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Diversity studies in genetic resources of Solanum spp. (section Petota) by comparative application of ISAP markers

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Abstract

The Genebank at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) harbours three different potato collections comprising 2846 wild potato accessions, 2757 accessions of cultivars, landraces and breeding material of Solanum tuberosum L. and 579 Solanum clones originating mainly from South and Central America (as of July 2016). The three collections are maintained via seeds, in vitro culture, cryopreservation or in the field. All four processes are labour and cost intensive. Therefore, methods facilitating the efficient management and maintenance of the collections are needed. We describe the experimental application of the retrotransposon-based Inter-SINE amplified polymorphism (ISAP) marker system for supporting the management of potato collections. Three ISAP primer combinations were evaluated on a set of 259 cultivated and 89 wild potato accessions focussing on three different aspects: diversity analysis, duplicate identification and phylogenetic studies. Compared to up to 29 microsatellites, ISAPs were similarly efficient in monitoring genetic diversity and detecting duplicated accessions. In addition, the three ISAP primer combinations could be applied to wild potato species, although their use in phylogenetic studies is limited due to their highly polymorphic nature. Generally, ISAPs are a very valuable tool in the maintenance of clonally maintained potato collections and for the verification of the identity of accessions.

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Acknowledgements

We gratefully acknowledge the German Federal Ministry of Education and Research for funding this project (KMU-Innovativ, Grants Nos. 0315425 and 0315864).

Author contributions

KD carried out the ISAP and SSR marker analyses at IPK and drafted the manuscript. KMS optimized and adjusted the ISAP marker system. KM carried out the ISAP marker analyses at NORIKA. TW developed the ISAP marker system. HJ conceived the project and coordinated it. TS conceived the project and coordinated the ISAP marker development at TUD. KJD conceived and coordinated the study at IPK. All authors read and approved the final manuscript.

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Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Parkweg 3a, 18190, Gross Luesewitz, Germany

    Kerstin Diekmann & Klaus J. Dehmer

  2. Institute of Botany, Technische Universitaet Dresden, 01062, Dresden, Germany

    Kathrin M. Seibt, Torsten Wenke & Thomas Schmidt

  3. NORIKA GmbH, Parkweg 4, 18190, Gross Luesewitz, Germany

    Katja Muders & Holger Junghans

Authors
  1. Kerstin Diekmann
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  2. Kathrin M. Seibt
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  3. Katja Muders
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  4. Torsten Wenke
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  5. Holger Junghans
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  6. Thomas Schmidt
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  7. Klaus J. Dehmer
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Corresponding author

Correspondence to Klaus J. Dehmer.

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The authors declare that they have no conflict of interests.

Electronic supplementary material

Below is the link to the electronic supplementary material.

10722_2016_484_MOESM1_ESM.pdf

Online Resource 1: Overview of the accessions used for the diversity and duplicate (bold) analyses; accessions written in italics were used in both studies. (PDF 164 kb)

10722_2016_484_MOESM2_ESM.pdf

Online Resource 2: Overview of the wild potato accessions used for the taxonomic analyses. Only one genotype of GLKS 30733, GLKS 32370 but three of GLKS 30716 were analysed. (PDF 114 kb)

10722_2016_484_MOESM3_ESM.pdf

Online Resource 3: Overview of the microsatellite markers used in this study, their amplicon lengths, concentration in the reaction, annealing temperatures (Ta in °C), original sources and how they were multiplexed. For the diversity analysis all multiplexes were used, for the duplicate study only multiplexes 1, 2 and 9 (PDF 94 kb)

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Diekmann, K., Seibt, K.M., Muders, K. et al. Diversity studies in genetic resources of Solanum spp. (section Petota) by comparative application of ISAP markers. Genet Resour Crop Evol 64, 1937–1953 (2017). https://doi.org/10.1007/s10722-016-0484-y

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  • DOI: https://doi.org/10.1007/s10722-016-0484-y

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