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| Registros recuperados : 9 | |
| 1. |  | LEITE, D. C. A.; BALIEIRO, F. C.; C. A. PIRES; MADARI, B. E.; ROSADO, A. S.; COUTINHO, H. L. C.; PEIXOTO, R. S. Comparison of DNA extraction protocols for microbial communities from soil treated with biochar. Brazilian Journal of Microbiology, São Paulo, v. 45, n. 1, p. 175-183, 2014.| Biblioteca(s): Embrapa Arroz e Feijão; Embrapa Solos. |
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| 2. | | LEITE, D. C. A.; BALIEIRO, F. de C.; LEITE, L. F. C.; MADARI, B. E.; RIBEIRO, A. de F.; PEIXOTO, R. S.; ROSADO, A. S. Integrated crop-livestock-forest system presents a different soil microbial structure in comparison to other land uses. In: WORLD CONGRESS ON INTEGRATED CROP-LIVESTOCK-FOREST SYSTEMS; INTERNATIONAL SYMPOSIUM ON INTEGRATED CROP-LIVESTOCK SYSTEMS, 3., 2015, Brasília, DF. Towards sustainable intensification: proceedings. Brasília, DF: Embrapa, 2015.| Biblioteca(s): Embrapa Arroz e Feijão; Embrapa Meio-Norte. |
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| 3. | | LEITE, D. C. A.; BALIEIRO, F. de C.; LEITE, L. F. C.; MADARI, B. E.; RIBEIRO, A. de F.; PEIXOTO, R. S.; ROSADO, A. S. Integrated crop-livestock-forest system presents a different soil microbial structure in comparison to other land uses. In: WORLD CONGRESS ON INTEGRATED CROP-LIVESTOCK-FOREST SYSTEMS; INTERNATIONAL SYMPOSIUM ON INTEGRATED CROP-LIVESTOCK SYSTEMS, 3., 2015, Brasília, DF. Towards sustainable intensification: proceedings. Brasília, DF: Embrapa, 2015.| Biblioteca(s): Embrapa Solos. |
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| 4. | | RACHID, C. T. C. C.; LEITE, D. C. A.; CHAER, G. M.; BALIEIRO, F. de C.; PICCOLO, M. de C.; ROSADO, A. S.; PEIXOTO, R. Acacia mangium affects soil nitrogen nd microbial community an ctivity in mixed plantations with eucalyptus urograndis. In: ACACIA, 2014, Hue, Vietnan. Resumo.... Vienna, Austria: IUFRO, 2014. 1 p.| Biblioteca(s): Embrapa Solos. |
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| 5. | | LEITE, D. C. A.; BALIEIRO, F. de C.; MADARI, B. E.; PIRES, C. A.; COUTINHO, H. L. C.; ROSADO, A. S. Alterações na estrutura da comunidade bacteriana associada à rizosferas de plantas de arroz (Oryza sativa), cultivar BRSMG Curinga, sob efeito de diferentes carvões. In: CONGRESSO BRASILEIRO DE MICROBIOLOGIA, 26., 2011, Foz do Iguaçu. Anais... São Paulo: Sociedade Brasileira de Microbiologia, 2011.| Biblioteca(s): Embrapa Solos. |
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| 6. | | RACHID, C. T. C. C.; PIRES, C. A.; LEITE, D. C. A.; COUTINHO, H. L. C.; PEIXOTO, R. S.; ROSADO, A. S.; SALTON, J.; ZANATTA, J. A.; MERCANTE, F. M.; ANGELINI, G. A. R.; BALIEIRO, F. de C. Sugarcane trash levels in soil affects the fungi but not bacteria in a short-term field experiment. Brazilian Journal of Microbiology, São Paulo, v. 47, n. 2, p. 322-326, abr./jun. 2016.| Biblioteca(s): Embrapa Agropecuária Oeste; Embrapa Florestas; Embrapa Solos. |
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| 7. | | PIRES, C. A.; LEITE, D. C. A.; COSTA, C. T. R. C.; ANGELINI, G. A. R.; PEIXOTO, R. S.; ROSADO, A. S.; COUTINHO, H. L. C.; ZANATTA, J.; SALTON, J.; BALIEIRO, F. C. Impacto de diferentes níveis de palhada de cana-de-açúcar sobre comunidade fúngica total de latossolo do cerrado. In: CONGRESSO BRASILEIRO DE CIÊNCIA DO SOLO, 33., 2011, Uberlândia. Solos nos biomas brasileiros: sustentabilidade e mudanças climáticas: anais. [Uberlândia]: SBCS: UFU, ICIAG, 2011.| Biblioteca(s): Embrapa Solos. |
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| 8. | | RACHID, C. T. C. C.; SANTOS, L. A.; LEITE, D. C. A.; PICCOLO, M. C.; BALIEIRO, F.; COUTINHO, H. L. C.; TIEDJE, J. M.; PEIXOTO, R. S.; ROSADO, A. S. Pirosequenciamento revela alta diversidade e mudanças estruturais significativas da comunidade basteriana de solo sob Cerrado e cana-de-açúcar. In: CONGRESSO BRASILEIRO DE MICROBIOLOGIA, 26., 2011, Foz do Iguaçu. Anais... São Paulo: Sociedade Brasileira de Microbiologia, 2011.| Biblioteca(s): Embrapa Solos. |
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| 9. | | RACHID, C. T. C. C.; PICCOLO, M. C.; LEITE, D. C. A.; BALIEIRO, F. de C.; COUTINHO, H. L. da C.; ELSAS, J. D. van; PEIXOTO, R. S.; ROSADO, A. S. Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems. BMC Microbiology, v. 12, 170, 2012.| Biblioteca(s): Embrapa Solos. |
