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 | Acesso ao texto completo restrito à biblioteca da Embrapa Florestas. Para informações adicionais entre em contato com cnpf.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Florestas. |
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Data corrente: |
24/10/2012 |
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Data da última atualização: |
20/02/2015 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
RESENDE JUNIOR, M. F. R.; MUÑOZ, P.; RESENDE, M. D. V. de; GARRICK, D. J.; FERNANDO, R. L.; DAVIS, J. M.; JOKELA, E. J.; MARTIN, T. A.; PETER, G. F.; KIRST, M. |
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Afiliação: |
M. F. R. RESENDE JUNIOR, UNIVERSITY OF FLORIDA; P. MUÑOZ, UNIVERSITY OF FLORIDA; MARCOS DEON VILELA DE RESENDE, CNPF; D. J. GARRICK, IOWA STATE UNIVERSITY; R. L. FERNANDO, IOWA STATE UNIVERSITY; J. M. DAVIS, UNIVERSITY OF FLORIDA; E. J. JOKELA, UNIVERSITY OF FLORIDA; T. A. MARTIN, UNIVERSITY OF FLORIDA; G. F. PETER, UNIVERSITY OF FLORIDA; M. KIRST, UNIVERSITY OF FLORIDA. |
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Título: |
Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.). |
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Ano de publicação: |
2012 |
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Fonte/Imprenta: |
Genetics, v. 190, p. 1503-1510, April 2012. |
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Idioma: |
Inglês |
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Conteúdo: |
Genomic selection can increase genetic gain per generation through early selection. Genomic selection is expected to be particularly valuable for traits that are costly to phenotype and expressed late in the life cycle of long-lived species. Alternative approaches to genomic selection prediction models may perform differently for traits with distinct genetic properties. Here the performance of four different original methods of genomic selection that differ with respect to assumptions regarding distribution of marker effects, including (i) ridge regression–best linear unbiased prediction (RR–BLUP), (ii) Bayes A, (iii) Bayes Cp, and (iv) Bayesian LASSO are presented. In addition, a modified RR–BLUP (RR–BLUP B) that utilizes a selected subset of markers was evaluated. The accuracy of these methods was compared across 17 traits with distinct heritabilities and genetic architectures, including growth, development, and disease-resistance properties, measured in a Pinus taeda (loblolly pine) training population of 951 individuals genotyped with 4853 SNPs. The predictive ability of the methods was evaluated using a 10-fold, cross-validation approach, and differed only marginally for most method/trait combinations. Interestingly, for fusiform rust disease-resistance traits, Bayes Cp, Bayes A, and RR–BLUB B had higher predictive ability than RR–BLUP and Bayesian LASSO. Fusiform rust is controlled by few genes of large effect. A limitation of RR–BLUP is the assumption of equal contribution of all markers to the observed variation. However, RR-BLUP B performed equally well as the Bayesian approaches.The genotypic and phenotypic data used in this study are publically available for comparative analysis of genomic selection prediction models. MenosGenomic selection can increase genetic gain per generation through early selection. Genomic selection is expected to be particularly valuable for traits that are costly to phenotype and expressed late in the life cycle of long-lived species. Alternative approaches to genomic selection prediction models may perform differently for traits with distinct genetic properties. Here the performance of four different original methods of genomic selection that differ with respect to assumptions regarding distribution of marker effects, including (i) ridge regression–best linear unbiased prediction (RR–BLUP), (ii) Bayes A, (iii) Bayes Cp, and (iv) Bayesian LASSO are presented. In addition, a modified RR–BLUP (RR–BLUP B) that utilizes a selected subset of markers was evaluated. The accuracy of these methods was compared across 17 traits with distinct heritabilities and genetic architectures, including growth, development, and disease-resistance properties, measured in a Pinus taeda (loblolly pine) training population of 951 individuals genotyped with 4853 SNPs. The predictive ability of the methods was evaluated using a 10-fold, cross-validation approach, and differed only marginally for most method/trait combinations. Interestingly, for fusiform rust disease-resistance traits, Bayes Cp, Bayes A, and RR–BLUB B had higher predictive ability than RR–BLUP and Bayesian LASSO. Fusiform rust is controlled by few genes of large effect. A limitation of RR–BLUP is the assumption of equal contrib... Mostrar Tudo |
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Palavras-Chave: |
Precisão. |
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Thesagro: |
Pinus Taeda; Seleção Genética. |
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Categoria do assunto: |
-- |
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Marc: |
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001 1937733
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100 1 $aRESENDE JUNIOR, M. F. R.
