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Characterization of single nucleotide polymorphism in Tunisian grapevine genome and their potential for population genetics and evolutionary studies

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Abstract

In this study, two gene fragments corresponding to the VvMYBA1 and VvMYBA2 loci were sequenced on a sample of grapes including cultivated and wild accessions originating from Tunisia, Germany and France. A total of 42 SNPs were detected in the sequenced fragments giving an average of 1 SNP every 33 bp. High level of polymorphism was observed in the samples either in cultivated or wild accessions. Pattern of nucleotide diversity indicates a non departure from neutrality expectations for wild grapevine sample for gene VvMYBA1 and VvMYBA2 and for cultivated sample for gene VvMYBA1. However, a linkage to a selective sweep was revealed for cultivated grapevine gene pool in gene VvMYBA2. A genetic structure of the studied sample according to accession taxonomic status was revealed by the UPGMA clustering with a considerable overlap. This result was confirmed by significant but low genetic differentiation values between cultivated and wild sample. The number of migrants Nm based on sequence data information between Tunisian cultivars and Tunisian wild accessions showed a low level of gene flow between those germplasms. This finding indicates that Tunisian cultivars do not derive directly from local wild populations but could mostly correspond to imported materials introduced during historical times. However, the possibility that some cultivars derived from ancestral events of local domestication or cross hybridization with native wild plants was not completely excluded for Tunisian grapevine accessions.

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Acknowledgments

The authors are grateful to INRA, Montpellier France, and to the Tunisian Ministry of Higher Education, Scientific Research and Technology for financial support.

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Authors and Affiliations

  1. Laboratoire de Physiologie Moléculaire des Plantes, Centre de Biotechnologie Borj Cedria, B.P. 901, 2050, Hammam-Lif, Tunisia

    Leila Riahi, Nejia Zoghlami & Ahmed Mliki

  2. Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA

    Alexandre Fournier-Level

  3. UMR RPB (IRD-UM2-CIRAD) Résistance des Plantes aux Bioagresseurs, IRD, 911, avenue Agropolis, BP 64501, 34394, Montpellier, France

    Alexis Dereeper

  4. Equipe DAVEM, UMR AGAP 1334, INRA SupAgro, 2 place Pierre Viala, 34060, Montpellier, France

    Loïc Le Cunff, Valérie Laucou & Patrice This

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  1. Leila Riahi
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  2. Nejia Zoghlami
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Riahi, L., Zoghlami, N., Fournier-Level, A. et al. Characterization of single nucleotide polymorphism in Tunisian grapevine genome and their potential for population genetics and evolutionary studies. Genet Resour Crop Evol 60, 1139–1151 (2013). https://doi.org/10.1007/s10722-012-9910-y

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