Skip to main content
SpringerLink
Log in

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

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Alix K, Paulet F, Glaszmann JC, D’Hont A (1999) Inter-Alu-like species-specific sequences in the Saccharum complex. Theor Appl Genet 99:962–968

    Article  CAS  Google Scholar 

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    Article  CAS  Google Scholar 

  • Ashkenazi V, Chani E, Lavi U, Levy D, Hillel J, Veilleux RE (2001) Development of microsatellite markers in potato and their use in phylogenetic and fingerprinting analyses. Genome 44:50–62

    Article  PubMed  CAS  Google Scholar 

  • Bannikova AA, Lavrenchenko LA, Kramerov DA (2005) Phylogenetic relationships between Afrotropical and Palaearctic Crocidura species inferred from inter-SINE-PCR. Biochem Syst Ecol 33:45–59

    Article  CAS  Google Scholar 

  • Baurens FC, Noyer JL, Lanaud C, Lagoda PJL (1998) Inter-Alu PCR like genomic profiling in banana. Euphytica 99:137–142

    Article  CAS  Google Scholar 

  • Bennetzen JL (1996) The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol 4:347–353

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95:127–132

    Article  PubMed  CAS  Google Scholar 

  • Campbell B, LeMare S, Piperidis G, Godwin I (2011) IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Mol Breed 27:193–206

    Article  Google Scholar 

  • Desel C, Jung C, Cai DG, Kleine M, Schmidt T (2001) High-resolution mapping of YACs and the single-copy gene Hs1(pro)-1 on Beta vulgaris chromosomes by multi-colour fluorescence in situ hybridization. Plant Mol Biol 45:113–122

    Article  PubMed  CAS  Google Scholar 

  • Flavell AJ, Knox MR, Pearce SR, Ellis THN (1998) Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16:643–650

    Article  PubMed  CAS  Google Scholar 

  • Ghislain M, Spooner DM, Rodriguez F, Villamon F, Nunez J, Vasquez C, Waugh R, Bonierbale M (2004) Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet 108:881–890

    Article  PubMed  CAS  Google Scholar 

  • Ghislain M, Núñez J, del Rosario HerreraM, Pignataro J, Guzman F, Bonierbale M, Spooner D (2009) Robust and highly informative microsatellite-based genetic identity kit for potato. Mol Breed 23:377–388

    Article  CAS  Google Scholar 

  • Hamon P, Duroy PO, Dubreuil-Tranchant C et al (2011) Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae). Mol Genet Genomics 285:447–460

    Article  PubMed  CAS  Google Scholar 

  • Hirochika H (1993) Activation of tobacco retrotransposons during tissue-culture. EMBO J 12:2521–2528

    PubMed  CAS  Google Scholar 

  • Hosaka K, Sanetomo R (2009) Comparative differentiation in mitochondrial and chloroplast DNA among cultivated potatoes and closely related wild species. Genes Genet Syst 84:371–378

    Article  PubMed  CAS  Google Scholar 

  • Huang SW, Xu X, Pan SK et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:U189–U194

    Article  Google Scholar 

  • Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270

    Google Scholar 

  • Jacobs MM, van den Berg RG, Vleeshouwers VG, Visser M, Mank R, Sengers M, Hoekstra R, Vosman B (2008) AFLP analysis reveals a lack of phylogenetic structure within Solanum section Petota. BMC Evol Biol 8:145

    Article  PubMed  Google Scholar 

  • Jacobs MMJ, Smulders MJM, van den Berg RG, Vosman B (2011) What’s in a name; genetic structure in Solanum section Petota studied using population-genetic tools. BMC Evol Biol 11:42

    Article  PubMed  Google Scholar 

  • Jurka J, Kohany O, Pavlicek A, Kapitonov VV, Jurka MV (2005) Clustering, duplication and chromosomal distribution of mouse SINE retrotransposons. Cytogenet Genome Res 110:117–123

    Article  PubMed  CAS  Google Scholar 

  • Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711

    Article  CAS  Google Scholar 

  • Kalendar R, Antonius K, Smykal P, Schulman AH (2010) iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 121:1419–1430

    Article  PubMed  CAS  Google Scholar 

  • Kamm A, Galasso I, Schmidt T, Heslop-Harrison JS (1995) Analysis of a repetitive DNA family from Arabidopsis arenosa and relationship between Arabidopsis species. Plant Mol Biol 27:853–862

    Article  PubMed  CAS  Google Scholar 

  • Kass DH, Batzer MA (1995) Inter-Alu polymerase chain reaction: advancements and applications. Anal Biochem 228:185–193

    Article  PubMed  CAS  Google Scholar 

  • Kostia S, Ruohonen-Lehto M, Vainola R, Varvio SL (2000) Phylogenetic information in inter-SINE and inter-SSR fingerprints of the Artiodactyla and evolution of the Bov-tA SINE. Heredity 84:37–45

