Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)
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 ch...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2024
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| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12123/20324 https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1361418/full https://doi.org/10.3389/fgene.2024.1361418 |
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| author | Aguirre, Natalia Cristina Villalba, Pamela Victoria Garcia, Martin Nahuel Filippi, Carla Valeria Rivas, Juan Gabriel Martinez, Maria Carolina Acuña, Cintia Vanesa Lopez, Javier Augusto Lopez, Juan Adolfo Pathauer, Pablo Santiago Palazzini, Dino Harrand, Leonel Oberschelp, Gustavo Pedro Javier Marco, Martin Alberto Cisneros, Esteban F. Carreras, Rocío Alves, Ana Rodrigues, Jose Hopp, Horacio Esteban Grattapaglia, Dario Cappa, Eduardo Pablo Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi |
| author_browse | Acuña, Cintia Vanesa Aguirre, Natalia Cristina Alves, Ana Cappa, Eduardo Pablo Carreras, Rocío Cisneros, Esteban F. Filippi, Carla Valeria Garcia, Martin Nahuel Grattapaglia, Dario Harrand, Leonel Hopp, Horacio Esteban Lopez, Javier Augusto Lopez, Juan Adolfo Marco, Martin Alberto Marcucci Poltri, Susana Noemi Martinez, Maria Carolina Oberschelp, Gustavo Pedro Javier Palazzini, Dino Paniego, Norma Beatriz Pathauer, Pablo Santiago Rivas, Juan Gabriel Rodrigues, Jose Villalba, Pamela Victoria |
| author_facet | Aguirre, Natalia Cristina Villalba, Pamela Victoria Garcia, Martin Nahuel Filippi, Carla Valeria Rivas, Juan Gabriel Martinez, Maria Carolina Acuña, Cintia Vanesa Lopez, Javier Augusto Lopez, Juan Adolfo Pathauer, Pablo Santiago Palazzini, Dino Harrand, Leonel Oberschelp, Gustavo Pedro Javier Marco, Martin Alberto Cisneros, Esteban F. Carreras, Rocío Alves, Ana Rodrigues, Jose Hopp, Horacio Esteban Grattapaglia, Dario Cappa, Eduardo Pablo Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi |
| author_sort | Aguirre, Natalia Cristina |
| collection | INTA Digital |
| description | 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. |
| format | info:ar-repo/semantics/artículo |
| id | INTA20324 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | INTA203242024-11-19T11:44:09Z Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden) Aguirre, Natalia Cristina Villalba, Pamela Victoria Garcia, Martin Nahuel Filippi, Carla Valeria Rivas, Juan Gabriel Martinez, Maria Carolina Acuña, Cintia Vanesa Lopez, Javier Augusto Lopez, Juan Adolfo Pathauer, Pablo Santiago Palazzini, Dino Harrand, Leonel Oberschelp, Gustavo Pedro Javier Marco, Martin Alberto Cisneros, Esteban F. Carreras, Rocío Alves, Ana Rodrigues, Jose Hopp, Horacio Esteban Grattapaglia, Dario Cappa, Eduardo Pablo Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi Genotyping-by-sequencing Single Nucleotide Polymorphisms Population Genetics Marker-assisted Selection Genotipado mediante Secuenciación Polimorfismos de Nucleótido Único Genética de Poblaciones Selección asistida por Marcadores Eucalyptus Eucalyptus dunnii 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. Instituto de Biotecnología Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Aguirre, Natalia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Villalba, Pamela Victoria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Villalba, Pamela Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Garcia, Martin Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Garcia, Martin Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Filippi, Carla Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Filippi, Carla Valeria. Universidad de la República. Facultad de Agronomía. Departamento de Biología Vegetal. Laboratorio de Bioquímica; Uruguay Fil: Rivas, Juan Gabriel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Rivas, Juan Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Martinez, Maria Carolina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Martinez, Maria Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Acuña, Cintia Vanesa. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Acuña, Cintia Vanesa. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Lopez, Javier Augusto. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bella Vista; Argentina Fil: Lopez, Juan Adolfo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bella Vista; Argentina Fil: Pathauer, Pablo Santiago. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Palazzini, Dino. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Harrand, Leonel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Concordia; Argentina Fil: Oberschelp, Gustavo Pedro Javier. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Concordia; Argentina Fil: Marco, Martin Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Concordia; Argentina Fil: Cisneros, Esteban F. Universidad Nacional de Santiago del Estero. Facultad de Ciencias Forestales; Argentina Fil: Carreras, Rocío. Universidad Nacional de Santiago del Estero. Facultad de Ciencias Forestales; Argentina Fil: Alves, Ana. Universidade de Lisboa. Instituto Superior de Agronomia. Centro de Estudos Florestais e Laboratório Associado TERRA; Portugal Fil: Rodrigues, Jose. Universidade de Lisboa. Instituto Superior de Agronomia. Centro de Estudos Florestais e Laboratório Associado TERRA; Portugal Fil: Hopp, Horacio Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Hopp, Horacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Grattapaglia, Dario. Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Recursos Genéticos e Biotecnologia; Brasil Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Cappa, Eduardo Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Paniego, Norma Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Marcucci Poltri, Susana Noemi. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina 2024-11-19T11:28:55Z 2024-11-19T11:28:55Z 2024-03 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/20324 https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1361418/full 1664-8021 https://doi.org/10.3389/fgene.2024.1361418 eng info:eu-repograntAgreement/INTA/2019-PE-E6-I114-001, Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf Frontiers Media Frontiers in Genetics 15 : 1361418 (March 2024) |
| spellingShingle | Genotyping-by-sequencing Single Nucleotide Polymorphisms Population Genetics Marker-assisted Selection Genotipado mediante Secuenciación Polimorfismos de Nucleótido Único Genética de Poblaciones Selección asistida por Marcadores Eucalyptus Eucalyptus dunnii Aguirre, Natalia Cristina Villalba, Pamela Victoria Garcia, Martin Nahuel Filippi, Carla Valeria Rivas, Juan Gabriel Martinez, Maria Carolina Acuña, Cintia Vanesa Lopez, Javier Augusto Lopez, Juan Adolfo Pathauer, Pablo Santiago Palazzini, Dino Harrand, Leonel Oberschelp, Gustavo Pedro Javier Marco, Martin Alberto Cisneros, Esteban F. Carreras, Rocío Alves, Ana Rodrigues, Jose Hopp, Horacio Esteban Grattapaglia, Dario Cappa, Eduardo Pablo Paniego, Norma Beatriz Marcucci Poltri, Susana Noemi Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden) |
| title | Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden) |
| title_full | Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden) |
| title_fullStr | Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden) |
| title_full_unstemmed | Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden) |
| title_short | Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden) |
| title_sort | comparison of ddradseq and euchip60k snp genotyping systems for population genetics and genomic selection in eucalyptus dunnii maiden |
| topic | Genotyping-by-sequencing Single Nucleotide Polymorphisms Population Genetics Marker-assisted Selection Genotipado mediante Secuenciación Polimorfismos de Nucleótido Único Genética de Poblaciones Selección asistida por Marcadores Eucalyptus Eucalyptus dunnii |
| url | http://hdl.handle.net/20.500.12123/20324 https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1361418/full https://doi.org/10.3389/fgene.2024.1361418 |
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