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Species relationships within the genus Vitis based on molecular and morphological data

Author

Listed:
  • Jean-Pierre Péros
  • Amandine Launay
  • André Peyrière
  • Gilles Berger
  • Catherine Roux
  • Thierry Lacombe
  • Jean-Michel Boursiquot

Abstract

The grape genus Vitis L. includes the domesticated V. vinifera, which is one of the most important fruit crop, and also close relatives recognized as valuable germplasm resources for improving cultivars. To resolve some standing problems in the species relationships within the Vitis genus we analyzed diversity in a set of 90 accessions comprising most of Vitis species and some putative hybrids. We discovered single nucleotide polymorphisms (SNPs) in SANGER sequences of twelve loci and genotyped accessions at a larger number of SNPs using a previously developed SNP array. Our phylogenic analyses consistently identified: three clades in North America, one in East Asia, and one in Europe corresponding to V. vinifera. Using heterozygosity measurement, haplotype reconstruction and chloroplast markers, we identified the hybrids existing within and between clades. The species relationships were better assessed after discarding these hybrids from analyses. We also studied the relationships between phylogeny and morphological traits and found that several traits significantly correlated with the phylogeny. The American clade that includes important species such as V. riparia and V. rupestris showed a major divergence with all other clades based on both DNA polymorphisms and morphological traits.

Suggested Citation

  • Jean-Pierre Péros & Amandine Launay & André Peyrière & Gilles Berger & Catherine Roux & Thierry Lacombe & Jean-Michel Boursiquot, 2023. "Species relationships within the genus Vitis based on molecular and morphological data," PLOS ONE, Public Library of Science, vol. 18(7), pages 1-24, July.
    • Handle: RePEc:plo:pone00:0283324
    DOI: 10.1371/journal.pone.0283324
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    References listed on IDEAS

    as
    1. Sean Myles & Jer-Ming Chia & Bonnie Hurwitz & Charles Simon & Gan Yuan Zhong & Edward Buckler & Doreen Ware, 2010. "Rapid Genomic Characterization of the Genus Vitis," PLOS ONE, Public Library of Science, vol. 5(1), pages 1-9, January.
    2. Lê, Sébastien & Josse, Julie & Husson, François, 2008. "FactoMineR: An R Package for Multivariate Analysis," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 25(i01).
    3. Jason Sawler & Bruce Reisch & Mallikarjuna K Aradhya & Bernard Prins & Gan-Yuan Zhong & Heidi Schwaninger & Charles Simon & Edward Buckler & Sean Myles, 2013. "Genomics Assisted Ancestry Deconvolution in Grape," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-1, November.
    4. Allison J Miller & Naim Matasci & Heidi Schwaninger & Mallikarjuna K Aradhya & Bernard Prins & Gan-Yuan Zhong & Charles Simon & Edward S Buckler & Sean Myles, 2013. "Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-11, November.
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