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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.
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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Registro completo
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Biblioteca(s): |
Catálogo Coletivo de Periódicos Embrapa; Embrapa Acre; Embrapa Agropecuária Oeste; Embrapa Algodão; Embrapa Amapá; Embrapa Amazônia Oriental; Embrapa Cerrados; Embrapa Florestas; Embrapa Instrumentação; Embrapa Meio-Norte; Embrapa Pecuária Sudeste; Embrapa Rondônia; Embrapa Semiárido; Embrapa Soja; Embrapa Solos; Embrapa Trigo; Embrapa Uva e Vinho. MenosCatálogo Coletivo de Periódicos Embrapa; Embrapa Acre; Embrapa Agropecuária Oeste; Embrapa Algodão; Embrapa Amapá; Embrapa Amazônia Oriental; Embrapa Cerrados; Embrapa Florestas; Embrapa Instrumentação; Embrapa Meio-Norte... Mostrar Todas |
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Identificador: |
3547 |
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Data corrente: |
09/05/2002 |
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Data da última atualização: |
15/05/2017 |
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Código do título: |
0900701 |
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Código CCN: |
095505-1 |
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Título e Subtítulo: |
A GRANJA DO ANO |
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Título anterior: |
QUEM E QUEM NA AGRICULTURA BRASILEIRA |
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Entidade: |
Editora Centaurus Ltda. |
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Local de publicação: |
Porto Alegre, RS |
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Periodicidade: |
Anual |
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Editora: |
Centaurus Ltda. |
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Inicio de publicação: |
1986 |
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Coleções da unidade: |
Embrapa Acre
1986-89 (1-4); 1999/2000 (14)
Classificação: 630.5
Embrapa Agropecuária Oeste
1986-93 1-7; 1994-02 9-16; 2003-07 18-21; 2009-11 24-27; 2014 (29); 2015 (30); 2016 (31); 2017/2018 (32)
Embrapa Algodão
1987/2005 1987-1990; 1995/96; 2001/2002; 2004/2005
Classificação: 630.5
Embrapa Amapá
1987 2; 1988 (3); 1990 5; 1991/92 6; 1992/93 7
Embrapa Amazônia Oriental
1986 1(1); 1987 1(2); 1988 1(3); 1989 1(4); 1990 1(5); 1992/93 1(7)
Classificação: 630.5G3
Embrapa Cerrados
1986(1); 1988(3); 1989(4); 1990(5); 1991/92(6); 1992/93(7); 1993/94(8); 1994/95(9); 1995/96(10); 1996/97(11); 1997/98(12); 1998/99(13); 1999/2000(14); 2000/01(15); 2001/02(16); 2006/07(21)
Classificação: 630.5
Embrapa Florestas
1987/1988 (2); 1988(3); 1998/1999 (13); 1999/2000 (14); 2000/2001 (15); 2002/2003 (17); 2007/2008 (22)
Embrapa Instrumentação
1999/2000 (14); 2001/2002 (16); 2002/2003 (17); 2003/2004 (18); 2005/2006 (20).
Classificação: 636.505
Embrapa Meio-Norte
1987-1995/96 (2-10); 1996/97 (11); 1997/98 (12); 1998/99 (13); 1999/2000 (14); 2002/03(17); 2003/04(18); 2004/2005(19); 2019/2020 (34)
Classificação: 630.5
Embrapa Pecuária Sudeste
1987 2; 1983 3; 1989 4; 1990 5; 1991 6; 1992 7; 2010 (24); 2012 26 27; 2013 28
Embrapa Rondônia
1978 (Ed/78); 1986 1(1); 1987/88 (2-3); 1990 (5); 1991/92 (6); 1994/95 (9); 1995/96 (10); 1999/00 (14); 2002/04 (17/18); 2004/05 19; 2005/06 20; 2006/2007 26; 2012/2013 27; 2013/2014 28; 2014/2015 2015/2016 30; 2017/2018 32; 2018/2019
Classificação: 630.5
Embrapa Semiárido
1987,1988 2; 1988 3; 1989 4; 1991,1992 6; 1992,1993 7; 1994,1995 9; 1995,1996 10; 1998/1999 13; 1999/2000 14; 2000/2001 15; 2001/2002 16; 2002/2003 17; 2004/2005 19; 2005/2006; 2008/2009; 2009/2010; 2010/2011.
Embrapa Soja
1987-89 (2-4); 1991-94 (6-8); 1995/96 (10); 1998-99 (13-14); 2000/01 (15); 2001/02 (16); 2002/03 (17); 2003/04 (18); 2005/06 (20); 2006/07 (21); 2008/2009 (23); 2009/10 (24); 2010/2011 (25); 2011/2012 (26); 2015/2016 (30-31); 2017/2018 (32); 2019/2020 (34); 2020/2021 (35); 2021/2022 (36);
Embrapa Solos
1986-89 (1-4); 1995-99 (10-13); 1999/2000 (14); 2000/2001 (15); 2001/2002 (16); 2002/2003 (17); 2003/2004 (18); 2004/2005 (19)
Classificação: 630.5
Embrapa Trigo
1986 (1); 1987 (2); 1988 (3); 1989 (4); 1992 (7); 1993 (8); 1994 (9); 1995 (10); 1997 (12); 1998 (13); 1999 (14); 2002 (17); 2006 (20); 2010 (25); 2011 (26); 2013 (28); 2014 (29); 2015 (30); 2016 (31); 2018 (33); 2019 (34), 2021(36); 2022/2023(37); 2023/2024
Classificação: 630.5
Embrapa Uva e Vinho
1986 1; 1988-89 3-4; 1992-93 7-8; 1996/1997(11); 1999 14; 2000/2001(15); 2001/2002(16); 2002/2003(17); 2004-05 (19); 2006(21); 2007/2008(22); 2008/2009(23); 2011/2012(26)
Classificação: 630 |
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