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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. |
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Registro Completo |
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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: |
LEADER 03680naa a2200469 a 4500
001 2163774
005 2024-04-22
008 2024 bl uuuu u00u1 u #d
024 7 $a10.3389/fgene.2024.1361418$2DOI
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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Registro original: |
Embrapa Recursos Genéticos e Biotecnologia (CENARGEN) |
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Registro Completo
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Biblioteca(s): |
Embrapa Gado de Corte. |
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Data corrente: |
09/12/2020 |
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Data da última atualização: |
09/12/2020 |
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Tipo da produção científica: |
Nota Técnica/Nota Científica |
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Autoria: |
BARRIOS, S. C. L.; CARROMEU, C.; SILVA, M. A. I. da; MATSUBARA, E. T.; VALLE, C. B. do; JANK, L.; SANTOS, M. F.; ASSIS, G. M. L. de; CRIVELLARO, L. L.; GONÇALVES, T. D. T.; QUEIROZ JÚNIOR, J. M.; CANDIDO, A. R.; MACHADO, W. K. R.; GOUVEIA, B. T.; NOBRE, A. A. A.; ZANELLA, A. L. |
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Afiliação: |
SANZIO CARVALHO LIMA BARRIOS, CNPGC; CAMILO CARROMEU, CNPGC; MÁRCIO APARECIDO INÁCIO DA SILVA, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil.; EDSON TAKASHI MATSUBARA, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brasil; CACILDA BORGES DO VALLE; LIANA JANK, CNPGC; MATEUS FIGUEIREDO SANTOS, CNPGC; GISELLE MARIANO LESSA DE ASSIS, CPAF-AC; LEONARDO LAZARINO CRIVELLARO, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brasil.; THALLYSON DANCHEN TEIXEIRA GONÇALVES, Universidade para o Desenvolvimento do Estado e da Região do Pantanal–Anhanguera/Uniderp, Campo Grande, MS, Brasil; JOSÉ MARCOS QUEIROZ JÚNIOR, Universidade Católica Dom Bosco, Campo Grande, MS, Brasil; ANDERSON RAMIRES CANDIDO, Universidade Estadual de Mato Grosso do Sul; WYVERSON KIM ROCHA MACHADO, Universidade Estadual de Mato Grosso do Sul; BEATRIZ TOMÉ GOUVEIA, Universidade Federal de Lavras, Lavras, MG, Brasil; ALANA APARECIDA AMARILHA NOBRE, Universidade Federal de Lavras, Lavras, MG, Brasil; AYHAN LIELL ZANELLA, Universidade Católica Dom Bosco, Campo Grande, MS, Brasil. |
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Título: |
Pasto Certo® version 2.0 - An application about Brazilian tropical forage cultivars for mobile and desktop devices. |
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Ano de publicação: |
2020 |
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Fonte/Imprenta: |
Tropical Grasslands-Forrajes Tropicales, v. 8, n. 2, p. 162?166, 2020. |
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Idioma: |
Português |
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Thesaurus NAL: |
Grasses; Megathyrsus maximus; Pastures; Urochloa. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/219034/1/1-Pasto-Certo-version-2.0-An-application-about-Brazilian-tropical-forage-cultivars-for-mobile-and-desktop-devices.pdf
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Marc: |
LEADER 01018naa a2200337 a 4500
001 2127940
005 2020-12-09
008 2020 bl uuuu u00u1 u #d
100 1 $aBARRIOS, S. C. L.
245 $aPasto Certo® version 2.0 - An application about Brazilian tropical forage cultivars for mobile and desktop devices.$h[electronic resource]
260 $c2020
650 $aGrasses
650 $aMegathyrsus maximus
650 $aPastures
650 $aUrochloa
700 1 $aCARROMEU, C.
700 1 $aSILVA, M. A. I. da
700 1 $aMATSUBARA, E. T.
700 1 $aVALLE, C. B. do
700 1 $aJANK, L.
700 1 $aSANTOS, M. F.
700 1 $aASSIS, G. M. L. de
700 1 $aCRIVELLARO, L. L.
700 1 $aGONÇALVES, T. D. T.
700 1 $aQUEIROZ JÚNIOR, J. M.
700 1 $aCANDIDO, A. R.
700 1 $aMACHADO, W. K. R.
700 1 $aGOUVEIA, B. T.
700 1 $aNOBRE, A. A. A.
700 1 $aZANELLA, A. L.
773 $tTropical Grasslands-Forrajes Tropicales$gv. 8, n. 2, p. 162?166, 2020.
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