Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers
Background: Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity...
| Autores principales: | , , , , , , , , , , , , |
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| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
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BMC
2019
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| Materias: | |
| Acceso en línea: | https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0360-x http://hdl.handle.net/20.500.12123/4267 https://doi.org/10.1186/s12870-014-0360-x |
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| author | Filippi, Carla Valeria Aguirre, Natalia Cristina Rivas, Juan Gabriel Zubrzycki, Jeremias Enrique Puebla, Andrea Fabiana Cordes, Diego Darío Moreno, Maria Valeria Fusari, Corina Mariana Alvarez, Daniel Heinz, Ruth Amelia Hopp, Horacio Esteban Paniego, Norma Beatriz Lia, Veronica Viviana |
| author_browse | Aguirre, Natalia Cristina Alvarez, Daniel Cordes, Diego Darío Filippi, Carla Valeria Fusari, Corina Mariana Heinz, Ruth Amelia Hopp, Horacio Esteban Lia, Veronica Viviana Moreno, Maria Valeria Paniego, Norma Beatriz Puebla, Andrea Fabiana Rivas, Juan Gabriel Zubrzycki, Jeremias Enrique |
| author_facet | Filippi, Carla Valeria Aguirre, Natalia Cristina Rivas, Juan Gabriel Zubrzycki, Jeremias Enrique Puebla, Andrea Fabiana Cordes, Diego Darío Moreno, Maria Valeria Fusari, Corina Mariana Alvarez, Daniel Heinz, Ruth Amelia Hopp, Horacio Esteban Paniego, Norma Beatriz Lia, Veronica Viviana |
| author_sort | Filippi, Carla Valeria |
| collection | INTA Digital |
| description | Background: Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated.
Results: The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation.
Conclusion: The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent estimations of genetic diversity and population structure in sunflower breeding materials. The generated knowledge about the levels of diversity and population structure of sunflower germplasm is an important contribution to this crop breeding and conservation. |
| format | info:ar-repo/semantics/artículo |
| id | INTA4267 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | BMC |
| publisherStr | BMC |
| record_format | dspace |
| spelling | INTA42672019-01-15T14:03:26Z Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers Filippi, Carla Valeria Aguirre, Natalia Cristina Rivas, Juan Gabriel Zubrzycki, Jeremias Enrique Puebla, Andrea Fabiana Cordes, Diego Darío Moreno, Maria Valeria Fusari, Corina Mariana Alvarez, Daniel Heinz, Ruth Amelia Hopp, Horacio Esteban Paniego, Norma Beatriz Lia, Veronica Viviana Helianthus Annuus Genética Marcadores Genéticos Variación Genética Germoplasma Genetics Genetic Markers Genetic Variation Germplasm Girasol Marcadores Moleculares Background: Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. Results: The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. Conclusion: The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent estimations of genetic diversity and population structure in sunflower breeding materials. The generated knowledge about the levels of diversity and population structure of sunflower germplasm is an important contribution to this crop breeding and conservation. Instituto de Biotecnología Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Rivas, Juan Gabriel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Zubrzycki, Jeremias Enrique. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Cordes, Diego Darío. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina Fil: Moreno, Maria Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina Fil: Fusari, Corina Mariana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Max Planck Institute of Molecular Plant Physiology; Alemania Fil: Alvarez, Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina Fil: Heinz, Ruth Amelia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina Fil: Hopp, Horacio Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina 2019-01-15T14:02:09Z 2019-01-15T14:02:09Z 2015-02 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0360-x http://hdl.handle.net/20.500.12123/4267 1471-2229 https://doi.org/10.1186/s12870-014-0360-x eng 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 BMC BMC Plant Biology 15 : 52 (2015) |
| spellingShingle | Helianthus Annuus Genética Marcadores Genéticos Variación Genética Germoplasma Genetics Genetic Markers Genetic Variation Germplasm Girasol Marcadores Moleculares Filippi, Carla Valeria Aguirre, Natalia Cristina Rivas, Juan Gabriel Zubrzycki, Jeremias Enrique Puebla, Andrea Fabiana Cordes, Diego Darío Moreno, Maria Valeria Fusari, Corina Mariana Alvarez, Daniel Heinz, Ruth Amelia Hopp, Horacio Esteban Paniego, Norma Beatriz Lia, Veronica Viviana Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers |
| title | Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers |
| title_full | Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers |
| title_fullStr | Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers |
| title_full_unstemmed | Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers |
| title_short | Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers |
| title_sort | population structure and genetic diversity characterization of a sunflower association mapping population using ssr and snp markers |
| topic | Helianthus Annuus Genética Marcadores Genéticos Variación Genética Germoplasma Genetics Genetic Markers Genetic Variation Germplasm Girasol Marcadores Moleculares |
| url | https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0360-x http://hdl.handle.net/20.500.12123/4267 https://doi.org/10.1186/s12870-014-0360-x |
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