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Open Access Research article

Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa

Loïc Le Cunff1*, Alexandre Fournier-Level1, Valérie Laucou1, Silvia Vezzulli2, Thierry Lacombe1, Anne-Françoise Adam-Blondon3, Jean-Michel Boursiquot1 and Patrice This1

Author Affiliations

1 UMR 1097 DIA-PC, Equipe « génétique Vigne », INRA-Supagro, 2 place Viala, F-34060 Montpellier, France

2 IASMA Research Center, 38010 San Michele all'Adige (TN), Italy

3 UMR 1165 INRA-CNRS-Université d'Evry Génomique Végétale, 2, rue Gaston Crémieux CP 5708, F-91057 EVRY cedex, France

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BMC Plant Biology 2008, 8:31  doi:10.1186/1471-2229-8-31

Published: 2 April 2008

Abstract

Background

The first high quality draft of the grape genome sequence has just been published. This is a critical step in accessing all the genes of this species and increases the chances of exploiting the natural genetic diversity through association genetics. However, our basic knowledge of the extent of allelic variation within the species is still not sufficient. Towards this goal, we constructed nested genetic core collections (G-cores) to capture the simple sequence repeat (SSR) diversity of the grape cultivated compartment (Vitis vinifera L. subsp. sativa) from the world's largest germplasm collection (Domaine de Vassal, INRA Hérault, France), containing 2262 unique genotypes.

Results

Sub-samples of 12, 24, 48 and 92 varieties of V. vinifera L. were selected based on their genotypes for 20 SSR markers using the M-strategy. They represent respectively 58%, 73%, 83% and 100% of total SSR diversity. The capture of allelic diversity was analyzed by sequencing three genes scattered throughout the genome on 233 individuals: 41 single nucleotide polymorphisms (SNPs) were identified using the G-92 core (one SNP for every 49 nucleotides) while only 25 were observed using a larger sample of 141 individuals selected on the basis of 50 morphological traits, thus demonstrating the reliability of the approach.

Conclusion

The G-12 and G-24 core-collections displayed respectively 78% and 88% of the SNPs respectively, and are therefore of great interest for SNP discovery studies. Furthermore, the nested genetic core collections satisfactorily reflected the geographic and the genetic diversity of grape, which are also of great interest for the study of gene evolution in this species.