Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers

BMC Plant Biology

Research Article

Diego Cordes¹  Daniel Alvarez¹  Maria V Moreno¹  Juan G Rivas²  Andrea Puebla²  Natalia Aguirre²  Jeremias Zubrzycki³  Norma B Paniego³  Carla V Filippi³  Veronica V Lia⁴  Ruth A Heinz⁴  Corina M Fusari⁵  Horacio E Hopp⁶ 

[1] Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA), Argentina;Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina;Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina;Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA, Ciudad Autónoma de Buenos Aires, Argentina;Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina;Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA, Ciudad Autónoma de Buenos Aires, Argentina;Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina;Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina;Currently at System Regulation Group, Metabolic Networks Department, Max Planck Institute of Molecular Plant Physiology, Am Mühlemberg 1, D-14476, Potsdam-Golm, Germany;Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina;Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina;

关键词: Sunflower breeding;    Genetic resources;    SNP;    SSR;    Association mapping;   

DOI  :  10.1186/s12870-014-0360-x

 received in 2014-03-27, accepted in 2014-11-27,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundArgentina 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.ResultsThe 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.ConclusionThe 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.

【 授权许可】

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© Filippi et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.