed for validation. Genotypes of 98 individuals with 4 and more offspring were completely masked and imputed. Imputation algorithms FImpute and Beagle v3.3 and v4 were used. Imputation accuracies were measured using the correlation and allelic correct rate. FImpute resulted in highest accuracies, whereas Beagle 3.3 gave the least-accurate imputations. Accuracies evaluated as correlation (allelic correct rate) ranged from 0.910 (0.942) to 0.961 (0.974) using 50K as HDP and with 3K (7K) as low-density panels. With GGP-75Ki as HDP, accuracies were moderate for 3K, 7K, and 50K, but high for SGGP-20Ki. The use of HD-777K as HDP resulted in accuracies of 0.888 (3K), 0.941 (7K), 0.980 (SGGP-20Ki), 0.982 (50K), and 0.993 (GGP-75Ki). Ungenotyped individuals were imputed with an average accuracy of 0.970. The average top 5 kinship coefficients between reference and imputed individuals was a strong predictor of imputation accuracy. FImpute was faster and used less memory than Beagle v4. Beagle v4 outperformed Beagle v3.3 in accuracy and speed of computation. A genotyping strategy that uses the HD-777K SNP chip as a reference panel and SGGP-20Ki as the lower-density SNP panel should be adopted as accuracy was high and similar to that of the 50K. However, the effect of using imputed HD-777K genotypes from the SGGP-20Ki on genomic evaluation is yet to be studied. MenosGenotype imputation is widely used as a cost-effective strategy in genomic evaluation of cattle. Key determinants of imputation accuracies, such as linkage disequilibrium patterns, marker densities, and ascertainment bias, differ between Bos indicus and Bos taurus breeds. Consequently, there is a need to investigate effectiveness of genotype imputation in indicine breeds. Thus, the objective of the study was to investigate strategies and factors affecting the accuracy of genotype imputation in Gyr (Bos indicus) dairy cattle. Four imputation scenarios were studied using 471 sires and 1,644 dams genotyped on Illumina BovineHD (HD-777K; San Diego, CA) and BovineSNP50 (50K) chips, respectively. Scenarios were based on which reference high-density single nucleotide polymorphism (SNP) panel (HDP) should be adopted [HD-777K, 50K, and GeneSeek GGP-75Ki (Lincoln, NE)]. Depending on the scenario, validation animals had their genotypes masked for one of the lower-density panels: Illumina (3K, 7K, and 50K) and GeneSeek (SGGP-20Ki and GGP-75Ki). We randomly selected 171 sires as reference and 300 as validation for all the scenarios. Additionally, all sires were used as reference and the 1,644 dams were imputed for validation. Genotypes of 98 individuals with 4 and more offspring were completely masked and imputed. Imputation algorithms FImpute and Beagle v3.3 and v4 were used. Imputation accuracies were measured using the correlation and allelic correct rate. FImpute resulted in highest ... Mostrar Tudo |
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Palavras-Chave: |
FImpute; Gyr; Imputation. |
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Thesaurus Nal: |
Beagle. |
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Categoria do assunto: |
L Ciência Animal e Produtos de Origem Animal |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/138978/1/Cnpgl-2015-JDairySci-Strategies.pdf
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Marc: |
LEADER 03421naa a2200265 a 4500
001 2036928
005 2024-02-06
008 2015 bl uuuu u00u1 u #d
100 1 $aBOISON, S. A.
