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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Corte. |
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Data corrente: |
30/12/2019 |
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Data da última atualização: |
30/12/2019 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
LARA, L. A. de C.; SANTOS, M. F.; JANK, L.; CHIARI, L.; VILELA, M. de M.; AMADEU, R. R.; SANTOS, J. P. R. dos; SILVA, F. G. da; ZENG, Z.-B.; GARCIA, A. A. F. |
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Afiliação: |
Letícia A. de C. Lara, Universidade de São Paulo -USP/Faculdade de Agricultura Luiz de Queiroz - ESALQ; MATEUS FIGUEIREDO SANTOS, CNPGC; LIANA JANK, CNPGC; LUCIMARA CHIARI, CNPGC; MARIANE DE MENDONCA VILELA, CNPGC; Rodrigo R. Amadeu, Universidade de São Paulo -USP/Faculdade de Agricultura Luiz de Queiroz - ESALQ; Jhonathan P. R. dos Santos, Universidade de São Paulo -USP/Faculdade de Agricultura Luiz de Queiroz - ESALQ; FRANCISCO GUILHERME DA SILVA, CNPGL; Zhao-Bang Zeng, North Carolina State University - NCSU; Antonio Augusto F. Garcia, Universidade de São Paulo -USP/Faculdade de Agricultura Luiz de Queiroz - ESALQ. |
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Título: |
Genomic Selection with Allele Dosage in Panicum maximum Jacq. |
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Ano de publicação: |
2019 |
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Fonte/Imprenta: |
G3: Genes|Genomes|Genetics, v. 9, p. 2463-2475, August 2019. |
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Idioma: |
Inglês |
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Conteúdo: |
Genomic selection is an efficient approach to get shorter breeding cycles in recurrent selection programs and greater genetic gains with selection of superior individuals. Despite advances in genotyping techniques, genetic studies for polyploid species have been limited to a rough approximation of studies in diploid species. The major challenge is to distinguish the different types of heterozygotes present in polyploid populations. In this work, we evaluated different genomic prediction models applied to a recurrent selection population of 530 genotypes of Panicum maximum, an autotetraploid forage grass. We ,also investigated the effect of the allele dosage in the prediction, i.e., considering tetraploid (GS-TD) or diploid (GS-DD) allele dosage. A longitudinal linear mixed model was fitted for each one of the six phenotypic traits, considering different covariance matrices for genetic and residual effects. A total of 41,424 genotypingby- sequencing markers were obtained using 96-plex and Pst1 restriction enzyme, and quantitative genotype calling was performed. Six predictive models were generalized to tetraploid species and predictive ability was estimated by a replicated fivefold cross-validation process. GS-TD and GS-DD models were performed considering 1,223 informative markers. Overall, GS-TD data yielded higher predictive abilities than with GS-DD data. However, different predictive models had similar predictive ability performance. In this work, we provide bioinformatic and modeling guidelines to consider tetraploid dosage and observed that genomic selection may lead to additional gains in recurrent selection program of P. maximum. MenosGenomic selection is an efficient approach to get shorter breeding cycles in recurrent selection programs and greater genetic gains with selection of superior individuals. Despite advances in genotyping techniques, genetic studies for polyploid species have been limited to a rough approximation of studies in diploid species. The major challenge is to distinguish the different types of heterozygotes present in polyploid populations. In this work, we evaluated different genomic prediction models applied to a recurrent selection population of 530 genotypes of Panicum maximum, an autotetraploid forage grass. We ,also investigated the effect of the allele dosage in the prediction, i.e., considering tetraploid (GS-TD) or diploid (GS-DD) allele dosage. A longitudinal linear mixed model was fitted for each one of the six phenotypic traits, considering different covariance matrices for genetic and residual effects. A total of 41,424 genotypingby- sequencing markers were obtained using 96-plex and Pst1 restriction enzyme, and quantitative genotype calling was performed. Six predictive models were generalized to tetraploid species and predictive ability was estimated by a replicated fivefold cross-validation process. GS-TD and GS-DD models were performed considering 1,223 informative markers. Overall, GS-TD data yielded higher predictive abilities than with GS-DD data. However, different predictive models had similar predictive ability performance. In this work, we provide bioinformati... Mostrar Tudo |
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Thesaurus Nal: |
Genomics; Genotyping; Guinea; Plant breeding; Polyploidy; Prediction. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/207993/1/Genomic-Selection-with-Allele-Dosage.pdf
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Marc: |
LEADER 02472naa a2200301 a 4500
001 2117941
005 2019-12-30
008 2019 bl uuuu u00u1 u #d
100 1 $aLARA, L. A. de C.