245 $aAccuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.).$h[electronic resource]
260 $c2012
520 $aGenomic selection can increase genetic gain per generation through early selection. Genomic selection is expected to be particularly valuable for traits that are costly to phenotype and expressed late in the life cycle of long-lived species. Alternative approaches to genomic selection prediction models may perform differently for traits with distinct genetic properties. Here the performance of four different original methods of genomic selection that differ with respect to assumptions regarding distribution of marker effects, including (i) ridge regression–best linear unbiased prediction (RR–BLUP), (ii) Bayes A, (iii) Bayes Cp, and (iv) Bayesian LASSO are presented. In addition, a modified RR–BLUP (RR–BLUP B) that utilizes a selected subset of markers was evaluated. The accuracy of these methods was compared across 17 traits with distinct heritabilities and genetic architectures, including growth, development, and disease-resistance properties, measured in a Pinus taeda (loblolly pine) training population of 951 individuals genotyped with 4853 SNPs. The predictive ability of the methods was evaluated using a 10-fold, cross-validation approach, and differed only marginally for most method/trait combinations. Interestingly, for fusiform rust disease-resistance traits, Bayes Cp, Bayes A, and RR–BLUB B had higher predictive ability than RR–BLUP and Bayesian LASSO. Fusiform rust is controlled by few genes of large effect. A limitation of RR–BLUP is the assumption of equal contribution of all markers to the observed variation. However, RR-BLUP B performed equally well as the Bayesian approaches.The genotypic and phenotypic data used in this study are publically available for comparative analysis of genomic selection prediction models.
650 $aPinus Taeda
650 $aSeleção Genética
653 $aPrecisão
700 1 $aMUÑOZ, P.
700 1 $aRESENDE, M. D. V. de
700 1 $aGARRICK, D. J.
700 1 $aFERNANDO, R. L.
700 1 $aDAVIS, J. M.
700 1 $aJOKELA, E. J.
700 1 $aMARTIN, T. A.
700 1 $aPETER, G. F.
700 1 $aKIRST, M.
773 $tGenetics$gv. 190, p. 1503-1510, April 2012.
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Registro original: |
Embrapa Florestas (CNPF) |
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| Registros recuperados : 19 | |
| 2. |  | MUNOZ, P.; RESENDE JUNIOR, M.; RESENDE, M. D. V. de; GEZAN, S.; KIRST, M.; PETER, G. The re-discovery of the dominance variation by using the observed relationship matrix and itis implications in breeding. In: INTERNATIONAL CONFERENCE ON QUANTITATIVE GENETICS, 4., 2012, Edinburgh. Understanding Variation in Complex Traits. . [S.l.: s.n], 2012. Poster abstracts. P-367.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
|    |
| 3. | | RIOS, E.; RESENDE, M.; KIRST, M.; RESENDE, M. D. V. de; ALMEIDA FILHO, J. E. de; MUNOZ, P. Predictive ability of Genomic Estimated Family Values (GEFV). In: PLANT & ANIMAL GENOME CONFERENCE, 24., 2016, San Diego. [Abstracts...]. San Diego: [s.n.], 2016. Pôster P1186.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 4. | | RESENDE JUNIOR, M. F. R.; MUÑOZ, P.; ACOSTA, J. J.; PETER, G. F.; DAVIS, J. M.; GRATTAPAGLIA, D.; RESENDE, M. D. V. de; KIRST, M. Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytologist, v. 193, p. 617-624, 2012.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Florestas; Embrapa Recursos Genéticos e Biotecnologia. |
|  |
| 5. | | ALMEIDA FILHO, J. E. de; GUIMARÃES, J. F. R.; SILVA, F. F. e; RESENDE, M. D. V. de; MUÑOZ, P.; KIRST, M.; RESENDE JUNIOR, M. F. R. The contribution of dominance to phenotype prediction in a pine breeding and simulated population. Heredity, v. 117, p. 33-41, July 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Florestas. |
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| 6. | | RESENDE JUNIOR, M.; RESENDE, M. D. V. de; MUNOZ, P. R.; TAKAHASHI, E. K.; PETROLI, C.; SANSALONI, C.; KIRST, M.; GRATTAPAGLIA, D. Increase in efficiency of genomic selection sing epistatic interactions and detection of candidate genes for rust resistance in Eucalyptus. In: INTERNATIONAL PLANT & ANIMAL GENOME, 21., 2013, San Diego. Abstracts... Jersey City: Scherago International, 2013. W287.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 7. | | RESENDE JUNIOR, M.; DELL VALLE, P. R. M.; RESENDE, M. D. V. de; GARRICK, D. J.; FERNANDO, R.; DAVIS, J. M.; PETER, G.; KIRST, M. Improvement of genomic selection using a ridge regression approach with selected markers. In: INTERNATIONAL CONFERENCE ON QUANTITATIVE GENETICS, 4., 2012, Edinburgh. Understanding Variation in Complex Traits. . [S.l.: s.n], 2012. Poster abstracts. P-199.