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| Registros recuperados : 48 | |
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| 22. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| 23. | | HOEKENGA, O. A.; BUCKLER, E.; MARON, L.; MAGALHAES, J. V. de; KIRST, M.; KRILL, A.; LYI, S. M.; ROSE, J.; THANNHAUSER, T.; KOCHIAN, L. Joint linkage-association analysis of aluminum tolerance in maize. In: INTERNATIONAL PLANT & ANIMAL GENOMES CONFERENCE, 15., 2007, San Diego, CA. [Proceedings...]. [S. l.: s.n.], 2007.| Biblioteca(s): Embrapa Milho e Sorgo. |
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| 24. | | HOEKENGA, O. A.; BUCKLER, E. S.; KIRST, M.; KRILL, A. M.; LYI, S. M.; MAGALHAES, J. V. de; MARON, L. G.; KOCHIAN, L. V. Joint linkage-association analysis of aluminum tolerance in maize. In: INTERNATIONAL SYMPOSIUM ON PLANT-SOIL INTERACTIONS AT LOW pH, 7., 2009, Guangzhou. Plant-soil interactions at low pH: nutriomic approach: proceedings. Guangzhou: South China University of Technology, 2009. p. 136-137.| Biblioteca(s): Embrapa Milho e Sorgo. |
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| 27. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| 28. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| 29. | | 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.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 30. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| 31. | | 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.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 32. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| 33. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| 34. | | FERREYRA RAMOS, S. L.; DEQUIGIOVANNI, G.; SEBBENN, A. M.; LOPES, M. T. G.; KAGEYAMA, P. Y.; MACEDO, J. L. V. de; KIRST, M.; VEASEY, E. A. Spatial genetic structure, genetic diversity and pollen dispersal in a harvested population of Astrocaryum aculeatum in the Brazilian Amazon. BMC Genetics, 23 Apr. 2016.| Biblioteca(s): Embrapa Amazônia Ocidental. |
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| 35. | | 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.| Biblioteca(s): Embrapa Amazônia Ocidental. |
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| 36. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| 37. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| 38. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| 39. | | MULLER, B. S. F.; NEVES, L. G.; LIMA, B. M.; GARCIA, C. C.; MISSIAGGIA, A.; AGUIAR, A. M.; TAKAHASHI, E. K.; SILVA JUNIOR, O. B. da; KIRST, M.; GRATTAPAGLIA, D. Joint GWAS analysis for growth traits across four Eucalyptus breeding populations. In: PLANT AND ANIMAL GENOME CONFERENCE, 25., 2017, San Diego. [Abstracts...]. San Diego, CA: [s.n.], 2017. W338.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 40. | | 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.| Biblioteca(s): Embrapa Florestas. |
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| Registros recuperados : 48 | |
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Registro Completo
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Biblioteca(s): |
Embrapa Florestas; Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
20/11/2017 |
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Data da última atualização: |
20/11/2017 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
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. |
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Afiliação: |
Bárbara S. F. Müller, UnB; Leandro G. Neves, RAPiD Genomics LLC; Janeo E. de Almeida Filho, University of Florida; Márcio F. R. Resende Junior, RAPiD Genomics LLC; Patricio R. Muñoz, University of Florida; PAULO EDUARDO TELLES DOS SANTOS, CNPF; ESTEFANO PALUDZYSZYN FILHO, CNPF; Matias Kirst, University of Florida; DARIO GRATTAPAGLIA, Cenargen. |
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Título: |
Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus. |
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Ano de publicação: |
2017 |
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Fonte/Imprenta: |
BMC Genomics, v. 18, article 524, 2017. 17 p. |
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DOI: |
10.1186/s12864-017-3920-2 |
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Idioma: |
Inglês
Português |
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Conteúdo: |
Background: The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted it to a genome-wide association study (GWAS) for growth traits in breeding populations of Eucalyptus benthamii (n =505) and Eucalyptus pellita (n =732). Both species are of increasing commercial interest for the development of germplasm adapted to environmental stresses. Results: Predictive ability reached 0.16 in E. benthamii and 0.44 in E. pellita for diameter growth. Predictive abilities using either Genomic BLUP or different Bayesian methods were similar, suggesting that growth adequately fits the infinitesimal model. Genomic prediction models using ~5000?10,000 SNPs provided predictive abilities equivalent to using all 13,787 and 19,506 SNPs genotyped in the E. benthamii and E. pellita populations, respectively. No difference was detected in predictive ability when different sets of SNPs were utilized, based on position (equidistantly genome-wide, inside genes, linkage disequilibrium pruned or on single chromosomes), as long as the total number of SNPs used was above ~5000. Predictive abilities obtained by removing relatedness between training and validation sets fell near zero for E. benthamii and were halved for E. pellita. These results corroborate the current view that relatedness is the main driver of genomic prediction, although some short-range historical linkage disequilibrium (LD) was likely captured for E. pellita. A GWAS identified only one significant association for volume growth in E. pellita, illustrating the fact that while genome-wide regression is able to account for large proportions of the