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Biblioteca(s): |
Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
22/04/2024 |
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Data da última atualização: |
22/04/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
AGUIRRE, N. C.; VILLALBA, P. V.; GARCÍA, M. N.; FILIPPI, C. V.; RIVAS, J. G.; MARTÍNEZ, M. C.; ACUÑA, C. V.; LÓPEZ, A. J.; LÓPEZ, J. A.; PATHAUER, P.; PALAZZINI, D.; HARRAND, L.; OBERSCHELP, J.; MARCÓ, M. A.; CISNEROS, E. F.; CARRERAS, R.; ALVES, A. M. M.; RODRIGUES, J. C.; HOPP, H. E.; GRATTAPAGLIA, D.; CAPPA, E. P.; PANIEGO, N. B.; POLTRI, S. N. M. |
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Afiliação: |
NATALIA CRISTINA AGUIRRE, UEDD INTA-CONICET; PAMELA VICTORIA VILLALBA, UEDD INTA-CONICET; MARTÍN NAHUEL GARCÍA, UEDD INTA-CONICET; CARLA VALERIA FILIPPI, UEDD INTA-CONICET; JUAN GABRIEL RIVAS, UEDD INTA-CONICET; MARÍA CAROLINA MARTÍNEZ, UEDD INTA-CONICET; CINTIA VANESA ACUÑA, UEDD INTA-CONICET; AUGUSTO J. LÓPEZ, INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA; JUAN ADOLFO LÓPEZ, INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA; PABLO PATHAUER, INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA; DINO PALAZZINI, INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA; LEONEL HARRAND, INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA; JAVIER OBERSCHELP, INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA; MARTÍN ALBERTO MARCÓ, INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA; ESTEBAN FELIPE CISNEROS, UNIVERSIDAD NACIONAL DE SANTIAGO DEL ESTERO (UNSE); ROCÍO CARRERAS, UNIVERSIDAD NACIONAL DE SANTIAGO DEL ESTERO (UNSE); ANA MARIA MARTINS ALVES, UNIVERSIDADE DE LISBOA; JOSÉ CARLOS RODRIGUES, UNIVERSIDADE DE LISBOA; H. ESTEBAN HOPP, UEDD INTA-CONICET; DARIO GRATTAPAGLIA, CENARGEN; EDUARDO PABLO CAPPA, INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA; NORMA BEATRIZ PANIEGO, UEDD INTA-CONICET; SUSANA NOEMÍ MARCUCCI POLTRI, UEDD INTA-CONICET. |
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Título: |
Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden). |
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Ano de publicação: |
2024 |
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Fonte/Imprenta: |
Frontiers in Genetics, 2024. |
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DOI: |
10.3389/fgene.2024.1361418 |
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Idioma: |
Inglês |
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Conteúdo: |
Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed. MenosEucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic... Mostrar Tudo |
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Palavras-Chave: |
ABLUP; Double digest restriction-site associated DNA sequencing; GBLUP; Genomic prediction; Genotyping by sequencing; SNP array. |
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Categoria do assunto: |
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Marc: |
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100 1 $aAGUIRRE, N. C.
245 $aComparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden).$h[electronic resource]
260 $c2024
520 $aEucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed.
653 $aABLUP
653 $aDouble digest restriction-site associated DNA sequencing
653 $aGBLUP
653 $aGenomic prediction
653 $aGenotyping by sequencing
653 $aSNP array
700 1 $aVILLALBA, P. V.
700 1 $aGARCÍA, M. N.
700 1 $aFILIPPI, C. V.
700 1 $aRIVAS, J. G.
700 1 $aMARTÍNEZ, M. C.
700 1 $aACUÑA, C. V.
700 1 $aLÓPEZ, A. J.
700 1 $aLÓPEZ, J. A.
700 1 $aPATHAUER, P.
700 1 $aPALAZZINI, D.
700 1 $aHARRAND, L.
700 1 $aOBERSCHELP, J.
700 1 $aMARCÓ, M. A.
700 1 $aCISNEROS, E. F.
700 1 $aCARRERAS, R.
