Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape
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Open Access
- 7 March 2013
- journal article
- Published by Springer Science and Business Media LLC in BMC Plant Biology
- Vol. 13 (1), 39
- https://doi.org/10.1186/1471-2229-13-39
Abstract
Background: The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation ofVitisresources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples.Results: We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevineV. viniferassp.sativa, its wild relativeV. viniferassp.sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions ofV. viniferaand non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability.Conclusions: The comprehensive molecular characterization of our grape germplasm collection contributes to the knowledge about levels and distribution of genetic diversity in the existing resources ofVitisand provides insights into genetic subdivision within the European germplasm. Genotypic and phenotypic information compared in this study may efficiently guide further exploration of this diversity for facilitating its practical use.Keywords
This publication has 69 references indexed in Scilit:
- STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno methodConservation Genetics Resources, 2011
- High throughput analysis of grape genetic diversity as a tool for germplasm collection managementTheoretical and Applied Genetics, 2011
- The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic originTheoretical and Applied Genetics, 2010
- Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markersTheoretical and Applied Genetics, 2010
- Untranslated leader region polymorphism of Tvv1, a retrotransposon family, is a novel marker useful for analyzing genetic diversity and relatedness in the genus VitisTheoretical and Applied Genetics, 2007
- A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.)Theoretical and Applied Genetics, 2007
- SSR analysis of the Medicago truncatula SARDI core collection reveals substantial diversity and unusual genotype dispersal throughout the Mediterranean basinTheoretical and Applied Genetics, 2006
- Development of a standard set of microsatellite reference alleles for identification of grape cultivarsTheoretical and Applied Genetics, 2004
- Evidence of a secondary grapevine domestication centre detected by SSR analysisTheoretical and Applied Genetics, 2003
- Evaluating the potential of SSR flanking regions for examining taxonomic relationships in the VitaceaeTheoretical and Applied Genetics, 2002