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Registro Completo |
Biblioteca(s): |
Embrapa Gado de Leite. |
Data corrente: |
16/11/2017 |
Data da última atualização: |
09/02/2024 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
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. |
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. |
Título: |
Genotype imputation in a tropical crossbred dairy cattle population. |
Ano de publicação: |
2017 |
Fonte/Imprenta: |
Journal of Dairy Science, v. 100, n. 12, p. 9623-9634, 2017. |
DOI: |
https://doi.org/10.3168/jds.2017-12732 |
Idioma: |
Inglês |
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 |
Palavras-Chave: |
Impute. |
Thesaurus Nal: |
genotype; single nucleotide polymorphism. |
Categoria do assunto: |
G Melhoramento Genético |
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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Registros recuperados : 38 | |
1. | | GATTI, M.; CHUD, T. C. S.; NASCIMENTO, G. B. do; THOLON, P.; MUNARI, D. P. Principal components analysis for growth traits in Canchim cattle. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 54., 2017, Foz do Iguaçu, PR. Proceedings... Brasília, DF: SBZ, 2017. p. 505.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Pecuária Sudeste. |
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4. | | CHUD, T. C. S.; VENTURA, R. V.; SCHENKEL. F. S.; URBINATI, I.; CARVALHEIRO, R.; REGITANO, L. C. de A.; MARCONDES, C. R.; MINARI, D. P. Accuracy of genotype imputation in Canchim cattle using FImpute and Beagle software. In: INTERNATIONAL SYMPOSIUM ON ANIMAL FUNCTIONAL GENOMICS, 5., 2013, Guarujá. Abstract... Guarujá:[ s.n.], 2013. AB.20.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Pecuária Sudeste. |
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5. | | CHUD, T. C. S.; BICKHART, D. M.; ZERLOTINI NETO, A.; COLE, J. B.; SILVA, M. V. G. B.; MUNARI, D. P. Copy number variation in dairy cattle using next-generation sequencing. In: PLANT AND ANIMAL GENOME CONFERENCE, 26., 2018, San Diego. Abstracts... [S.l.: s.n.], 2018. 1 p. PAG 2018. P0490. Na publicação: Adhemar Zerlotini, Marcos Vinicius B. da Silva.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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6. | | BUZANSKAS, M. E.; CHUD, T. C. S.; PANETTO, J. C. do C.; MACHADO, M. A.; SILVA, L. O. C. da; SILVA, M. V. G. B.; MUNARI, D. P. Breeding structure and genetic variability in nelore and gyr breeds from brazil na índia. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 55.; CONGRESSO BRASILEIRO DE ZOOTECNIA, 28., 2018, Goiânia. Construindo saberes, formando pessoas e transformando a produção animal: anais eletrônicos. Goiânia: Sociedade Brasileira de Zootecnia, 2018.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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8. | | ROSA, J. O.; PIRES, B. C.; CHUD, T. C. S.; BUZANSKAS, M. E.; CRUZ, V. A. R.; LEDUR, M. C.; SCHMIDT, G. S.; MUNARI, D. P. Genetic parameters reproductive traits in a strain if laying hens. In: CONGRESSO BRASILEIRO DE GENÉTICA, 60., 2014, Guarujá. Resumos? Ribeirão Preto: Sociedade Brasileira de Genética, 2014. p. 24Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Suínos e Aves. |
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9. | | OLIVEIRA JUNIOR, G. A.; CARMO, A. S.; UTSUNOMIYA, A. T. H.; CHUD, T. C. S.; REY, F. S. B.; FERRAZ, J. B. S.; SILVA, M. V. G. B. Common copy number variation regions affecting dairy traits in Gyr cattle. In: ADSA ASAS JOINT ANNUAL MEETING, 2015, Orlando. Proceedings... Orlando: ADSA: ASAS, 2015.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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10. | | CHUD, T. C. S.; SILVA, M. V. G. B.; CARMO, A. S.; SILVA, T. B. R.; OLIVEIRA JUNIOR, G. A.; REY, F. S. B.; MUNARI, D. P. Identification of copy number variation in Brazilian synthetic dairy cattle breed. In: ADSA ASAS JOINT ANNUAL MEETING, 2015, Orlando. Proceedings... Orlando: ADSA: ASAS, 2015.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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11. | | URBITANI, I.; BUZANSKAS, M. E.; CHUD, T. C. S.; MORKRY, F. B; HIGA, R. H.; REGITANO, L. C. de A.; MUNARI, D. P. Selection signatures in Canchim beef cattle. In:WORLD CONGRESS OF GENETICS APPLIED TO LIVESTOCK PRODUCTION, 10., 2014, Vancouver. Proceedings...Vancouver: WCGALP: Amarican Society of Animal Science, 2014.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Pecuária Sudeste. |