700 1 $aALVES, A. M. M.
700 1 $aRODRIGUES, J. C.
700 1 $aHOPP, H. E.
700 1 $aGRATTAPAGLIA, D.
700 1 $aCAPPA, E. P.
700 1 $aPANIEGO, N. B.
700 1 $aPOLTRI, S. N. M.
773 $tFrontiers in Genetics, 2024.
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Embrapa Recursos Genéticos e Biotecnologia (CENARGEN) |
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| Registros recuperados : 7 | |
| 1. |  | GOMES-MESSIAS, L. M.; VIANELLO, R. P.; RODRIGUES, L. A.; PEREIRA, H. S.; MELO, L. C.; SOUZA, T. L. P. O. de. Piramidação de alelos de resistência à antracnose, mancha-angular e murcha-de-fusário em feijão carioca com escurecimento lento dos grãos. In: CONGRESSO NACIONAL DE PESQUISA DE FEIJÃO, 13., 2021, Goiânia. Conectividade tecnológica, intensificação sustentável: resumos. Brasília, DF: Embrapa; Santo Antônio de Goiás: Embrapa Arroz e Feijão, 2021. p. 104. Evento online.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 2. | | TORRES, M. H. R. M.; VIANELLO, R. P.; SOUZA, T. L. P. O. de; MELO, L. C.; MARTINS, S. M.; GOMES-MESSIAS, L. M.; PEREIRA, H. S. Identification of QTLs and validation of molecular markers associated with reaction to Fusarium wilt in the common bean cultivar BRS FP403. Crop Science, v. 64, n. 3, p. 1729-1742, May/June 2024.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 3. | | GOMES-MESSIAS, L. M.; MARINHO, G. R.; RESENDE, M. P. M.; VIANELLO, R. P.; PEREIRA, H. S.; MELO, L. C.; SOUZA, T. L. P. O. Inheritance of anthracnose resistance in the andean common bean cultivar BRSMG Realce. Annual Report of the Bean Improvement Cooperative, v. 64, p. 7-8, May 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 3 |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 4. | | COÊLHO, L. M.; GOMES-MESSIAS, L. M.; TORGA, P. P.; VIANELLO, R. P.; COSTA, J. G. C. da; SOUZA, T. L. P. O. de. Validação de marcador SNP associado à resistência do Crestamento Bacteriano Comum no acesso de feijão-comum CB911921 (QTL-SU91). In: CONGRESSO NACIONAL DE PESQUISA DE FEIJÃO, 13., 2021, Goiânia. Conectividade tecnológica, intensificação sustentável: resumos. Brasília, DF: Embrapa; Santo Antônio de Goiás: Embrapa Arroz e Feijão, 2021. p. 84. Evento online.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 5. | | GOMES-MESSIAS, L. M.; VIANELLO, R. P.; MARINHO, G. R.; RODRIGUES, L. A.; COELHO, A. S. G.; PEREIRA, H. S.; MELO, L. C.; SOUZA, T. L. P. O. de. Genetic mapping of the Andean anthracnose resistance gene present in the common bean cultivar BRSMG Realce. Frontiers in Plant Science, v, 13, 1033687, Nov. 2022.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 6. | | GOMES-MESSIAS, L. M.; VIANELLO, R. P.; MONTEIRO-JÚNIOR, J. P.; RODRIGUES, L. A.; MOTA, A. P. S.; PEREIRA, H. S.; MELO, L. C.; RAATZ, B.; SOUZA, T. L. P. O. de. Molecular characterization of parental lines and validation of SNP markers for anthracnose and angular leaf spot in common bean. Euphytica, v. 218, n. 5, May 2022.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 7. | | SOUZA, I. P. de; AZEVEDO, B. R. de; COELHO, A. S. G.; SOUZA, T. L. P. O. de; VALDISSER, P. A. M. R.; GOMES-MESSIAS, L. M.; FUNICHELI, B. W.; BRONDANI, C.; VIANELLO, R. P. Whole-genome resequencing of common bean elite breeding lines. Scientific Reports, v. 13, 12721, 2023.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| Registros recuperados : 7 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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