    Article  PubMed  CAS  Google Scholar 

  • Kramerov DA, Vassetzky NS (2005) Short retroposons in eukaryotic genomes. Int Rev Cytol 247:165–221

    Article  PubMed  CAS  Google Scholar 

  • Kubis S, Schmidt T, Heslop-Harrison JS (1998) Repetitive DNA elements as a major component of plant genomes. Ann Bot 82:45–55

    Article  CAS  Google Scholar 

  • Kumar A, Pearce SR, McLean K, Harrison G, Heslop-Harrison JS, Waugh R, Flavell AJ (1997) The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers. Genetica 100:205–217

    Article  PubMed  CAS  Google Scholar 

  • Lara-Cabrera SI, Spooner DM (2004) Taxonomy of North and Central American diploid wild potato (Solanum sect. Petota) species: AFLP data. Plant Syst Evol 248:129–142

    Article  CAS  Google Scholar 

  • Lara-Cabrera SI, Spooner DM (2005) Taxonomy of Mexican diploid wild potatoes (Solanum sect. Petota): morphological and microsatellite data. Monogr Syst Bot Mo Bot Gard 104:199–205

    Google Scholar 

  • Lenoir A, Lavie L, Prieto JL, Goubely C, Cote JC, Pelissier T, Deragon JM (2001) The evolutionary origin and genomic organization of SINEs in Arabidopsis thaliana. Mol Biol Evol 18:2315–2322

    Article  PubMed  CAS  Google Scholar 

  • Li X, van Eck HJ, Rouppe van der Voort JNAM, Huigen D-J, Stam P, Jacobsen E (1998) Autotetraploids and genetic mapping using common AFLP markers: the R2 allele conferring resistance to Phytophthora infestans mapped on potato chromosome 4. Theor Appl Genet 96:1121–1128

    Article  CAS  Google Scholar 

  • Lightbourn GJ, Jelesko JG, Veilleux RE (2007) Retrotransposon-based markers from potato monoploids used in somatic hybridization. Genome 50:492–501

    Article  PubMed  CAS  Google Scholar 

  • Luan DD, Korman MH, Jakubczak JL, Eickbush TH (1993) Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site—a mechanism for non-LTR retrotransposition. Cell 72:595–605

    Article  PubMed  CAS  Google Scholar 

  • Ma JX, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410

    Article  PubMed  CAS  Google Scholar 

  • McGregor CE, Lambert CA, Greyling MM, Louw JH, Warnich L (2000) A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica 113:135–144

    Article  CAS  Google Scholar 

  • Moisan-Thiery M, Marhadour S, Kerlan M, Dessenne N, Perramant M, Gokelaere T, Le Hingrat Y (2005) Potato cultivar identification using simple sequence repeats markers (SSR). Potato Res 48:191–200

    Article  Google Scholar 

  • Nelson DL, Ledbetter SA, Corbo L, Victoria MF, Ramirez-Solis R, Webster TD, Ledbetter DH, Caskey CT (1989) Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc Natl Acad Sci USA 86:6686–6690

    Article  PubMed  CAS  Google Scholar 

  • Nováková A, Šimáčková K, Bárta J, Čurn V (2009) Potato variety identification by molecular markers based on retrotransposon analyses. Czech J Genet Plant Breed 45:1–10

    Google Scholar 

  • Okada N (1991) SINEs. Curr Opin Genet Dev 1:498–504

    Article  PubMed  CAS  Google Scholar 

  • Oliver KR, Greene WK (2009) Transposable elements: powerful facilitators of evolution. Bioessays 31:703–714

    Article  PubMed  CAS  Google Scholar 

  • Ovchinnikova A, Krylova E, Gavrilenko T, Smekalova T, Zhuk M, Knapp S, Spooner DM (2011) Taxonomy of cultivated potatoes (Solanum section Petota: Solanaceae). Bot J Linn Soc 165:107–155

    Article  Google Scholar 

  • Pieterse L, Hils U (2009) World Catalogue of Potato Varieties 2009/10 Agrimedia

  • Reid A, Kerr EM (2007) A rapid simple sequence repeat (SSR)-based identification method for potato cultivars. Plant Genet Resour 5:7–13

    Article  CAS  Google Scholar 

  • Reid A, Hof L, Esselink D, Vosman B (2009) Potato cultivar genome analysis. In: Burns R (ed) Plant pathology: techniques and protocols. Humana, New York, pp 295–308

    Google Scholar 

  • Reid A, Hof L, Felix G et al (2011) Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU Common Catalogue. Euphytica 182:239–249

    Article  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  • Schmidt T (1999) LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol Biol 40:903–910

    Article  PubMed  CAS  Google Scholar 

  • Schmidt T, Junghans H, Metzlaff M (1990) Construction of Beta procumbens-specific DNA probes and their application for the screening of B.vulgaris × B.procumbens (2n = 19) addition lines. Theor Appl Genet 79:177–181