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 9. | | AGUIAR, A. V. de; LOPES, M. T. G.; GAIOTTO, F. A.; BITTENCOURT, F.; DERVINIS, C.; MULLER, B. S. F.; SANTOS, R. F. dos; QUISEN, R. C.; KIRST, M. Transcriptome analysis of Euterpe edulis and identification of microsatellite markers. In: IUFRO GENOMICS & FOREST TREE GENETICS, 2016, Arcachon. Book of abstracts. [S.l.]: IUFRO, 2016. p. 90-91.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 10. | | ALMEIDA FILHO, J. E. de A.; RODRIGUES, J. F. G.; SILVA, F. F. e; RESENDE, M. D. V. de; RESENDE JÚNIOR, M.; MUÑOZ, P.; KIRST, M. Genomic prediction of assitive and non-additive effects using genetic markers and pedigrees in pines breeding. In: CONGRESSO BRASILEIRO DE MELHORAMENTO DE PLANTAS, 8., 2015, Goiânia. O melhoramento de plantas, o futuro da agricultura e a soberania nacional: anais. Goiânia: SBMP: UFG, 2015. Resumo.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 11. | | MÜLLER, B. S. F.; NEVES, L. G.; RESENDE JÚNIOR, M. F. R.; MUÑOZ, P. R.; KIRST, M.; SANTOS, P. E. T. dos; PALUDZYSZYN FILHO, E.; GRATTAPAGLIA, D. Genomic selection for growth traits in Eucalyptus benthamii and E. pellita populations using a genome-wide Eucalyptus 60K SNPs chip. In: IUFRO TREE BIOTECHNOLOGY CONFERENCE, 2015, Florence. Forests: the importance to the planet and society. [S.l.]: IBBR: ICCOM, 2015. Pen-drive.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 12. | | GUIMARÃES, J. F. R.; ALMEIDA FILHO, J. E.; RESENDE JÚNIOR, M. F.; RESENDE, M. D. V. de; SILVA, F. F. e; MUÑOZ, P.; KIRST, M. Predictive ability behavior across sites after discard of SNPS with unstable effects. In: CONGRESSO BRASILEIRO DE MELHORAMENTO DE PLANTAS, 8., 2015, Goiânia. O melhoramento de plantas, o futuro da agricultura e a soberania nacional: anais. Goiânia: SBMP: UFG, 2015. Resumo.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 13. | | MUÑOZ, P. R.; RESENDE JUNIOR, M. F. R.; GEZAN, S. A.; RESENDE, M. D. V. de; CAMPOS, G. de los; KIRST, M.; HUBER, D.; PETER, G. F. Unraveling additive from nonadditive effects using genomic relationship matrices. Genetics, v. 198, p. 1759-1768, Dec. 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Florestas. |
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| 14. | | RESENDE JUNIOR, M. F. R.; MUÑOZ, P.; RESENDE, M. D. V. de; GARRICK, D. J.; FERNANDO, R. L.; DAVIS, J. M.; JOKELA, E. J.; MARTIN, T. A.; PETER, G. F.; KIRST, M. Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.). Genetics, v. 190, p. 1503-1510, April 2012.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Florestas. |
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| 15. | | ALMEIDA FILHO, J. E. de A.; GUIMARÃES, J. F. R.; SILVA, F. F. e; RESENDE, M. D. V. de; MUÑOZ, P.; KIRST, M.; RESENDE JÚNIOR, M. F. R. de. Genomic prediction of additive and non-additive effects using genetic markers and pedigrees. G3: Genes, Genomes, Genetics, v. 9, p. 2739-2748, Aug. 2019.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Florestas. |
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| 16. | | MÜLLER, B. S. F.; NEVES, L. G.; ALMEIDA FILHO, J. E. de; RESENDE JUNIOR, M. F. R.; MUÑOZ, P. R.; SANTOS, P. E. T. dos; PALUDZYSZYN FILHO, E.; KIRST, M.; GRATTAPAGLIA, D. Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus. BMC Genomics, v. 18, article 524, 2017. 17 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Florestas; Embrapa Recursos Genéticos e Biotecnologia. |
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| 17. | | MUNOZ, P. R.; RESENDE JUNIOR, M. F. R.; HUBER, D. A.; QUESADA, T.; RESENDE, M. D. V. de; NEALE, D. B.; WEGRZYN, J. L.; KIRST, M.; PETER, G. F. Genomic relationship matrix for correcting pedigree errors in breeding populations: impact on genetic parameters and genomic selection accuracy. Crop Science, v. 54, p. 115-1123, May/June 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Florestas. |
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| 18. | | LOPES, M. T. G.; GAIOTTO, F. A.; AGUIAR, A. V. de; FAHRENKROG, A.; BITTENCOURT, F.; DERVINIS, C.; MULLER, B. S. F.; SANTOS, R. F. dos; QUISEN, R. C.; KIRST, M. Next-generation transcriptome assembly of an Amazon palm (Euterpe precatoria). In: IUFRO GENOMICS & FOREST TREE GENETICS, 2016, Arcachon. Book of abstracts. [S.l.]: IUFRO, 2016. p. 90.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 19. | | LOPES, M. T. G.; AGUIAR, A. V. de; GAIOTTO, F. A.; FAHRENKROG, A.; BITTENCOURT, F.; DERVINIS, C.; MÜLLER, B. S. F.; SANTOS, R. F. dos; QUISEN, R. C.; KIRST, M. Next generation transcriptome assembly for Euterpe oleracea. In: GLOBAL CONFERENCE ON PLANT SCIENCE AND MOLECULAR BIOLOGY, 2., 2018, Rome. Accentuate innovations and emerging novel research in plant sciences: book of abstracts. Rome: 2018. p. 94.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| Registros recuperados : 19 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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