Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

  1. Emanuelli, F. 1
  2. Lorenzi, S. 1
  3. Grzeskowiak, L. 1
  4. Catalano, V. 1
  5. Stefanini, M. 1
  6. Troggio, M. 1
  7. Myles, S. 2
  8. Martinez-Zapater, J.M. 3
  9. Zyprian, E. 5
  10. Moreira, F.M. 14
  11. Grando, M.S. 1
  1. 1 Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN 38010, Italy
  2. 2 Dalhousie University
    info

    Dalhousie University

    Halifax, Canadá

    ROR https://ror.org/01e6qks80

  3. 3 Instituto de Ciencias de la Vid y del Vino
    info

    Instituto de Ciencias de la Vid y del Vino

    Logroño, España

    ROR https://ror.org/01rm2sw78

  4. 4 Instituto Federal de Santa Catarina, Rua José Lino Kretzer 608 - Praia Comprida, São José, Santa Catarina 88130-310, Brazil
  5. 5 Julius Kühn-Institut
    info

    Julius Kühn-Institut

    Quedlinburg, Alemania

    ROR https://ror.org/022d5qt08

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Revue:
BMC Plant Biology

ISSN: 1471-2229

Année de publication: 2013

Volumen: 13

Número: 1

Pages: 1-17

Type: Article

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DOI: 10.1186/1471-2229-13-39 PMID: 23497049 SCOPUS: 2-s2.0-84874597356 GOOGLE SCHOLAR lock_openAccès ouvert editor

D'autres publications dans: BMC Plant Biology

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Résumé

Background: The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources 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 grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. 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 of V. vinifera and 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 of Vitis and 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. © 2013 Emanuelli et al.; licensee BioMed Central Ltd.