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Registro Completo |
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Biblioteca(s): |
Embrapa Pecuária Sudeste; Embrapa Pesca e Aquicultura. |
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Data corrente: |
09/07/2019 |
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Data da última atualização: |
08/01/2020 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
FERREIRA FILHO, D.; BUENO FILHO, J. S. de S.; REGITANO, L. C. de A.; ALENCAR, M. M. de; ALVES, R. R.; BAENA, M. M.; MEIRELLES, S. L. C. |
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Afiliação: |
Diógenes Ferreira Filho, UFRRJ; Júio Sílvio de Sousa Bueno Filho, UFLA; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; MAURICIO MELLO DE ALENCAR, CPPSE; ROSIANA RODRIGUES ALVES, CNPASA; Marielle Moura Baena, UFLA; Sarah Laguna Conceição Meirelles, UFLA. |
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Título: |
Tournaments between markers as a strategy to enhance genomic predictions. |
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Ano de publicação: |
2019 |
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Fonte/Imprenta: |
Plos One, v. 14, n. 7, e0219448, p. 1-17, 2019. |
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DOI: |
10.1371/journal.pone.0219448 |
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Idioma: |
Inglês |
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Conteúdo: |
Analysis of a large number of markers is crucial in both genome-wide association studies (GWAS) and genome-wide selection (GWS). However there are two methodological issues that restrict statistical analysis: high dimensionality (p>>n) and multicollinearity. Although there are methodologies that can be used to fit models for data with high dimensionality (eg,the Bayesian Lasso), a big problem that can occurs in this cases is that the predictive ability of the model should perform well for the individuals used to fit the model, but should not perform well for other individuals, restricting the applicability of the model. This problem can be circumvent by applying some selection methodology to reduce the number of markers (but keeping the markers associated with the phenotypic trait) before adjusting a model to predict GBVs. We revisit a tournament-based strategy between marker samples, where each sample has good statistical properties for estimation: n>p and low collinearity. Such tournaments are elaborated using multiple linear regression to eliminate markers. This method is adapted from previous works found in the literature. We used simulated data as well as real data derived from a study with SNPs in beef cattle. Tournament strategies not only circumvent the p>>n issue, but also minimize spurious associations. For real data, when we selected a few more than 20 markers, we obtained correlations greater than 0.70 between predicted Genomic Breeding Values (GBVs) and phenotypes in validation groups of a cross-validation scheme; and when we selected a larger number of markers (more than 100), the correlations exceeded 0.90, showing the efficiency in identifying relevant SNPs (or segregations) for both GWAS and GWS. In the simulation study, we obtained similar results. MenosAnalysis of a large number of markers is crucial in both genome-wide association studies (GWAS) and genome-wide selection (GWS). However there are two methodological issues that restrict statistical analysis: high dimensionality (p>>n) and multicollinearity. Although there are methodologies that can be used to fit models for data with high dimensionality (eg,the Bayesian Lasso), a big problem that can occurs in this cases is that the predictive ability of the model should perform well for the individuals used to fit the model, but should not perform well for other individuals, restricting the applicability of the model. This problem can be circumvent by applying some selection methodology to reduce the number of markers (but keeping the markers associated with the phenotypic trait) before adjusting a model to predict GBVs. We revisit a tournament-based strategy between marker samples, where each sample has good statistical properties for estimation: n>p and low collinearity. Such tournaments are elaborated using multiple linear regression to eliminate markers. This method is adapted from previous works found in the literature. We used simulated data as well as real data derived from a study with SNPs in beef cattle. Tournament strategies not only circumvent the p>>n issue, but also minimize spurious associations. For real data, when we selected a few more than 20 markers, we obtained correlations greater than 0.70 between predicted Genomic Breeding Values (GBVs) and phenotyp... Mostrar Tudo |
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Palavras-Chave: |
Genome-wide; Genomic Breeding Values; GWAS; GWS; SNPs. |
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Thesagro: |
Genoma; Genótipo; Marcador Genético; Seleção Genética. |
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Thesaurus Nal: |
Genetic markers; Genomics; Genotyping. |
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Categoria do assunto: |
G Melhoramento Genético |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/199471/1/Tournaments-between-markers-as-a-strategy-correcao.pdf
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Marc: |
LEADER 02769naa a2200349 a 4500
001 2110534
005 2020-01-08
008 2019 bl uuuu u00u1 u #d
024 7 $a10.1371/journal.pone.0219448$2DOI
100 1 $aFERREIRA FILHO, D.