245 $aStrategies for single nucleotide polymorphism (SNP) genotyping to enhance genotype imputation in Gyr (Bos indicus) dairy cattle$bComparison of commercially available SNP chips.$h[electronic resource]
260 $c2015
520 $aGenotype imputation is widely used as a cost-effective strategy in genomic evaluation of cattle. Key determinants of imputation accuracies, such as linkage disequilibrium patterns, marker densities, and ascertainment bias, differ between Bos indicus and Bos taurus breeds. Consequently, there is a need to investigate effectiveness of genotype imputation in indicine breeds. Thus, the objective of the study was to investigate strategies and factors affecting the accuracy of genotype imputation in Gyr (Bos indicus) dairy cattle. Four imputation scenarios were studied using 471 sires and 1,644 dams genotyped on Illumina BovineHD (HD-777K; San Diego, CA) and BovineSNP50 (50K) chips, respectively. Scenarios were based on which reference high-density single nucleotide polymorphism (SNP) panel (HDP) should be adopted [HD-777K, 50K, and GeneSeek GGP-75Ki (Lincoln, NE)]. Depending on the scenario, validation animals had their genotypes masked for one of the lower-density panels: Illumina (3K, 7K, and 50K) and GeneSeek (SGGP-20Ki and GGP-75Ki). We randomly selected 171 sires as reference and 300 as validation for all the scenarios. Additionally, all sires were used as reference and the 1,644 dams were imputed for validation. Genotypes of 98 individuals with 4 and more offspring were completely masked and imputed. Imputation algorithms FImpute and Beagle v3.3 and v4 were used. Imputation accuracies were measured using the correlation and allelic correct rate. FImpute resulted in highest accuracies, whereas Beagle 3.3 gave the least-accurate imputations. Accuracies evaluated as correlation (allelic correct rate) ranged from 0.910 (0.942) to 0.961 (0.974) using 50K as HDP and with 3K (7K) as low-density panels. With GGP-75Ki as HDP, accuracies were moderate for 3K, 7K, and 50K, but high for SGGP-20Ki. The use of HD-777K as HDP resulted in accuracies of 0.888 (3K), 0.941 (7K), 0.980 (SGGP-20Ki), 0.982 (50K), and 0.993 (GGP-75Ki). Ungenotyped individuals were imputed with an average accuracy of 0.970. The average top 5 kinship coefficients between reference and imputed individuals was a strong predictor of imputation accuracy. FImpute was faster and used less memory than Beagle v4. Beagle v4 outperformed Beagle v3.3 in accuracy and speed of computation. A genotyping strategy that uses the HD-777K SNP chip as a reference panel and SGGP-20Ki as the lower-density SNP panel should be adopted as accuracy was high and similar to that of the 50K. However, the effect of using imputed HD-777K genotypes from the SGGP-20Ki on genomic evaluation is yet to be studied.
650 $aBeagle
653 $aFImpute
653 $aGyr
653 $aImputation
700 1 $aSANTOS, D. J. A.
700 1 $aUTSONOMIYA, A. H. T.
700 1 $aCARVALHEIRO, R.
700 1 $aNEVES, H. H. R.
700 1 $aO'BRIEN, A. M. P.
700 1 $aGARCIA, J. F.
700 1 $aSÖLKNER, J.
700 1 $aSILVA, M. V. G. B.
773 $tJournal of Dairy Science$gv. 98, n. 7, p. 4969-4989, 2015.
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Esconder MarcMostrar Marc Completo |
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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Biblioteca |
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Tipo/Formato |
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| Registros recuperados : 31 | |
| 1. |  | COSTA JÚNIOR, D, S. Avaliação clonal e pós-colheita de híbridos de abacaxi ornamental. 2014. 99f. il. Dissertação (Mestrado em Ciência Agrárias)- Universidade Federal do Recôncavo da Bahia, Cruz das Almas. Orlentadora: Profa. Dra. Maria Angélica Pereira de Carvalho Costa; Coorientadores: Dr. Márclo Eduardo Canto Pereira (CNMPF); Dra. Fernanda Vldigal Duarte Souza (CNMPF).| Tipo: Orientação de Tese de Pós-Graduação |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
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| 9. | | OLIVEIRA, M. F.; PEREIRA, M. E. C.; COSTA JÚNIOR, D. S.; SOUZA, F. V. D. Vida útil pós-colheita de hastes florais de abacaxi ornamental armazenadas com embalagem plástica ou tratadas com cera de carnaúba. In: JORNADA CIENTÍFICA EMBRAPA MANDIOCA E FRUTICULTURA, 8., 2014, Cruz das Almas, Ba. Pesquisa: despertando mentes para a inovação e transformando o futuro: [anais]. Cruz das Almas, BA, Embrapa Mandioca e Fruticultura, 2014.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
