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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. |
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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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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.
Download
Esconder MarcMostrar Marc Completo |
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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Biblioteca |
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| Registros recuperados : 133 | |
| 101. |  | 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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| 102. | | 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.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 103. | | SOMAVILLA, A. L.; REGITANO, L. C. de A.; ROSA, G. J. M.; MOKRY, F. B.; MUDADU, M. de A.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; SOUZA, M. M. de; COUTINHO, L. L.; MUNARI, D. P. Genome-enabled prediction of breeding values for feedlot average daily weight gain in nelore cattle. G3: Genes, Genomes, Genetics, v. 7, p. 1-17, 2017.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sudeste. |
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| 104. | | 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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| 105. | | STAFUZZA, N. B.; SILVA, R. M. de O.; PERIPOLLI, E.; BEZERRA, L. A. F.; LOBO, R. B.; MAGNABOSCO, C. de U.; DI CROCE, F.; OSTERSTOCK, J.; MUNARI, D. P.; LOURENCO, D. A. L.; BALDI, F. Genome-wide association study provides insights into genes related with horn development in Nelore beef cattle. PLoS ONE, v. 13, n. 8, e0202978, August 30, 2018.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Cerrados. |
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| 106. | | 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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| 107. | | BUZANSKAS, M. E.; SAVEGNAGO, R. P.; GROSSI, D. A.; VENTURINI, G. C.; QUEIROZ, S. A.; SILVA, L. O. C. da; TORRES JUNIOR, R. A. de A.; MUNARI, D. P.; ALENCAR, M. M. de. Genetic parameter estimates and principal component analysis of breeding values of reproduction and growth traits in female Canchim cattle. Reproduction, Fertility and Development, 7 p. Aug. 2012. http://dx.doi.org/10.1071/RD12132.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Gado de Corte; Embrapa Pecuária Sudeste. |
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| 108. | | RAGOGNETTI, B. do N. N; STAFUZZA, N. B.; SILVA, T. B. R. da; CHUD, T. C. S.; GRUPIONI, V. A. R.; CRUZ, V. A. R.; DANTAS, J. de O.; NONES, K.; LEDUR, M. C.; MUNARI, D. P. Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilers. Genetics and Molecular Research, v. 14, n. 4, p. 17544-17554, 2015.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Suínos e Aves. |
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| 109. | | DUARTE, I. N. H.; BESSA, A. F. DE O.; ROLA, L. D.; GENUÍNO, M. V. H.; ROCHA, I. M.; MARCONDES, C. R.; REGITANO, L. C. de A.; MUNARI, D. P.; BERRY, D. P.; BUZANSKAS, M. E. Cross-population selection signatures in Canchim composite beef cattle. Plos One, v.17, n.4, 2022, e0264279. 15 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 110. | | 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.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 111. | | 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.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 112. | | BUZANSKAS, M. E.; GENUÍNO, M. V. H.; DUARTE, I. N. H.; BESSA, A. F. DE O.; ROLA, L. D.; ROCHA, I. M.; MARCONDES, C. R.; REGITANO, L. C. de A.; BERRY, D. P.; MUNARI, D. P. Overlapping haplotype blocks indicate shared genomic regions between a composite beef cattle breed and its founder breeds. Livestock Science, v.254, 104747, dec. 2021. 6 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 113. | | GRUPIONI, N. V.; CRUZ, V. A. R. da; STAFUZZA, N. B.; FREITAS, L. A.; RAMOS, S. B.; SAVEGNAGO, R. P.; PEIXOTO, J. de O.; LEDUR, M. C.; MUNARI, D. P. Phenotypic, genetic and environmental parameters for traits related to femur bone integrity and body weight at 42 days of age in a broiler population. Poultry Science, Sep. 15 2015.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Suínos e Aves. |
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| 114. | | FREITAS, L. A. de; SAVEGNAGO, R. P.; GRUPIONI, N. V.; RAMOS, S. B.; STAFUZZA, N. B.; FIGUEIREDO, E. A. P. de; SCHMIDT, G. S.; LEDUR, M. C.; MUNARI, D. P. Reduced-rank estimation of genetic parameters for egg production traits and cluster analyses with predicted breeding values. Acta Agriculturae Scandinavica, Section A ? Animal Science, v. 68, n. 2, p. 81-86, 2019| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Suínos e Aves. |
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| 115. | | URBINATI, I.; STAFUZZA, N. B.; OLIVEIRA, M. T.; CHUD, T. C. S.; HIGA, R. H.; REGITANO, L. C. de A.; ALENCAR, M. M. de; BUZANSKAS, M. E.; MUNARI, D. P. Selection signatures in Canchim beef cattle Journal of Animal Science and Biotechnology, v. 7, p. 1-9, 2016. Na publicação: Luciana Correia de Almeida Regitano.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 3 |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sudeste. |
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| 116. | | CHUD, T. C. S.; VENTURA, R. V.; SCHENKEL, F. S.; CARVALHEIRO, R.; BUZANSKAS, M. E.; ROSA, J. O.; MUDADU, M. de A.; SILVA, M. V. G. B.; MARCONDES, C. R.; REGITANO, L. C. de A.; MUNARI, D. P. Strategies for genotype imputation in composite beef cattle BMC Genetics, v. 16, p. 99, 2015. 10 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Gado de Leite. |
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| 117. | | STARLING, J. M. C.; RIBEIRO, A. R. B.; ALENCAR, M. M. de; MUNARI, D. P.; SAVEGNAGO, R. P.; FERNANDES JÚNIOR, J. A.; PAÇO, A. L.; IBELLI, A. M. G.; REGITANO, L. C. de A. Termorregulação de novilhas Senepol submetidas a um teste de tolerância ao calor na região Sudeste do Brasil. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA ZOOTECNIA, 47., 2010, Salvador. Empreendorismo e progresso científicos na zootecnia brasileira de vanguarda - anais. Salvador: SBZ: UFBA, 2010.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 118. | | PERIPOLLI, E.; METZGER, J.; LEMOS, M. V. A. de; STAFUZZA, N. B.; KLUSKA, S.; OLIVIERI, B. F.; FEITOSA, F. L. B.; BERTON, M. P.; LOPES, F. B.; MUNARI, D. P.; LOBO, R. B.; MAGNABOSCO, C. de U.; DI CROCE, F.; OSTERSTOCK, J.; DENISE, S.; PEREIRA, A. S. C.; BALDI, F. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits. BMC Genomics, v. 19, 680, 2018.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Cerrados. |
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| 119. | | BUZANSKAS, M. E.; VENTURA, R. V.; CHUD, T. C. S.; SANTOS, D. J. A.; BERNARDES, P. A.; SILVA, T. B. R.; MUDADU, M. A.; REGITANO, L. C. A.; SILVA, M. V. G. B.; LI, C.; SCHENKEL, F. S.; ALENCAR, M. M.; MUNARI, D. P. Admixture analysis in Brazillian synthetic 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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| 120. | | ROSA, J. O.; VENTURINI, G. C.; CHUD, T. C. S.; PIRES, B. C.; BUZANSKAS, M. E.; STAFUZZA, N. B.; FURQUIM, G. R.; CRUZ, V. A. R. da; SCHMIDT, G. S.; FIGUEIREDO, E. A. P. de; LIMA, V. F. M. H. de; LEDUR, M. C.; MUNARI, D. P. Bayesian inference of genetic parameters for reproductive and performance traits in white leghorn hens. Czech Journal of Animal Science, v. 63 n. 6, p. 230-236, 2018.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Suínos e Aves. |
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| Registros recuperados : 133 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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