245 $aTournaments between markers as a strategy to enhance genomic predictions.$h[electronic resource]
260 $c2019
520 $aAnalysis of a large number of markers is crucial in both genome-wide association studies (GWAS) and genome-wide selection (GWS). However there are two methodological issues that restrict statistical analysis: high dimensionality (p>>n) and multicollinearity. Although there are methodologies that can be used to fit models for data with high dimensionality (eg,the Bayesian Lasso), a big problem that can occurs in this cases is that the predictive ability of the model should perform well for the individuals used to fit the model, but should not perform well for other individuals, restricting the applicability of the model. This problem can be circumvent by applying some selection methodology to reduce the number of markers (but keeping the markers associated with the phenotypic trait) before adjusting a model to predict GBVs. We revisit a tournament-based strategy between marker samples, where each sample has good statistical properties for estimation: n>p and low collinearity. Such tournaments are elaborated using multiple linear regression to eliminate markers. This method is adapted from previous works found in the literature. We used simulated data as well as real data derived from a study with SNPs in beef cattle. Tournament strategies not only circumvent the p>>n issue, but also minimize spurious associations. For real data, when we selected a few more than 20 markers, we obtained correlations greater than 0.70 between predicted Genomic Breeding Values (GBVs) and phenotypes in validation groups of a cross-validation scheme; and when we selected a larger number of markers (more than 100), the correlations exceeded 0.90, showing the efficiency in identifying relevant SNPs (or segregations) for both GWAS and GWS. In the simulation study, we obtained similar results.
650 $aGenetic markers
650 $aGenomics
650 $aGenotyping
650 $aGenoma
650 $aGenótipo
650 $aMarcador Genético
650 $aSeleção Genética
653 $aGenome-wide
653 $aGenomic Breeding Values
653 $aGWAS
653 $aGWS
653 $aSNPs
700 1 $aBUENO FILHO, J. S. de S.
700 1 $aREGITANO, L. C. de A.
700 1 $aALENCAR, M. M. de
700 1 $aALVES, R. R.
700 1 $aBAENA, M. M.
700 1 $aMEIRELLES, S. L. C.
773 $tPlos One$gv. 14, n. 7, e0219448, p. 1-17, 2019.
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Registro original: |
Embrapa Pecuária Sudeste (CPPSE) |
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Registro Completo
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Biblioteca(s): |
Embrapa Amazônia Oriental. |
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Data corrente: |
19/04/1999 |
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Data da última atualização: |
13/06/2022 |
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Tipo da produção científica: |
Artigo em Anais de Congresso |
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Autoria: |
LUDOVINO, R. M. R.; LOBO, I. J. B.; PESSOA, R. O.; TOURRAND, J.-F.; VEIGA, J. B. da. |
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Afiliação: |
JONAS BASTOS DA VEIGA, CPATU. |
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Título: |
A pecuária nos sistemas de produção familiar do sul e sudeste do Pará. |
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Ano de publicação: |
1998 |
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Fonte/Imprenta: |
In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 35., 1998, Botucatu. Anais. Botucatu: SBZ, 1998. |
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Páginas: |
v. 4, p. 141-143. |
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Idioma: |
Português |
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Palavras-Chave: |
Brasil; Diagnostic; Itupiranga; Marabá; Pará; Production system; Rendenção; Rondon do Pará; São João do Araguaia; Tipologia; Typology; Xinguara. |
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Thesagro: |
Agricultura Familiar; Diagnostico; Pecuária; Sistema de Produção. |
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Thesaurus NAL: |
Amazonia; family farms; livestock. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/236011/1/A-pecuaria-nos-sistemas-de-producao.pdf
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Marc: |
LEADER 01069nam a2200385 a 4500
001 1394918
005 2022-06-13
008 1998 bl uuuu u00u1 u #d
100 1 $aLUDOVINO, R. M. R.
