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| Registros recuperados : 23 | |
| 3. |  | MOREIRA, G. C. M.; CESAR, A. S. M.; GODOY, T. F.; BOSCHIERO, C.; LEDUR, M. C.; GARRICK, D. J.; MOURA, A. S. A. M. T.; COUTINHO, L. L. Genome-wide association studies reveal genomic windows and candidate genes related to fat deposition in chickens. In: PLANT & ANIMAL GENOME CONFERENCE, 24., 2016, San Diego, CA. [Abstracts...]. San Diego: [s.n.], 2016. Pôster P0647.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 4. | | OLIVEIRA JUNIOR, G. A.; VENTURA, R.; FREITAS, B. G. de; SANTANA, M. H. A.; SILVA, M. V. G. B.; FERRAZ, J. B. S.; GARRICK, D. J. Genome-wide association study in reproductive trait of Nellore heifers. In: PLANT & ANIMAL GENOME, 24., 2016, San Diego. [Proceedings...] San Diego: [s.n.], 2016.| Biblioteca(s): Embrapa Gado de Leite. |
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| 5. | | RESENDE JUNIOR, M.; DELL VALLE, P. R. M.; RESENDE, M. D. V. de; GARRICK, D. J.; FERNANDO, R.; DAVIS, J. M.; PETER, G.; KIRST, M. Improvement of genomic selection using a ridge regression approach with selected markers. In: INTERNATIONAL CONFERENCE ON QUANTITATIVE GENETICS, 4., 2012, Edinburgh. Understanding Variation in Complex Traits. . [S.l.: s.n], 2012. Poster abstracts. P-199.| Biblioteca(s): Embrapa Florestas. |
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| 6. | | RESENDE JUNIOR, M. F. R.; MUÑOZ, P.; RESENDE, M. D. V. de; GARRICK, D. J.; FERNANDO, R. L.; DAVIS, J. M.; JOKELA, E. J.; MARTIN, T. A.; PETER, G. F.; KIRST, M. Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.) Genetics, v. 190, p. 1503-1510, April 2012.| Biblioteca(s): Embrapa Florestas. |
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| 7. | | 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. Genotype imputation in a tropical crossbred dairy cattle population. Journal of Dairy Science, v. 100, n. 12, p. 9623-9634, 2017.| Biblioteca(s): Embrapa Gado de Leite. |
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| 8. | | VERARDO, L. L.; STAFUZZA, N. B.; MUNARI, D. P.; ZERLOTINI NETO, A.; CHUD, T. C. S.; GARRICK, D. J.; COLE, J. B.; PANETTO, J. C. do C.; MACHADO, M. A.; MARTINS, M. F.; SILVA, M. V. G. B. A gene-transcription factor network associated with residual feed intake based on SNVs/InDels identified in Gir, Girolando and Holstein cattle breeds. In: WORLD CONGRESS ON GENETICS APPLIED TO LIVESTOCK PRODUCTION, 11., 2018, Auckland. Proceedings... [S.l.: s.n.], 2018.| Biblioteca(s): Embrapa Gado de Leite. |
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| 9. | | VERARDO, L. L.; STAFUZZA, N. B.; MUNARI, D. P.; ZERLOTINI NETO, A.; CHUD, T. C. S.; GARRICK, D. J.; COLE, J. B.; PANETTO, J. C. do C.; MACHADO, M. A.; MARTINS, M. F.; SILVA, M. V. G. B. A gene-transcription factor network associated with residual feed intake based on SNVs/InDels identified in Gir, Girolando and Holstein cattle breeds. In: WORLD CONGRESS ON GENETICS APPLIED TO LIVESTOCK PRODUCTION, 11., 2018, Auckland. Proceedings... [S.l.: s.n.], 2018. 6 p. Na publicação: A. Zerlotini, J. C. C. Panetto. WCGALP 2018.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 10. | | MOREIRA, G. C. M.; BOSCHIERO, C.; CESAR, A. S. M.; REECY, J. M.; GODOY, T. F.; PÉRTILLE, F.; LEDUR, M. C.; MOURA, A. S. A. M. T. M.; GARRICK, D. J.; COUTINHO, L. L. Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken. Scientific Reports, v. 8, n. 16222, 2018.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 11. | | ZERLOTINI NETO, A.; STAFUZZA, N. B.; 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.; SILVA, M. V. G. B. Detection of potential genetic variants affecting gene function in Guzerat cattle. In: INTERNATIONAL CONFERENCE OF THE AB3C, 12., 2016, Belo Horizonte. Proceedings... [S.l.]: AB3C, 2016. p. 47. X-meeting 2016.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 12. | | ZERLOTINI NETO, A.; STAFUZZA, N. B.; 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.; SILVA, M. V. G. B. Detection of potential genetic variants affecting gene function in Guzerat cattle. In: INTERNATIONAL CONFERENCE OF THE AB3C, 12., 2016, Belo Horizonte. Proceedings... [S.l.]: AB3C, 2016. p. 47. X-meeting 2016.