Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs

  1. Laucou, V. 1
  2. Launay, A. 1
  3. Bacilieri, R. 1
  4. Lacombe, T. 18
  5. Adam-Blondon, A.-F. 2
  6. Bérard, A. 2
  7. Chauveau, A. 2
  8. De Andrés, M.T. 4
  9. Hausmann, L. 5
  10. Ibáñez, J. 3
  11. Le Paslier, M.-C. 2
  12. Maghradze, D. 7
  13. Martinez-Zapater, J. 3
  14. Maul, E. 5
  15. Ponnaiah, M. 26
  16. Töpfer, R. 5
  17. Péros, J.-P. 1
  18. Boursiquot, J.-M. 18
  1. 1 University of Montpellier
    info

    University of Montpellier

    Montpellier, Francia

    ROR https://ror.org/051escj72

  2. 2 University of Paris-Saclay
    info

    University of Paris-Saclay

    Gif-sur-Yvette, Francia

    ROR https://ror.org/03xjwb503

  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 Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario
    info

    Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario

    Madrid, España

  5. 5 Julius Kühn-Institut
    info

    Julius Kühn-Institut

    Quedlinburg, Alemania

    ROR https://ror.org/022d5qt08

  6. 6 Pierre and Marie Curie University
    info

    Pierre and Marie Curie University

    París, Francia

  7. 7 National Wine Agency of Georgia, Tbilisi, Georgia
  8. 8 Institut Francais de la Vigne et du Vin
    info

    Institut Francais de la Vigne et du Vin

    Le Grau-du-Roi, Francia

    ROR https://ror.org/03synvw58

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Revista:
PLoS ONE

ISSN: 1932-6203

Año de publicación: 2018

Volumen: 13

Número: 2

Tipo: Artículo

DOI: 10.1371/JOURNAL.PONE.0192540 SCOPUS: 2-s2.0-85041736711 WoS: WOS:000424517900090 GOOGLE SCHOLAR

Otras publicaciones en: PLoS ONE

Repositorio institucional: lock_openAcceso abierto Editor

Resumen

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ∼47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genomewide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine. © 2018 Laucou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.