245 $aA pecuária nos sistemas de produção familiar do sul e sudeste do Pará.
260 $aIn: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 35., 1998, Botucatu. Anais. Botucatu: SBZ$c1998
300 $av. 4, p. 141-143.
650 $aAmazonia
650 $afamily farms
650 $alivestock
650 $aAgricultura Familiar
650 $aDiagnostico
650 $aPecuária
650 $aSistema de Produção
653 $aBrasil
653 $aDiagnostic
653 $aItupiranga
653 $aMarabá
653 $aPará
653 $aProduction system
653 $aRendenção
653 $aRondon do Pará
653 $aSão João do Araguaia
653 $aTipologia
653 $aTypology
653 $aXinguara
700 1 $aLOBO, I. J. B.
700 1 $aPESSOA, R. O.
700 1 $aTOURRAND, J.-F.
700 1 $aVEIGA, J. B. da
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Registro original: |
Embrapa Amazônia Oriental (CPATU) |
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| 161. |  | 5153958, ANNALS OF MATHEMATICAL STATISTICS, Institute of Mathematical Statistics, Ann Arbor, Mich., US
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Unidades Centrais. |   |
| 163. | | 0905093, ANUARIO ESTATISTICO DO AMAPA, Secretaria de Planejamento e Coordenacao, Macapa, AP
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Amapá; Embrapa Amazônia Oriental. | |
| 164. | | 0350129, ARCHIV FUR TIERZUCHT, Akademi Verlag, Dummerstof-Alemanha
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Suínos e Aves. | |
| 165. | | 1350046, ARROZ (BOGOTA), Federacion Nacional de Arroceros, Bogota, CO
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Agropecuária Oeste; Embrapa Amapá; Embrapa Amazônia Oriental; Embrapa Arroz e Feijão; Embrapa Meio-Norte; Embrapa Solos. | |
| 166. | | 0600633, AUSTRALIAN SEPTORIA NEWSLETTER, Wheat Industry Research Council of Australia, Australia
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Trigo. | |
| 168. | | 0900360, BAHIA RURAL, Cooperativa Central Instituto de Pecuaria da Bahia, Salvador, BA
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Semiárido. | |
| 170. | | 2450182, BIOTECHNOLOGY AND DEVELOPMENT MONITOR, Dept. of International Relations and Public International Law of University Amsterdam, Amsterdam-Holanda
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Amapá; Embrapa Meio Ambiente; Embrapa Soja; Embrapa Trigo. | |
| 172. | | 0900808, BRASIL MOAGEIRO, Acao Moageira, Porto Alegre-RS
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Trigo. | |
| 174. | | 2000160, CAHIERS DE MEDECINE VETERINAIRE, Societe Parisiense d'Expansion Chimique, Paris-Franca
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Amazônia Oriental. | |
| 175. | | 5151638, CALIFORNIA TOMATO GROWER, California Tomato Growers Association, California-CA
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Hortaliças. | |
| 177. | | 0901626, SUÍNOS & CIA, Campinas - SP
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Suínos e Aves. |  |
| 178. | | 2000090, CHIMIE ANALYTIQUE, Societe de Productions Documentaires, Malmaison-Franca
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Agroindústria de Alimentos. | |
| 179. | | 5150982, COLEOPTERISTS BULLETIN, Coleopterists Society, Chicago-IL
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Acre; Embrapa Algodão; Embrapa Amazônia Oriental; Embrapa Arroz e Feijão; Embrapa Cerrados; Embrapa Gado de Corte; Embrapa Meio Norte / UEP-Parnaíba; Embrapa Semiárido; Embrapa Soja; Embrapa Suínos e Aves; Embrapa Trigo. MenosCatálogo Coletivo de Periódicos Embrapa; Embrapa Acre; Embrapa Algodão; Embrapa Amazônia Oriental; Embrapa Arroz e Feijão; Embrapa Cerrados; Embrapa Gado de Corte; Embrapa Meio Norte / UEP-Parnaíba; Embrapa Semiárido; Embrapa Soja... Mostrar Todas | |
| 180. | | 3600041, COMERCIO EXTERIOR. MEXICO, Banco Nacional de Comercio Exterior, Mexico-DF
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Semiárido. | |
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