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Theoretical and Applied Genetics

, Volume 125, Issue 1, pp 185–196 | Cite as

Development and application of SINE-based markers for genotyping of potato varieties

  • Kathrin M. Seibt
  • Torsten Wenke
  • Cora Wollrab
  • Holger Junghans
  • Katja Muders
  • Klaus J. Dehmer
  • Kerstin Diekmann
  • Thomas SchmidtEmail author
Original Paper

Abstract

Potato variety discrimination based on morphological traits is laborious and influenced by the environment, while currently applied molecular markers are either expensive or time-consuming in development or application. SINEs, short interspersed nuclear elements, are retrotransposons with a high copy number in plant genomes representing a potential source for new markers. We developed a marker system for potato genotyping, designated inter-SINE amplified polymorphism (ISAP). Based on nine potato SINE families recently characterized (Wenke et al. in Plant Cell 23:3117–3128, 2011), we designed species-specific SINE primers. From the resulting 153 primer combinations, highly informative primer sets were selected for potato variety analysis regarding number of bands, quality of the banding pattern, and the degree of polymorphism. Fragments representing ISAPs can be separated by conventional agarose gel electrophoresis; however, automation with a capillary sequencer is feasible. Two selected SINE families, SolS-IIIa and SolS-IV, were shown to be highly but differently amplified in Solanaceae, Solaneae tribe, including wild and cultivated potatoes, tomato, and eggplant. Fluorescent in situ hybridization demonstrated the genome-wide distribution of SolS-IIIa and SolS-IV along potato chromosomes, which is the basis for genotype discrimination and differentiation of somaclonal variants by ISAP markers.

Keywords

Amplify Fragment Length Polymorphism Simple Sequence Repeat Marker Long Terminal Repeat Prime Combination Potato Cultivar 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We gratefully acknowledge the German Federal Ministry of Education and Research for funding this project (KMU-Innovativ, grant no. 0315425). We thank the Science and Advice for Scottish Agriculture Organization (SASA, UK) for generously providing seed and plant material and I. Walter for technical support.

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Kathrin M. Seibt
    • 1
  • Torsten Wenke
    • 1
  • Cora Wollrab
    • 1
  • Holger Junghans
    • 2
  • Katja Muders
    • 2
  • Klaus J. Dehmer
    • 3
  • Kerstin Diekmann
    • 3
  • Thomas Schmidt
    • 1
    Email author
  1. 1.Institute of Botany, Dresden University of TechnologyDresdenGermany
  2. 2.NORIKA GmbHGroß LüsewitzGermany
  3. 3.Groß Lüsewitz Potato Collections (GLKS)Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Groß LüsewitzGermany

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