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Registro Completo |
Biblioteca(s): |
Embrapa Pecuária Sudeste. |
Data corrente: |
26/11/2015 |
Data da última atualização: |
15/03/2023 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
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.; MOKRY, F. B.; MARCONDES, C. R.; REGITANO, L. C. de A.; MUNARI, D. P. |
Afiliação: |
TATIANE C. S. CHUD, UNESP; RICARDO V. VENTURA, UNESP; FLAVIO S. SCHENKEL, University of Guelph; ROBERTO CARVALHEIRO, UNESP; MARCOS E. BUZANSKAS, UNESP; JAQUELINE O. ROSA, UNESP; MAURICIO DE ALVARENGA MUDADU, CPPSE; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL; FABIANA B. MOKRY, Federal University of São Carlos; CINTIA RIGHETTI MARCONDES, CPPSE; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; DANÍSIO P. MUNARI, UNESP. |
Título: |
Strategies for genotype imputation in composite beef cattle. |
Ano de publicação: |
2015 |
Fonte/Imprenta: |
BMC Genomics, v. 16, n. 99, 2015. |
Páginas: |
10 p. |
DOI: |
10.1186/s12863-015-0251-7 |
Idioma: |
Inglês |
Conteúdo: |
Genotype imputation has been used to increase genomic information, allow more animals in genome-wide analyses, and reduce genotyping costs. In Brazilian beef cattle production, many animals are resulting from crossbreeding and such an event may alter linkage disequilibrium patterns. Thus, the challenge is to obtain accurately imputed genotypes in crossbred animals. The objective of this study was to evaluate the best fitting and most accurate imputation strategy on the MA genetic group (the progeny of a Charolais sire mated with crossbred Canchim X Zebu cows) and Canchim cattle. The data set contained 400 animals (born between 1999 and 2005) genotyped with the Illumina BovineHD panel. Imputation accuracy of genotypes from the Illumina-Bovine3K (3K), Illumina-BovineLD (6K), GeneSeek-Genomic-Profiler (GGP) BeefLD (GGP9K), GGP-IndicusLD (GGP20Ki), Illumina-BovineSNP50 (50K), GGP-IndicusHD (GGP75Ki), and GGP-BeefHD (GGP80K) to Illumina-BovineHD (HD) SNP panels were investigated. Seven scenarios for reference and target populations were tested; the animals were grouped according with birth year (S1), genetic groups (S2 and S3), genetic groups and birth year (S4 and S5), gender (S6), and gender and birth year (S7). Analyses were performed using FImpute and BEAGLE software and computation run-time was recorded. Genotype imputation accuracy was measured by concordance rate (CR) and allelic R square (R2). |
Palavras-Chave: |
Canchim breed; Crossbred cattle; Genomic data; Low density panel. |
Thesaurus Nal: |
single nucleotide polymorphism. |
Categoria do assunto: |
G Melhoramento Genético |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/134135/1/regitano4.pdf
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Marc: |
LEADER 02356naa a2200337 a 4500 001 2029694 005 2023-03-15 008 2015 bl uuuu u00u1 u #d 024 7 $a10.1186/s12863-015-0251-7$2DOI 100 1 $aCHUD, T. C. S. 245 $aStrategies for genotype imputation in composite beef cattle.$h[electronic resource] 260 $c2015 300 $a10 p. 520 $aGenotype imputation has been used to increase genomic information, allow more animals in genome-wide analyses, and reduce genotyping costs. In Brazilian beef cattle production, many animals are resulting from crossbreeding and such an event may alter linkage disequilibrium patterns. Thus, the challenge is to obtain accurately imputed genotypes in crossbred animals. The objective of this study was to evaluate the best fitting and most accurate imputation strategy on the MA genetic group (the progeny of a Charolais