Filippi Carla V, Aguirre Natalia, Rivas Juan G, Zubrzycki Jeremias, Puebla Andrea, Cordes Diego, Moreno Maria V, Fusari Corina M, Alvarez Daniel, Heinz Ruth A, Hopp Horacio E, Paniego Norma B, Lia Veronica V
BMC Plant Biol. 2015 Feb 13;15:52. doi: 10.1186/s12870-014-0360-x.
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.
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.
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.
阿根廷有着悠久的向日葵育种传统，其种质是全球宝贵的遗传资源。然而，关于阿根廷种质的遗传构成和变异水平的知识仍然匮乏，使得栽培向日葵多样性的全球图谱并不完整。在本研究中，使用了42个微卫星位点和384个单核苷酸多态性（SNP）来表征用于向日葵数量性状基因座定位的首个关联作图群体，以及从阿根廷国家农业技术研究所种质库中挑选的相关开放授粉群体和复合群体。还评估了不同类型标记评估遗传多样性和群体结构的能力。
对本研究中所研究的向日葵种质集合的多态性分析表明，微卫星和SNP标记对于种质表征都具有信息性，尽管程度不同。总体而言，遗传变异估计值适中。通过期望杂合度量化的平均遗传多样性，SSR位点为0.52，SNP为0.29。在SSR标记中，来自非编码区的标记能够捕获比EST - SSR更高水平的多样性。在种质之间基于SSR和SNP的遗传距离之间发现了显著相关性。使用贝叶斯和多变量方法推断群体结构。在各个数据集（即SSR、SNP和SSR + SNP）中一致发现存在三个不同遗传组的证据，保持系/恢复系状态是与组划分相关的最普遍特征。
本研究是比较SSR和SNP标记在栽培向日葵群体遗传学分析中性能的首份报告。我们表明，此处检测的SSR和SNP面板，单独使用或联合使用，都能对向日葵育种材料的遗传多样性和群体结构进行一致估计。所产生的关于向日葵种质多样性水平和群体结构的知识是对这种作物育种和保护的重要贡献。
