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Development of a Potato Cultivar (Solanum tuberosum L.) Core Collection, a Valuable Tool to Prospect Genetic Variation for Novel Traits

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Abstract

This study presents the development of a core collection capturing the genetic diversity of a collection of 350 tetraploid cultivated potato varieties (Solanum tuberosum L.). The core collection was established by using simple sequence repeats (SSR) data and the M strategy, which aims at maximizing the allelic diversity. A 48-core collection was defined which captured 99.5% of the SSR alleles used to establish it, and 96.9% of the SSR alleles which belonged to an independent set of markers. The defined core collection was further validated by analysing 35 agro-morphological traits. The class coverage value and the estimates of the Shannon-Weaver diversity index indicated a good representation of the phenotypic diversity in the core collection. Furthermore, the core set included accessions having the most desirable status for several agronomic traits. A linkage disequilibrium (LD) analysis, using data obtained with the SolCAP SNP array on the defined core collection, was performed. The population structure analysis showed that the core collection did not present a clear genetic structure. The linkage disequilibrium analysis carried out between markers located on the same pseudomolecule within 10,000 bp concluded that 41.3% of these pairs of SNP markers have a significant LD. We conclude that this core collection, representative of the genetic diversity of cultivated potato varieties, is a relevant tool for a first screening for genetic variation regarding novel traits of interest.

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Acknowledgments

We would like to thank the Experimental Unit RGCO for participation to the multiplication of genetic resources. We are grateful for useful discussions with Dominique Brunel. We thank Anne-Marie Chèvre, Marie-Claire Kerlan and Bernadette Julier for their valuable comments on this paper. We also thank the editor for his relevant suggestions on the manuscript. Finally, we would like to thank the CEA-IG/CNG for performing the DNA QC in its DNA and Cell Bank service and for providing INRA-EPGV group access to their Illumina Genotyping Platform.

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Authors and Affiliations

  1. IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, F-29260, Ploudaniel, France

    Florence Esnault, Roland Pellé, Jean-Paul Dantec & Jean-Eric Chauvin

  2. EPGV, INRA, CEA-IG/CNG, F-91057, Evry, France

    Aurélie Bérard & Marie-Christine Le Paslier

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  1. Florence Esnault
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  2. Roland Pellé
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Correspondence to Florence Esnault.

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Esnault, F., Pellé, R., Dantec, JP. et al. Development of a Potato Cultivar (Solanum tuberosum L.) Core Collection, a Valuable Tool to Prospect Genetic Variation for Novel Traits. Potato Res. 59, 329–343 (2016). https://doi.org/10.1007/s11540-016-9332-x

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  • DOI: https://doi.org/10.1007/s11540-016-9332-x

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