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12. | | URBITANI, I.; BUZANSKAS, M. E.; CHUD, T. C. S.; MORKRY, F. B; REGITANO, L. C. A.; HIGA, R. H.; MUNARI, D. P. Selection signatures in Canchim beef cattle. In: WORLD CONGRESS OF GENETICS APPLIED TO LIVESTOCK PRODUCTION, 10., 2014, Vancouver. Proceedings... Champaign: ASAS, 2014. Não paginado.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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13. | | CRUZ, V. A. R. da; IBELLI, A. M. G.; BUZANSKAS, M. E.; ROSA, J. O.; CHUD, T. C. S.; LEDUR, M. C.; PEIXOTO, J. de O.; MUNARI, D. P. Association of Apolipoprotein B gene with carcass, performance, and organ traits in a paternal broiler line. In: REUNIÃO ANNUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 51, 2014, Barra dos Coqueiros. Anais ... Barra dos Coqueiros: SBZ, 2014. 1 CD-ROM.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Suínos e Aves. |
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14. | | MARCIANO, L. E. A.; MAIA, R. de O. G.; SANTOS; DUARTE, I. N. H.; BERNARDES, P. A.; CHUD, T. C. S.; REGITANO, L. C. de A.; BUZANSKAS, M. E. Estratégias de imputação em gado Canchim utilizando população de referência da raça Nelore. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 55.; CONGRESSO BRASILEIRO DE ZOOTECNIA, 28., 2018, Goiânia. Construindo saberes, formando pessoas e transformando a produção animal: anais eletrônicos. Goiânia: Sociedade Brasileira de Zootecnia, 2018.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Pecuária Sudeste. |
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15. | | 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.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Gado de Leite. |
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16. | | JOAQUIM, L. B.; CHUD, T. C. S.; MARCHESI, J. A. P.; SAVEGNAGO, R. P.; BUZANKAS, M. E.; ZANELLA, R.; CANTAO, M. E.; PEIXOTO, J. de O.; LEDUR, M. C.; IRGANG, R.; MUNARI, D. P. Genomic structure of a crossbred landrace pig population. Plos One, v. 14, n.2, e0212266, 2019.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Suínos e Aves. |
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17. | | BUZANSKAS, M. E.; GROSSI, D. A.; VENTURA, R. V.; CHUD, T. C. S.; URBINATI, I.; MEIRELLES, S. L. C.; MOKRY, F. B.; SCHENKEL, F. S.; REGITANO, L. C. de A.; MUNARI, D. P. Genome-wide association study on long-yearling scrotal circumference in Canchim cattle. In:WORLD CONGRESS OF GENETICS APPLIED TO LIVESTOCK PRODUCTION, 10., 2014, Vancouver. Proceedings...Vancouver: WCGALP: Amarican Society of Animal Science, 2014.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Pecuária Sudeste. |
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18. | | CARMO, A. S. do; OLIVEIRA JÚNIOR, G. A. de; CHUD, T. C. S.; PANETTO, J. C. do C.; VERNEQUE, R. da S.; MACHADO, M. A.; SILVA, M. V. G. B. Genome Wide CNVs analysis to identify variants associated with coat color in Gyr breed. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 52., 2015, Belo Horizonte. Zootecnia: otimizando recursos e potencialidades: anais. Belo Horizonte: Sociedade Brasileira de Zootecnia, 2015. 3 p.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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19. | | CHUD, T. C. S.; ROSA, J. O.; SILVA, M. V. G. B.; SILVA, T. B. R.; OLIVEIRA, G. A.; VENTURINI, G. C.; BALDI REY, F. S.; MUNARI, D. P. Genome-wide identification of copy number variation regions in Girolando cattle. In: CONGRESSO BRASILEIRO DE GENÉTICA, 61., 2015, Águas de Lindóia. Resumos... Ribeirão Preto: Sociedade Brasileira de Genética, 2015.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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20. | | 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.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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Registros recuperados : 38 | |
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