heritability, very little or none of it is captured into significant associations using GWAS in breeding populations of the size evaluated in this study. Conclusions: This study provides further experimental data supporting positive prospects of using genome-wide data to capture large proportions of trait heritability and predict growth traits in trees with accuracies equal or better than those attainable by phenotypic selection. Additionally, our results document the superiority of the whole-genome regression approach in accounting for large proportions of the heritability of complex traits such as growth in contrast to the limited value of the local GWAS approach toward breeding applications in forest trees. MenosBackground: The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted it to a genome-wide association study (GWAS) for growth traits in breeding populations of Eucalyptus benthamii (n =505) and Eucalyptus pellita (n =732). Both species are of increasing commercial interest for the development of germplasm adapted to environmental stresses. Results: Predictive ability reached 0.16 in E. benthamii and 0.44 in E. pellita for diameter growth. Predictive abilities using either Genomic BLUP or different Bayesian methods were similar, suggesting that growth adequately fits the infinitesimal model. Genomic prediction models using ~5000?10,000 SNPs provided predictive abilities equivalent to using all 13,787 and 19,506 SNPs genotyped in the E. benthamii and E. pellita populations, respectively. No difference was detected in predictive ability when different sets of SNPs were utilized, based on position (equidistantly genome-wide, inside genes, linkage disequilibrium pruned or on single chromosomes), as long as the total number of SNPs used was above ~5000. Predictive abilities obtained by removing relatedness between training and validation sets fell near zero for E. benthamii and were halved for E. pellita. These results corroborate the current view that relatedness is the main driver of genomic prediction, although some short-range h... Mostrar Tudo |
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Palavras-Chave: |
Espécie exótica; Genomic selection; GWAS; Seleção genômica; SNP genotyping. |
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Thesagro: |
Eucalipto; Melhoramento genético vegetal. |
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Thesaurus NAL: |
Eucalyptus benthamii; Eucalyptus pellita; genetic relationships; marker-assisted selection; plant breeding. |
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Categoria do assunto: |
--
G Melhoramento Genético |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/166929/1/2017-PauloE-BMCG-Genomic-prediction.pdf
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/181027/1/s12864-017-3920-2.pdf
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Marc: |
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024 7 $a10.1186/s12864-017-3920-2$2DOI
100 1 $aMÜLLER, B. S. F.
245 $aGenomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus.$h[electronic resource]
260 $c2017
520 $aBackground: The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted it to a genome-wide association study (GWAS) for growth traits in breeding populations of Eucalyptus benthamii (n =505) and Eucalyptus pellita (n =732). Both species are of increasing commercial interest for the development of germplasm adapted to environmental stresses. Results: Predictive ability reached 0.16 in E. benthamii and 0.44 in E. pellita for diameter growth. Predictive abilities using either Genomic BLUP or different Bayesian methods were similar, suggesting that growth adequately fits the infinitesimal model. Genomic prediction models using ~5000?10,000 SNPs provided predictive abilities equivalent to using all 13,787 and 19,506 SNPs genotyped in the E. benthamii and E. pellita populations, respectively. No difference was detected in predictive ability when different sets of SNPs were utilized, based on position (equidistantly genome-wide, inside genes, linkage disequilibrium pruned or on single chromosomes), as long as the total number of SNPs used was above ~5000. Predictive abilities obtained by removing relatedness between training and validation sets fell near zero for E. benthamii and were halved for E. pellita. These results corroborate the current view that relatedness is the main driver of genomic prediction, although some short-range historical linkage disequilibrium (LD) was likely captured for E. pellita. A GWAS identified only one significant association for volume growth in E. pellita, illustrating the fact that while genome-wide regression is able to account for large proportions of the heritability, very little or none of it is captured into significant associations using GWAS in breeding populations of the size evaluated in this study. Conclusions: This study provides further experimental data supporting positive prospects of using genome-wide data to capture large proportions of trait heritability and predict growth traits in trees with accuracies equal or better than those attainable by phenotypic selection. Additionally, our results document the superiority of the whole-genome regression approach in accounting for large proportions of the heritability of complex traits such as growth in contrast to the limited value of the local GWAS approach toward breeding applications in forest trees.
650 $aEucalyptus benthamii
650 $aEucalyptus pellita
650 $agenetic relationships
650 $amarker-assisted selection
650 $aplant breeding
650 $aEucalipto
650 $aMelhoramento genético vegetal
653 $aEspécie exótica
653 $aGenomic selection
653 $aGWAS
653 $aSeleção genômica
653 $aSNP genotyping
700 1 $aNEVES, L. G.
700 1 $aALMEIDA FILHO, J. E. de
700 1 $aRESENDE JUNIOR, M. F. R.
700 1 $aMUÑOZ, P. R.
700 1 $aSANTOS, P. E. T. dos
700 1 $aPALUDZYSZYN FILHO, E.
700 1 $aKIRST, M.
700 1 $aGRATTAPAGLIA, D.
773 $tBMC Genomics$gv. 18, article 524, 2017. 17 p.
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