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| Registros recuperados : 9 | |
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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. |
Registro Completo
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
16/11/2017 |
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Data da última atualização: |
09/02/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
OLIVEIRA JÚNIOR, G. A.; CHUD, T. C. S.; VENTURA, R. V.; GARRICK, D. J.; COLE, J. B.; MUNARI, D. P.; FERRAZ, J. B. S.; MULLART, E.; DeNISE, S.; SMITH, S.; SILVA, M. V. G. B. |
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Afiliação: |
Gerson A. Oliveira Júnior, USP; Tatiane C. S. Chud, UNESP; Ricardo V. Ventura, University of Guelph, Guelph, Canada; Dorian J. Garrick, Iowa State University, Ames; John B. Cole, United States Department of Agriculture, Agricultural Research Service, Maryland, USA; Danísio Prado Munari, UNESP Jaboticabal; José B. S. Ferraz, USP; Erik Mullart, CRV Holding B. V., Arnhem, 454, the Netherlands; SUE DeNISE, Zoetis, Kalamazoo, MI; SHANNON SMITH, Zoetis, Kalamazoo, MI; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL. |
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Título: |
Genotype imputation in a tropical crossbred dairy cattle population. |
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Ano de publicação: |
2017 |
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Fonte/Imprenta: |
Journal of Dairy Science, v. 100, n. 12, p. 9623-9634, 2017. |
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DOI: |
https://doi.org/10.3168/jds.2017-12732 |
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Idioma: |
Inglês |
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Conteúdo: |
The objective of this study was to investigate different strategies for genotype imputation in a population of crossbred Girolando (Gyr × Holstein) dairy cattle. The data set consisted of 478 Girolando, 583 Gyr, and 1,198 Holstein sires genotyped at high density with the Illumina BovineHD (Illumina, San Diego, CA) panel, which includes ∼777K markers. The accuracy of imputation from low (20K) and medium densities (50K and 70K) to the HD panel density and from low to 50K density were investigated. Seven scenarios using different reference populations (RPop) considering Girolando, Gyr, and Holstein breeds separately or combinations of animals of these breeds were tested for imputing genotypes of 166 randomly chosen Girolando animals. The population genotype imputation were performed using FImpute. Imputation accuracy was measured as the correlation between observed and imputed genotypes (CORR) and also as the proportion of genotypes that were imputed correctly (CR). This is the first paper on imputation accuracy in a Girolando population. The sample-specific imputation accuracies ranged from 0.38 to 0.97 (CORR) and from 0.49 to 0.96 (CR) imputing from low and medium densities to HD, and 0.41 to 0.95 (CORR) and from 0.50 to 0.94 (CR) for imputation from 20K to 50K. The CORRanim exceeded 0.96 (for 50K and 70K panels) when only Girolando animals were included in RPop (S1). We found smaller CORRanim when Gyr (S2) was used instead of Holstein (S3) as RPop. The same behavior was observed between S4 (Gyr + Girolando) and S5 (Holstein + Girolando) because the target animals were more related to the Holstein population than to the Gyr population. The highest imputation accuracies were observed for scenarios including Girolando animals in the reference population, whereas using only Gyr animals resulted in low imputation accuracies, suggesting that the haplotypes segregating in the Girolando population had a greater effect on accuracy than the purebred haplotypes. All chromosomes had similar imputation accuracies (CORRsnp) within each scenario. Crossbred animals (Girolando) must be included in the reference population to provide the best imputation accuracies. MenosThe objective of this study was to investigate different strategies for genotype imputation in a population of crossbred Girolando (Gyr × Holstein) dairy cattle. The data set consisted of 478 Girolando, 583 Gyr, and 1,198 Holstein sires genotyped at high density with the Illumina BovineHD (Illumina, San Diego, CA) panel, which includes ∼777K markers. The accuracy of imputation from low (20K) and medium densities (50K and 70K) to