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| 10. | | SOUZA, E. H. de; SOUZA, F. V. D.; COSTA JÚNIOR, D. S.; COSTA, M. A. P. de C. Avaliação de abacaxi ornamental em vaso. In: CONGRESSO BRASILEIRO DE CULTURA DE TECIDOS DE PLANTAS, 4.; 2009, Aracaju. Ciência, inovação e sustentabilidade: [anais...]. Aracaju: Embrapa Tabuleiros Costeiros; Cruz das Almas: Embrapa Mandioca e Fruticultura Tropical, 2009. 1 CD-ROM. (Embrapa Tabuleiros Costeiros. Documentos, 150). Organizadores: Ana da Silva Lédo; Fernanda Vidigal D. Souza; Vivian Loges; Everton Hilo de Souza; Ana Cecília R. de Castro.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
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| 12. | | COSTA JUNIOR, D. S.; SOUZA, E. H. de; COSTA, M. A. P. de C.; PEREIRA, M. E. C. Clonal evaluation of new ornamental pineapple hybrids to use as cut flowers. Acta Scientiarum, Maringá, v. 38, n. 4, p. 475-483, Oct.-Dec., 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
|  |
| 13. | | COSTA JUNIOR, D. S.; SOUZA, E. H. de; SOUZA, F. V. D.; COSTA, M. A. P. de C. Caracterização de Ananas macrodontes Morren para uso como planta ornamental. In: CONGRESSO BRASILEIRO DE FLORICULTURA E PLANTAS ORNAMENTAIS, 17.; CONGRESSO BRASILEIRO DE CULTURA DE TECIDOS DE PLANTAS, 4.; 2009, Aracaju. Ciência, inovação e sustentabilidade: [anais...]. Aracaju: Embrapa Tabuleiros Costeiros; Cruz das Almas: Embrapa Mandioca e Fruticultura Tropical, 2009. 1 CD-ROM. (Embrapa Tabuleiros Costeiros. Documentos, 150). Organizadores: Ana da Silva Lédo; Fernanda Vidigal D. Souza; Vivian Loges; Everton Hilo de Souza; Ana Cecília R. de Castro.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
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| 14. | | COSTA JÚNIOR, D. S.; SOUZA, F. V. D.; PEREIRA, M. E. C.; COSTA, M. A. P. de C. Desverdecimento de frutos de kumquat para fins ornamentais. In: SIMPÓSIO BRASILEIRO DE PÓS-COLHEITA DE FRUTAS, HORTALIÇAS E FLORES, 4.; ENCONTRO NACIONAL SOBRE PROCESSAMENTO MÍNIMO DE FRUTAS E HORTALIÇAS, 7., 2013, Ribeirão Preto. Internacionalizar para não perecer: anais. Ribeirão Preto: USP-Faculdade de Ciências Farmacêuticas de Ribeirão Preto, 2013. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
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| 16. | | SOUZA, F. V. D.; SOUZA, E. H. de; COSTA JÚNIOR, D. S.; LEDO, C. A. da S. Desenvolvimento e qualidade de hastes do híbrido ornamental de abacaxi. In: CONGRESSO BRASILEIRO DE RECURSOS GENÉTICOS, 2., 2012, Belém, PA. Anais... Brasília, DF: Sociedade Brasileira de Recursos Genéticos, 2012. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
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| 17. | | SOUZA, F. V. D.; SOUZA, E. H. de; COSTA, M. A. P. de C.; COSTA JUNIOR, D. S. Importância relativa de caracteres morfológicos quantitativos em abacaxizeiros ornamentais. In: CONGRESSO BRASILEIRO DE RECURSOS GENÉTICOS; WORKSHOP EM BIOPROSPECÇÃO E CONSERVAÇÃO DE PLANTAS NATIVAS DO SEMI-ÁRIDO, 3.; WORKSHOP INTERNACIONAL SOBRE BIOENERGIA E MEIO AMBIENTE, 2010, Salvador. Bancos de germoplasma: descobrir a riqueza, garantir o futuro: anais. Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2010. 1 CD-ROM (Embrapa Recursos Genéticos e Biotecnologia. Documentos, 304). PDF 372.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
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| 19. | | COSTA JÚNIOR, D. S.; SEREJO, J. A. dos S.; PEREIRA, M. E. C.; COSTA, M. A. P. de C. Uso de cera à base de carnaúba em minifrutos de um híbrido de bananeira ornamental. In: SIMPÓSIO BRASILEIRO DE PÓS-COLHEITA DE FRUTAS, HORTALIÇAS E FLORES, 4.; ENCONTRO NACIONAL SOBRE PROCESSAMENTO MÍNIMO DE FRUTAS E HORTALIÇAS, 7., 2013, Ribeirão Preto. Internacionalizar para não perecer: anais. Ribeirão Preto: USP-Faculdade de Ciências Farmacêuticas de Ribeirão Preto, 2013. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
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| 20. | | SOUZA, E. H. de; SOUZA, F. V. D.; COSTA, M. A. P. de C.; COSTA JUNIOR, D. S.; LEDO, C. A. da S. Dissimilaridade genética em abacaxizeiros com potencial ornamental. In: CONGRESSO BRASILEIRO DE RECURSOS GENÉTICOS; WORKSHOP EM BIOPROSPECÇÃO E CONSERVAÇÃO DE PLANTAS NATIVAS DO SEMI-ÁRIDO, 3.; WORKSHOP INTERNACIONAL SOBRE BIOENERGIA E MEIO AMBIENTE, 2010, Salvador. Bancos de germoplasma: descobrir a riqueza, garantir o futuro: anais. Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2010. 1 CD-ROM (Embrapa Recursos Genéticos e Biotecnologia. Documentos, 304). pdf 280.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Mandioca e Fruticultura. |
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| Registros recuperados : 31 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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