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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: |
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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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Biblioteca |
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| Registros recuperados : 26 | |
| 5. |  | VENERONI-GOUVEIA, G.; TIZIOTO, P. C.; MEIRELLES, S. L. C.; SANTIAGO, A. C.; ALENCAR, M. M. de; REGITANO, L. C. de A. Candidate genes for carcass traits in a tropical-adapted Brazilian composite beef breed. Genetics and Molecular Research, v. 14, n. 4, p. 16667-16674, 2015.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 6. | | MOKRY, F. B.; LIMA, A. O. de; MUDADU, M. A.; HIGA, R. H.; MEIRELLES, S. L. C.; REGITANO, L. C. de A. An insight into the linkage disequilibrium map of the Canchim beef cattle breed. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 8., 2012, Campinas. Abstract book... Ribeirão Preto: AB3C, 2012. Não paginado. X-MEETING 2012.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 7. | | SOUZA, F. A. C.; FERNANDES, T. J.; CUNHA, F. O.; RIBEIRO, R. A.; MUNIZ, F. R.; MEIRELLES, S. L. C.; MUNIZ, J. A.; MOURA, R. S. Morphometric characteristics of the Mangalarga Marchador horse breed determined by nonlinear models. Pesquisa Agropecuária Brasileira v. 54, e01145, jan./dez. 2019. Título em português: Características morfométricas de equinos da raça Mangalarga Marchador determinadas por modelos não lineares.| Biblioteca(s): Embrapa Unidades Centrais. |
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| 8. | | BAENA, M. M.; COSTA, A. C.; VIEIRA, G. R.; ROCHA, R. de F. B.; RIBEIRO, A. R. B.; IBELLI, A. M. G.; MEIRELLES, S. L. C. Heat tolerance responses in a Bos Taurus cattle herd raised in a Brazilian climate. Journal of Thermal Biology, v. 81, p. 162-169, 2019.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Suínos e Aves. |
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| 10. | | MORKY, F. B.; LIMA, A. O.; HIGA, R. H.; MUDADU, M. de A.; MEIRELLES, S. L. C.; REGITANO, L. C. de A. Predictive ability and genotype frequencies of a set of SNPs for backfat thickness in Canchim. In: ANNUAL MEETING BRAZILIAN SOCIETY OF ANIMAL SCIENCE, 50., 2013, Campinas. The integration of Knowledge in animal production - Abstracts. Campinas: SBZ, 2013 1 CD-ROM| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sudeste. |
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| 11. | | LIMA, A. O. de; MOKRY, F. B.; TIZIOTO, P. C.; MUDADU, M. de A.; HIGA, R. H.; MEIRELLES, S. L. C.; REGITANO, L. C. de A. Preliminary studies for identification of SNPs associated with ribeye area in Canchim cattle. In: INTERNATIONAL SYMPOSIUM ON ANIMAL FUNCTIONAL GENOMICS, 5., 2013, Guarujá. Programme and abstract book... [S.l.: s.n.], 2013. p. 43. ISAFG 2013. AB.36.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 13. | | 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. Tournaments between markers as a strategy to enhance genomic predictions. Plos One, v. 14, n. 7, e0219448, p. 1-17, 2019.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Pecuária Sudeste; Embrapa Pesca e Aquicultura. |
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| 14. | | ROCHA, R. F. B.; BAENA, M. M.; ESTOPA, A. de C.; GERVASIO, I. C.; IBELLI, A. M. G.; GIONBELLI, T. R. S.; GIONBELLI, M. P.; FREITAS, R. T. F. de; MEIRELLES, S. L. C. Differential expression of HSF1 and HSPA6 genes and physiological responses in Angus and Simmental cattle breeds. Journal of Thermal Biology, v. 84, p. 92-98, 2019.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Suínos e Aves. |
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| 15. | | MOKRY, F. B.; LIMA, A. O.; MUDADU, M. A.; HIGA, R. H.; MEIRELLES, S. L. C.; SILVA, M. V. B.; CARDOSO, F. F.; NICIURA, S. C. M.; ALENCAR, M. M.; REGITANO, L. C. A. Descriptive analysis of haplotypes in a population of Canchim beef cattle. In: CONGRESSO BRASILEIRO DE GENÉTICA, 58., 2012, Foz do Iguaçu. Resumos... Foz do Iguaçu: SBG, 2012. p. 1.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sul. |
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| 16. | | MOKRY, F. B.; LIMA, A. O.; MUDADU, M. de A.; HIGA, R. H.; MEIRELLES, S. L. C.; SILVA, M. V. G. B.; CARDOSO, F. F.; NICIURA, S. C. M. Descriptive analysis of haplotypes in a population of Canchim beef cattle. In: CONGRESSO BRASILEIRO DE GENÉTICA, 58., 2012, Foz do Iguaçu. Anais... Foz do Igauaçu: SBG, 2012. 1 CD-ROM| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 17. | | 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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| 18. | | GIACHETTO, P. F.; PEREIRA, F. C. P.; MOKRY, F. B.; HIGA, R. H.; MUDADU, M. A.; SILVA, M. V.; NICIURA, S. C. M.; CARDOSO, F. F.; ALENCAR, M. M.; MEIRELLES, S. L. C.; LIMA, A. O.; REGITANO, L. C. A. Initial analysis of copy number variations in canchim beef cattle with extreme phenotypes for ribeye area. In: INTERNATIONAL PLANT & ANIMAL GENOME, 21., 2013, San Diego. [Abstracts...]. [S.l.: s.n.], 2013. Não paginado. Pôster P0572.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sul. |
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| 19. | | TIZIOTO, P. C.; SOUZA, M. M. de; MUDADU, M. de A.; THOLON, P.; MEIRELLES, S. L. C.; TULLIO, R. R.; NASSU, R. T.; ROSA, A. do N.; MEDEIROS, S. R. de; SIQUEIRA, F.; FEIJO, G. L. D.; REGITANO, L. C. de A. Association of KCNJ11 gene variants with tenderness in Nelore breed. In: CONFERENCE OF INTERNATIONAL SOCIETY FOR ANIMAL GENETICS, 33., 2012, Cairns, AU. Abstracts... Cairns: ISAG, 2012. p.109-110 P4046| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Gado de Corte; Embrapa Pecuária Sudeste. |
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| 20. | | BUZANSKAS, M. E.; GROSSI, D. do A.; VENTURA, R. V.; SCHENKEL, F. S.; CHUD, T. C. S.; STAFUZZA, N. B.; ROLA, L. D.; MEIRELLES, S. L. C.; MOKRY, F. B.; MUDADU, M. de A.; HIGA, R. H.; SILVA, M. V. G. B.; ALENCAR, M. M. de; REGITANO, L. C. de A.; MUNARI, D. P. Candidate genes for male and female reproductive traits in Canchim beef cattle. Journal of Animal Science and Biotechnology, v. 8, p. 1-10, 2017. Artigo 67. Na publicação: Marcos Vinícius Gualberto Barbosa da Silva.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Gado de Leite; Embrapa Pecuária Sudeste. |
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| Registros recuperados : 26 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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