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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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Biblioteca(s): |
Embrapa Semiárido. |
Data corrente: |
02/06/1997 |
Data da última atualização: |
09/10/2023 |
Tipo da produção científica: |
Artigo em Anais de Congresso |
Autoria: |
QUEIROZ, M. A. de. |
Afiliação: |
MANOEL ABILIO DE QUEIROZ, CPATSA. |
Título: |
O papel da pesquisa agropecuaria como suporte ao desenvolvimento sustentavel do semi-arido brasileiro. |
Ano de publicação: |
1996 |
Fonte/Imprenta: |
In: REUNIAO ESPECIAL DA SBPC, 4.; JORNADA UNIVERSITARIA DA UEFS, 11., 1996, Feira de Santana, BA. Anais... Feira de Santana: SBPC/UEFS, 1996. |
Páginas: |
p. 99-103. |
Idioma: |
Português |
Conteúdo: |
Trata sobre vantagens comparativas da pesquisa agropecuaria como suporte ao desenvolvimento sustentavel no semi-arido brasileiro; agricultura irrigada; agropecuaria de sequeiro; vantagens competitivas. |
Palavras-Chave: |
Agropecuaria; Nordeste; Northeast; Regiao semi-arida; Semi-arid region; Sustainability. |
Thesagro: |
Agricultura; Desenvolvimento Sustentável. |
Thesaurus NAL: |
Agriculture; Livestock; Research; Sustainable development. |
Categoria do assunto: |
P Recursos Naturais, Ciências Ambientais e da Terra |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/196620/1/Jornada-Universitaria.pdf
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Marc: |
LEADER 01047nam a2200265 a 4500 001 1132941 005 2023-10-09 008 1996 bl uuuu u00u1 u #d 100 1 $aQUEIROZ, M. A. de 245 $aO papel da pesquisa agropecuaria como suporte ao desenvolvimento sustentavel do semi-arido brasileiro. 260 $aIn: REUNIAO ESPECIAL DA SBPC, 4.; JORNADA UNIVERSITARIA DA UEFS, 11., 1996, Feira de Santana, BA. Anais... Feira de Santana: SBPC/UEFS$c1996 300 $ap. 99-103. 520 $aTrata sobre vantagens comparativas da pesquisa agropecuaria como suporte ao desenvolvimento sustentavel no semi-arido brasileiro; agricultura irrigada; agropecuaria de sequeiro; vantagens competitivas. 650 $aAgriculture 650 $aLivestock 650 $aResearch 650 $aSustainable development 650 $aAgricultura 650 $aDesenvolvimento Sustentável 653 $aAgropecuaria 653 $aNordeste 653 $aNortheast 653 $aRegiao semi-arida 653 $aSemi-arid region 653 $aSustainability
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