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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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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: |
LEADER 03672naa a2200373 a 4500
001 2080081
005 2017-11-20
008 2017 bl uuuu u00u1 u #d
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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Registro original: |
Embrapa Florestas (CNPF) |
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 | Acesso ao texto completo restrito à biblioteca da Embrapa Recursos Genéticos e Biotecnologia. Para informações adicionais entre em contato com cenargen.biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Cerrados; Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
30/09/2019 |
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Data da última atualização: |
30/12/2020 |
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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: |
MORANDI, P. S.; MARIMON, B. S.; MARIMON-JUNIOR, B. H.; RATTER, J. A.; FELDPAUSCH, T. R.; COLLI, G. R.; MUNHOZ, C. B. R.; SILVA JÚNIOR, M. C. da; LIMA, E. de S.; HAIDAR, R. F.; ARROYO, L.; MURAKAMI, A. A.; AQUINO, F. de G.; WALTER, B. M. T.; RIBEIRO, J. F.; FRANÇOSO, R.; ELIAS, R.; OLIVEIRA, E. A. de; REIS, S. M.; OLIVEIRA, B. de; NEVES, E. C. das; NOGUEIRA, D. S.; LIMA, H. S.; CARVALHO, T. P. de; RODRIGUES, S. A.; VILLARROEL, D.; FELFILI, J. M.; PHILLIPS, O. L. |
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Afiliação: |
PAULO S. MORANDI, BIONORTE, UFAM–UNEMAT; BEATRIZ SCHWANTES MARIMON, BIONORTE, UFAM–UNEMAT; BEN HUR MARIMON-JUNIOR, BIONORTE, UFAM–UNEMAT; JAMES A. RATTER, ROYAL BOTANIC GARDEN, UK; TED R. FELDPAUSCH, UNIVERSITY OF EXETER, UK; GUARINO RINALDI COLLI, UNB; CÁSSIA BEATRIZ RODRIGUES MUNHOZ, UNB; MANOEL CLÁUDIO DA SILVA JÚNIOR, UNB; EDSON DE SOUZA LIMA, INSTITUTO PRÓ-CARNÍVOROS; RICARDO FLORES HAIDAR, UNB; LUZMILA ARROYO, UNIVERSIDAD AUTÓNOMA GABRIEL RENE MORENO, BOLIVIA; ALEJANDRO ARAUJO MURAKAMI, UNIVERSIDAD AUTÓNOMA GABRIEL RENE MORENO, BOLIVIA; FABIANA DE GOIS AQUINO, CPAC; BRUNO MACHADO TELES WALTER, Cenargen; JOSE FELIPE RIBEIRO, CPAC; RENATA FRANÇOSO, UNB; FERNANDO ELIAS, UNEMAT; EDMAR ALMEIDA DE OLIVEIRA, BIONORTE, UFAM–UNEMAT; SIMONE MATIAS REIS, BIONORTE, UFAM–UNEMAT; BIANCA DE OLIVEIRA, UNEMAT; EDER CARVALHO DAS NEVES, UNEMAT; DENIS SILVA NOGUEIRA, UNEMAT; HERSON SOUZA LIMA, INSTITUTO PRÓ-CARNÍVOROS; TATIANE PIRES DE CARVALHO, INSTITUTO PRÓ-CARNÍVOROS; SILVO ALVES RODRIGUES, UFMT; DANIEL VILLARROEL, UNIVERSIDAD AUTÓNOMA GABRIEL RENE MORENO, BOLIVIA; JEANINE M. FELFILI, UNB; OLIVER L. PHILLIPS, UNIVERSITY OF LEEDS, UK. |
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Título: |
Tree diversity and above-ground biomass in the South America Cerrado biome and their conservation implications. |
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Ano de publicação: |
2020 |
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Fonte/Imprenta: |
Biodiversity and Conservation, v. 29, n. 5, p. 1519-1536, 2020. |
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DOI: |
10.1007/s10531-018-1589-8 |
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Idioma: |
Inglês |
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Palavras-Chave: |
Carbon stocks; Core area; Diversity-biomass; Neotropics; Richness; Transition. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 01479naa a2200517 a 4500
001 2128856
005 2020-12-30
008 2020 bl uuuu u00u1 u #d
024 7 $a10.1007/s10531-018-1589-8$2DOI
100 1 $aMORANDI, P. S.
245 $aTree diversity and above-ground biomass in the South America Cerrado biome and their conservation implications.$h[electronic resource]
260 $c2020
653 $aCarbon stocks
653 $aCore area
653 $aDiversity-biomass
653 $aNeotropics
653 $aRichness
653 $aTransition
700 1 $aMARIMON, B. S.
700 1 $aMARIMON-JUNIOR, B. H.
700 1 $aRATTER, J. A.
700 1 $aFELDPAUSCH, T. R.
700 1 $aCOLLI, G. R.
700 1 $aMUNHOZ, C. B. R.
700 1 $aSILVA JÚNIOR, M. C. da
700 1 $aLIMA, E. de S.
700 1 $aHAIDAR, R. F.
700 1 $aARROYO, L.
700 1 $aMURAKAMI, A. A.
700 1 $aAQUINO, F. de G.
700 1 $aWALTER, B. M. T.
700 1 $aRIBEIRO, J. F.
700 1 $aFRANÇOSO, R.
700 1 $aELIAS, R.
700 1 $aOLIVEIRA, E. A. de
700 1 $aREIS, S. M.
700 1 $aOLIVEIRA, B. de
700 1 $aNEVES, E. C. das
700 1 $aNOGUEIRA, D. S.
700 1 $aLIMA, H. S.
700 1 $aCARVALHO, T. P. de
700 1 $aRODRIGUES, S. A.
700 1 $aVILLARROEL, D.
700 1 $aFELFILI, J. M.
700 1 $aPHILLIPS, O. L.
773 $tBiodiversity and Conservation$gv. 29, n. 5, p. 1519-1536, 2020.
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