245 $aGenomic Selection with Allele Dosage in Panicum maximum Jacq.$h[electronic resource]
260 $c2019
520 $aGenomic selection is an efficient approach to get shorter breeding cycles in recurrent selection programs and greater genetic gains with selection of superior individuals. Despite advances in genotyping techniques, genetic studies for polyploid species have been limited to a rough approximation of studies in diploid species. The major challenge is to distinguish the different types of heterozygotes present in polyploid populations. In this work, we evaluated different genomic prediction models applied to a recurrent selection population of 530 genotypes of Panicum maximum, an autotetraploid forage grass. We ,also investigated the effect of the allele dosage in the prediction, i.e., considering tetraploid (GS-TD) or diploid (GS-DD) allele dosage. A longitudinal linear mixed model was fitted for each one of the six phenotypic traits, considering different covariance matrices for genetic and residual effects. A total of 41,424 genotypingby- sequencing markers were obtained using 96-plex and Pst1 restriction enzyme, and quantitative genotype calling was performed. Six predictive models were generalized to tetraploid species and predictive ability was estimated by a replicated fivefold cross-validation process. GS-TD and GS-DD models were performed considering 1,223 informative markers. Overall, GS-TD data yielded higher predictive abilities than with GS-DD data. However, different predictive models had similar predictive ability performance. In this work, we provide bioinformatic and modeling guidelines to consider tetraploid dosage and observed that genomic selection may lead to additional gains in recurrent selection program of P. maximum.
650 $aGenomics
650 $aGenotyping
650 $aGuinea
650 $aPlant breeding
650 $aPolyploidy
650 $aPrediction
700 1 $aSANTOS, M. F.
700 1 $aJANK, L.
700 1 $aCHIARI, L.
700 1 $aVILELA, M. de M.
700 1 $aAMADEU, R. R.
700 1 $aSANTOS, J. P. R. dos
700 1 $aSILVA, F. G. da
700 1 $aZENG, Z.-B.
700 1 $aGARCIA, A. A. F.
773 $tG3: Genes|Genomes|Genetics$gv. 9, p. 2463-2475, August 2019.
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Registro original: |
Embrapa Gado de Corte (CNPGC) |
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| Registros recuperados : 7 | |
| 2. |  | MICHALCZECHEN LACERDA, V. A.; DRIESSEN, K.; FAGUNDES, N. S.; MELO, E. O.; RUMPF, R.; FRANCO, M. M. Análise de metilação de DNA em células doadoras de núcleo para clonagem de bovinos. In: ENCONTRO DO TALENTO ESTUDANTIL DA EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA, 13., 2008, Brasília, DF. Anais: resumos dos trabalhos. Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2008. Resumo 054. p. 96.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 3. | | FRANCO, M. M.; FAGUNDES, N. S.; MICHALCZECHEN-LACERDA, V. A.; CAIXETA, E. S.; RODRIGUES, F. de C.; MACHADO, G. M.; FERREIRA, A. R.; DODE, M. A. N. Characterisation of the methylation pattern in the intragenic CpG island of the IGF2 gene in Bos taurus indicus cumulus cells during in vitro maturation. Journal of Assisted Reproduction and Genetics, v. 31, n. 1, p. 115-120, 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 2 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 4. | | MICHALCZECHEN LACERDA, V. A.; DRIESSEN, K.; FAGUNDES, N. S.; SOUSA, R. V. de; MELO, E. de O.; RUMPF, R.; FRANCO, M. M. Efeito da reclonagem na metilação de DNA do receptor do fator de crescimento semelhante à insulina 2 (IGF2R) em bovinos. In: CONGRESSO BRASILEIRO DE GENÉTICA, 55., 2009, Águas de Lindóia, SP. Resumos... Ribeirão Preto: Sociedade Brasileira de Genética, 2009. p. 215. Apresentado também no ENCONTRO DO TALENTO ESTUDANTIL DA EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA, 14., 2009, Brasília, DF. Anais: resumos dos trabalhos. Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2009. Resumo 039, p. 78.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 5. | | FAGUNDES, N. S.; MICHALCZECHEN-LACERDA, V. A.; CAIXETA, E. S.; MACHADO, G. M.; RODRIGUES, F. C.; MELO, E. de O.; DODE, M. A. N.; FRANCO, M. M. Methylation status in the intragenic differentially methylated region of the IGF2 locus in Bos taurus indicus oocytes with different developmental competencies. Molecular Human Reproduction, v. 17, n. 2, p. 85-91, 2011.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 6. | | RODRIGUES, F. C.; MICHALCZECHEN-LACERDA, V. A.; FAGUNDES, N. S.; MACHADO, G. M.; CAIXETA, E. S.; DODE, M. A. N.; FRANCO, M. M. Padrão de metilação do gene igf2 em células do cumulus de vacas nelore. In: ENCONTRO DO TALENTO ESTUDANTIL DA EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA, 15., 2010, Brasília, DF. Anais: resumos dos trabalhos. Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2010. Resumo 048.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 7. | | RODRIGUES, F. C.; MICHALCZECHEN-LACERDA, V. A.; FAGUNDES, N. S.; MACHADO, G. M.; CAIXETA, E. S.; DODE, M. A. N.; FRANCO, M. M. Padrão de metilação da região diferencialmente metilada de éxon 10 do gene IGF2 em células do cumulus de vacas da raça Nelore. In: CONGRESSO BRASILEIRO DE GENÉTICA, 56., 2010, Guarujá. Resumos... Ribeirão Preto: Sociedade Brasileira de Genética, 2010. p. 71| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| Registros recuperados : 7 | |
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