the HD panel density and from low to 50K density were investigated. Seven scenarios using different reference populations (RPop) considering Girolando, Gyr, and Holstein breeds separately or combinations of animals of these breeds were tested for imputing genotypes of 166 randomly chosen Girolando animals. The population genotype imputation were performed using FImpute. Imputation accuracy was measured as the correlation between observed and imputed genotypes (CORR) and also as the proportion of genotypes that were imputed correctly (CR). This is the first paper on imputation accuracy in a Girolando population. The sample-specific imputation accuracies ranged from 0.38 to 0.97 (CORR) and from 0.49 to 0.96 (CR) imputing from low and medium densities to HD, and 0.41 to 0.95 (CORR) and from 0.50 to 0.94 (CR) for imputation from 20K to 50K. The CORRanim exceeded 0.96 (for 50K and 70K panels) when only Girolando animals were included in RPop (S1). We found smaller CORRanim when Gyr (S2) was used instead of Holstein (S3) as RPop. The same behavior was obse... Mostrar Tudo |
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Palavras-Chave: |
Impute. |
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Thesaurus NAL: |
genotype; single nucleotide polymorphism. |
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Categoria do assunto: |
G Melhoramento Genético |
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Marc: |
LEADER 03028naa a2200289 a 4500
001 2079937
005 2024-02-09
008 2017 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.3168/jds.2017-12732$2DOI
100 1 $aOLIVEIRA JÚNIOR, G. A.
245 $aGenotype imputation in a tropical crossbred dairy cattle population.$h[electronic resource]
260 $c2017
520 $aThe objective of this study was to investigate different strategies for genotype imputation in a population of crossbred Girolando (Gyr × Holstein) dairy cattle. The data set consisted of 478 Girolando, 583 Gyr, and 1,198 Holstein sires genotyped at high density with the Illumina BovineHD (Illumina, San Diego, CA) panel, which includes ∼777K markers. The accuracy of imputation from low (20K) and medium densities (50K and 70K) to the HD panel density and from low to 50K density were investigated. Seven scenarios using different reference populations (RPop) considering Girolando, Gyr, and Holstein breeds separately or combinations of animals of these breeds were tested for imputing genotypes of 166 randomly chosen Girolando animals. The population genotype imputation were performed using FImpute. Imputation accuracy was measured as the correlation between observed and imputed genotypes (CORR) and also as the proportion of genotypes that were imputed correctly (CR). This is the first paper on imputation accuracy in a Girolando population. The sample-specific imputation accuracies ranged from 0.38 to 0.97 (CORR) and from 0.49 to 0.96 (CR) imputing from low and medium densities to HD, and 0.41 to 0.95 (CORR) and from 0.50 to 0.94 (CR) for imputation from 20K to 50K. The CORRanim exceeded 0.96 (for 50K and 70K panels) when only Girolando animals were included in RPop (S1). We found smaller CORRanim when Gyr (S2) was used instead of Holstein (S3) as RPop. The same behavior was observed between S4 (Gyr + Girolando) and S5 (Holstein + Girolando) because the target animals were more related to the Holstein population than to the Gyr population. The highest imputation accuracies were observed for scenarios including Girolando animals in the reference population, whereas using only Gyr animals resulted in low imputation accuracies, suggesting that the haplotypes segregating in the Girolando population had a greater effect on accuracy than the purebred haplotypes. All chromosomes had similar imputation accuracies (CORRsnp) within each scenario. Crossbred animals (Girolando) must be included in the reference population to provide the best imputation accuracies.
650 $agenotype
650 $asingle nucleotide polymorphism
653 $aImpute
700 1 $aCHUD, T. C. S.
700 1 $aVENTURA, R. V.
700 1 $aGARRICK, D. J.
700 1 $aCOLE, J. B.
700 1 $aMUNARI, D. P.
700 1 $aFERRAZ, J. B. S.
700 1 $aMULLART, E.
700 1 $aDeNISE, S.
700 1 $aSMITH, S.
700 1 $aSILVA, M. V. G. B.
773 $tJournal of Dairy Science$gv. 100, n. 12, p. 9623-9634, 2017.
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Embrapa Gado de Leite (CNPGL) |
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