    Article  CAS  Google Scholar 

  • Schmidt T, Schwarzacher T, Heslop-Harrison JS (1994) Physical mapping of rRNA genes by fluorescent in situ hybridization and structural analysis of 5S rRNA genes and intergenic spacer sequences in sugar beet (Beta vulgaris). Theor Appl Genet 88:629–636

    Article  CAS  Google Scholar 

  • Schulman AH, Flavell AJ, Ellis THN (2004) The application of LTR retrotransposons as molecular markers in plants. In: Miller WJ, Capy P (eds) Mobile genetic elements. Humana, Totowa, pp 145–174

    Chapter  Google Scholar 

  • Schwarzacher T, Heslop-Harrison P (2000) Practical in situ hybridization. BIOS Scientific Publishers Ltd, Oxford

    Google Scholar 

  • Scotti N, Cozzolino S, Cardi T (2007) Mitochondrial DNA variation in cultivated and wild potato species (Solanum spp.). Genome 50:706–713

    Article  PubMed  CAS  Google Scholar 

  • Simko I, Jansky SH, Stephenson S, Spooner DM (2007) Genetics of resistance to pests and disease. In: Vreugdenhil D, Bradshaw J, Gebhardt C, Govers F, MacKerron DKL, Taylor MA, Ross HA (eds) Potato biology and biotechnology—advances and perspectives. Elsevier, Amsterdam, pp 117–155

    Google Scholar 

  • Spooner DM, Hijmans RJ (2001) Potato systematics and germplasm collecting, 1989–2000. Am J Potato Res 78:237–268

    Article  Google Scholar 

  • Spooner DM, Salas A (2006) Structure, biosystematics, and genetic resources. In: Gopal J, Khurana SMP (eds) Handbook of potato production, improvement, and postharvest management. Haworth’s Press, Binghamton, pp 1–39

    Google Scholar 

  • Spooner DM, McLean K, Ramsay G, Waugh R, Bryan GJ (2005a) A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping. Proc Natl Acad Sci USA 102:14694–14699

    Article  PubMed  CAS  Google Scholar 

  • Spooner DM, Nunez J, Rodriguez F, Naik PS, Ghislain M (2005b) Nuclear and chloroplast DNA reassessment of the origin of Indian potato varieties and its implications for the origin of the early European potato. Theor Appl Genet 110:1020–1026

    Article  PubMed  CAS  Google Scholar 

  • Spooner DM, Núñez J, Trujillo G, Del Rosario Herrera M, Guzmán F, Ghislain M (2007) Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proc Natl Acad Sci USA 104:19398–19403

    Article  PubMed  CAS  Google Scholar 

  • Sukhotu T, Hosaka K (2006) Origin and evolution of Andigena potatoes revealed by chloroplast and nuclear DNA markers. Genome 49:636–647

    Article  PubMed  CAS  Google Scholar 

  • Sukhotu T, Kamijima O, Hosaka K (2004) Nuclear and chloroplast DNA differentiation in Andean potatoes. Genome 47:46–56

    Article  PubMed  CAS  Google Scholar 

  • Van Berloo R, Hutten RCB, Van Eck HJ, Visser RGF (2007) An online potato pedigree database resource. Potato Res 50:45–57

    Article  Google Scholar 

  • Wenke T, Döbel T, Sörensen TR, Junghans H, Weisshaar B, Schmidt T (2011) Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes. Plant Cell 23:3117–3128

    Article  PubMed  CAS  Google Scholar 

  • Wu F, Tanksley SD (2010) Chromosomal evolution in the plant family Solanaceae. BMC Genomics 11:182

    Article  PubMed  Google Scholar 

  • Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, Kudrna D, Wing RA (2007) Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evol Biol 7:152

    Article  PubMed  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

  1. Institute of Botany, Dresden University of Technology, 01062, Dresden, Germany

    Kathrin M. Seibt, Torsten Wenke, Cora Wollrab & Thomas Schmidt

  2. NORIKA GmbH, 18190, Groß Lüsewitz, Germany

    Holger Junghans & Katja Muders

  3. Groß Lüsewitz Potato Collections (GLKS), Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Parkweg 3a, 18190, Groß Lüsewitz, Germany

    Klaus J. Dehmer & Kerstin Diekmann

Authors
  1. Kathrin M. Seibt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Torsten Wenke
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cora Wollrab
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Holger Junghans
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Katja Muders
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Klaus J. Dehmer
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Kerstin Diekmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Thomas Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Thomas Schmidt.

Additional information

Communicated by C. Gebhardt.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Seibt, K.M., Wenke, T., Wollrab, C. et al. Development and application of SINE-based markers for genotyping of potato varieties. Theor Appl Genet 125, 185–196 (2012). https://doi.org/10.1007/s00122-012-1825-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-012-1825-7

Keywords

Search

Navigation