sire mated with crossbred Canchim X Zebu cows) and Canchim cattle. The data set contained 400 animals (born between 1999 and 2005) genotyped with the Illumina BovineHD panel. Imputation accuracy of genotypes from the Illumina-Bovine3K (3K), Illumina-BovineLD (6K), GeneSeek-Genomic-Profiler (GGP) BeefLD (GGP9K), GGP-IndicusLD (GGP20Ki), Illumina-BovineSNP50 (50K), GGP-IndicusHD (GGP75Ki), and GGP-BeefHD (GGP80K) to Illumina-BovineHD (HD) SNP panels were investigated. Seven scenarios for reference and target populations were tested; the animals were grouped according with birth year (S1), genetic groups (S2 and S3), genetic groups and birth year (S4 and S5), gender (S6), and gender and birth year (S7). Analyses were performed using FImpute and BEAGLE software and computation run-time was recorded. Genotype imputation accuracy was measured by concordance rate (CR) and allelic R square (R2). 650 $asingle nucleotide polymorphism 653 $aCanchim breed 653 $aCrossbred cattle 653 $aGenomic data 653 $aLow density panel 700 1 $aVENTURA, R. V. 700 1 $aSCHENKEL, F. S. 700 1 $aCARVALHEIRO, R. 700 1 $aBUZANSKAS, M. E. 700 1 $aROSA, J. O. 700 1 $aMUDADU, M. de A. 700 1 $aSILVA, M. V. G. B. 700 1 $aMOKRY, F. B. 700 1 $aMARCONDES, C. R. 700 1 $aREGITANO, L. C. de A. 700 1 $aMUNARI, D. P. 773 $tBMC Genomics$gv. 16, n. 99, 2015.
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Registro original: |
Embrapa Pecuária Sudeste (CPPSE) |
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| Acesso ao texto completo restrito à biblioteca da Embrapa Gado de Corte. Para informações adicionais entre em contato com cnpgc.biblioteca@embrapa.br. |
Registro Completo
Biblioteca(s): |
Embrapa Gado de Corte. |
Data corrente: |
06/04/2006 |
Data da última atualização: |
06/04/2006 |
Autoria: |
MEDEIROS, S. R. de; CATTO, J. B.; ROSA, G. O.; BRAGAGNOLO, N. |
Afiliação: |
Embrapa Gado de Corte (Campo Grande, MS). |
Título: |
Ácidos graxos e colesterol do Longissimus dorsi de bovinos da sub-região da Nhecolândia, Pantanal. |
Ano de publicação: |
2002 |
Fonte/Imprenta: |
In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 39., 2002, Recife. A produção animal e a sociedade brasileira: anais. Recife: UFRPE: SBZ, 2002. |
Páginas: |
4 p. |
Descrição Física: |
1 CD-ROM. |
Idioma: |
Português |
Notas: |
CNPGC. |
Palavras-Chave: |
Animal fats; Brasil; Longissimus dorsi; Natural pastures; Nhecolândia; Quality. |
Thesagro: |
Ácido Graxo; Bovino; Carne; Colesterol; Composição de Alimento; Gordura Animal; Pastagem Nativa; Qualidade. |
Thesaurus NAL: |
Brazil; cattle; cholesterol; fatty acids; meat; Pantanal; proximate composition. |
Categoria do assunto: |
-- |
Marc: |
LEADER 01198naa a2200421 a 4500 001 1326026 005 2006-04-06 008 2002 bl uuuu u00u1 u #d 100 1 $aMEDEIROS, S. R. de 245 $aÁcidos graxos e colesterol do Longissimus dorsi de bovinos da sub-região da Nhecolândia, Pantanal. 260 $c2002 300 $a4 p.$c1 CD-ROM. 500 $aCNPGC. 650 $aBrazil 650 $acattle 650 $acholesterol 650 $afatty acids 650 $ameat 650 $aPantanal 650 $aproximate composition 650 $aÁcido Graxo 650 $aBovino 650 $aCarne 650 $aColesterol 650 $aComposição de Alimento 650 $aGordura Animal 650 $aPastagem Nativa 650 $aQualidade 653 $aAnimal fats 653 $aBrasil 653 $aLongissimus dorsi 653 $aNatural pastures 653 $aNhecolândia 653 $aQuality 700 1 $aCATTO, J. B. 700 1 $aROSA, G. O. 700 1 $aBRAGAGNOLO, N. 773 $tIn: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 39., 2002, Recife. A produção animal e a sociedade brasileira: anais. Recife: UFRPE: SBZ, 2002.
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