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 13. | | MOREIRA, G. C. M.; POLETI, M. D.; PÉRTILLE, F.; BOSCHIERO, C.; CESAR, A. S. M.; GODOY, T. F.; LEDUR, M. C.; REECY, J. M.; GARRICK, D. J.; COUTINHO, L. L. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. BMC Genetics, v. 20, n. 83, 2019.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 14. | | CESAR, A. S. M.; REGITANO, L. C. de A.; MOURÃO, G. B.; TULLIO, R. R.; LANNA, D. P. D.; NASSU, R. T.; MUDADU, M. de A.; OLIVEIRA, P. S. N.; NASCIMENTO, M. L. do; CHAVES, A. S.; ALENCAR, M. M. de; SONSTEGRAD, T. S.; GARRICK, D. J.; REECY, J. M.; COUTINHO, L. L. Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle. BMC Genetics, v. 15, p. 39, 2014| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 15. | | OLIVEIRA, P. S. N.; CESAR, A. S. M.; NASCIMENTO, M. L. do; CHAVES, A. S.; TIZIOTO, P. C.; TULLIO, R. R.; LANNA, D. P. D.; ROSA, A. do N.; SONSTEGARD, T. S.; MOURÃO, G. B.; REECY, J. M.; GARRICK, D. J.; MUDADU, M. de A.; COUTINHO, L. L.; REGITANO, L. C. de A. Identification of genomic regions associated with feed efficiency in Nelore cattle. BMC Genetics, v. 15, n. 1, 2014 10 p.| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 16. | | STAFUZZA, N. B.; ZERLOTINI, A.; LOBO, F. P.; YAMAGISHI, M. E. B.; BUZANSKAS, M. E.; CHUD, T. C.; CAETANO, A. R.; MUNARI, D. P.; GARRICK, D. J.; MACHADO, M. A.; MARTINS, M. F.; CARVALHO, M. R. S.; COLE, J. B.; SILVA, M. V. G. B. Genetic variants with potencial loss of function in Gyr, Girolando, and Guzerat cattle breeds by resequencing. Journal of Animal Science, v. 95, n. 4, p. 81, 2017. Edição dos abstracts do of Breeding and Genetics Symposium, Baltimore, 2017.| Biblioteca(s): Embrapa Gado de Leite. |
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| 17. | | STAFUZZA, N. B.; ZERLOTINI NETO, A.; LOBO, F. P.; YAMAGISHI, M. E. B.; BUZANSKAS, M. E.; 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. Genetic variants with potential loss of function in Gyr, Girolando, and Guzerat cattle breeds by resequencing. Journal of Animal Science, v. 95, p. 81, 2017. Suplemento 4, Resumo 165. Edição de Abstracts do ASAS-CSAS Annual Meeting and Trade Show, Baltimore, 2017. Na publicação: A. Zerlotini, M. V. G. B. da Silva.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 18. | | STAFUZZA, N. B.; ZERLOTINI NETO, A.; LOBO, F. P.; YAMAGISHI, M. E. B.; BUZANSKAS, M. E.; CHUD, T. C.; CAETANO, A. R.; MUNARI, D. P.; GARRICK, D. J.; MACHADO, M. A.; MARTINS, M. F.; CARVALHO, M. R. S.; COLE, J. B.; SILVA, M. V. G. B. Genetiv variants with potencial loss of function in Gyr, Girolando, and Guzerat cattle breeds by resequencing. Journal of Animal Science, v. 95, n. suppl. 4, p. 81, 2017. Abstract of Breeding and Genetics Symposium, Baltimore, 2017.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 19. | | OLIVEIRA, P. S. N.; CESAR, A. S. M.; NASCIMENTO, M. L. do; SOUZA, M. M.; TULLIO, R. R.; LANNA, D. P.; SONSTEGARD, T.; MOURÃO, G. B.; REECY, J. M.; GARRICK, D. J.; MUDADU, M. de A.; REGITANO, L. C. de A.; COUTINHO, L. L. Positional candidate genes for residual intake and gain in Nelore beef cattle. In:WORLD CONGRESS OF GENETICS APPLIED TO LIVESTOK PRODUCTION, 10; . 2014, Vancouver. Proceedings... Vancouver: American Society of animal Science, 2014| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 20. | | 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. Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. Plos One, v. 12, n. 3, p. 1-15, 2017. Artigo e0173954. Na publicação: Adhemar Zerlotini, Marcos Vinicius Gualberto Barbosa da Silva.| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Gado de Leite; Embrapa Recursos Genéticos e Biotecnologia. |
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| Registros recuperados : 23 | |
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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: |
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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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