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...
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todo:paper_14712229_v15_n1_p_Filippi2023-10-03T16:17:50Z Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers Filippi, C.V. Aguirre, N. Rivas, J.G. Zubrzycki, J. Puebla, A. Cordes, D. Moreno, M.V. Fusari, C.M. Alvarez, D. Heinz, R.A. Hopp, H.E. Paniego, N.B. Lia, V.V. Association mapping Genetic resources SNP SSR Sunflower breeding Helianthus microsatellite DNA Argentina Bayes theorem expressed sequence tag genetic polymorphism genetic variation genetics multivariate analysis plant breeding population genetics single nucleotide polymorphism sunflower Argentina Bayes Theorem Expressed Sequence Tags Genetic Variation Genetics, Population Helianthus Microsatellite Repeats Multivariate Analysis Plant Breeding Polymorphism, Genetic Polymorphism, Single Nucleotide 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. © 2015 Filippi et al.; licensee BioMed Central. Fil:Puebla, A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Moreno, M.V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Fusari, C.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Heinz, R.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Hopp, H.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Lia, V.V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_14712229_v15_n1_p_Filippi |
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Universidad de Buenos Aires |
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I-28 |
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R-134 |
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Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Association mapping Genetic resources SNP SSR Sunflower breeding Helianthus microsatellite DNA Argentina Bayes theorem expressed sequence tag genetic polymorphism genetic variation genetics multivariate analysis plant breeding population genetics single nucleotide polymorphism sunflower Argentina Bayes Theorem Expressed Sequence Tags Genetic Variation Genetics, Population Helianthus Microsatellite Repeats Multivariate Analysis Plant Breeding Polymorphism, Genetic Polymorphism, Single Nucleotide |
| spellingShingle |
Association mapping Genetic resources SNP SSR Sunflower breeding Helianthus microsatellite DNA Argentina Bayes theorem expressed sequence tag genetic polymorphism genetic variation genetics multivariate analysis plant breeding population genetics single nucleotide polymorphism sunflower Argentina Bayes Theorem Expressed Sequence Tags Genetic Variation Genetics, Population Helianthus Microsatellite Repeats Multivariate Analysis Plant Breeding Polymorphism, Genetic Polymorphism, Single Nucleotide Filippi, C.V. Aguirre, N. Rivas, J.G. Zubrzycki, J. Puebla, A. Cordes, D. Moreno, M.V. Fusari, C.M. Alvarez, D. Heinz, R.A. Hopp, H.E. Paniego, N.B. Lia, V.V. Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers |
| topic_facet |
Association mapping Genetic resources SNP SSR Sunflower breeding Helianthus microsatellite DNA Argentina Bayes theorem expressed sequence tag genetic polymorphism genetic variation genetics multivariate analysis plant breeding population genetics single nucleotide polymorphism sunflower Argentina Bayes Theorem Expressed Sequence Tags Genetic Variation Genetics, Population Helianthus Microsatellite Repeats Multivariate Analysis Plant Breeding Polymorphism, Genetic Polymorphism, Single Nucleotide |
| 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. © 2015 Filippi et al.; licensee BioMed Central. |
| format |
JOUR |
| author |
Filippi, C.V. Aguirre, N. Rivas, J.G. Zubrzycki, J. Puebla, A. Cordes, D. Moreno, M.V. Fusari, C.M. Alvarez, D. Heinz, R.A. Hopp, H.E. Paniego, N.B. Lia, V.V. |
| author_facet |
Filippi, C.V. Aguirre, N. Rivas, J.G. Zubrzycki, J. Puebla, A. Cordes, D. Moreno, M.V. Fusari, C.M. Alvarez, D. Heinz, R.A. Hopp, H.E. Paniego, N.B. Lia, V.V. |
| author_sort |
Filippi, C.V. |
| title |
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_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_sort |
population structure and genetic diversity characterization of a sunflower association mapping population using ssr and snp markers |
| url |
http://hdl.handle.net/20.500.12110/paper_14712229_v15_n1_p_Filippi |
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