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


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.


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.



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.


  1. Alix K, Paulet F, Glaszmann JC, D’Hont A (1999) Inter-Alu-like species-specific sequences in the Saccharum complex. Theor Appl Genet 99:962–968CrossRefGoogle Scholar
  2. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218CrossRefGoogle Scholar
  3. 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 44:50–62PubMedCrossRefGoogle Scholar
  4. Bannikova AA, Lavrenchenko LA, Kramerov DA (2005) Phylogenetic relationships between Afrotropical and Palaearctic Crocidura species inferred from inter-SINE-PCR. Biochem Syst Ecol 33:45–59CrossRefGoogle Scholar
  5. Baurens FC, Noyer JL, Lanaud C, Lagoda PJL (1998) Inter-Alu PCR like genomic profiling in banana. Euphytica 99:137–142CrossRefGoogle Scholar
  6. Bennetzen JL (1996) The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol 4:347–353PubMedCrossRefGoogle Scholar
  7. Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95:127–132PubMedCrossRefGoogle Scholar
  8. 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 27:193–206CrossRefGoogle Scholar
  9. 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 45:113–122PubMedCrossRefGoogle Scholar
  10. Flavell AJ, Knox MR, Pearce SR, Ellis THN (1998) Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16:643–650PubMedCrossRefGoogle Scholar
  11. 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 108:881–890PubMedCrossRefGoogle Scholar
  12. 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 23:377–388CrossRefGoogle Scholar
  13. 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 285:447–460PubMedCrossRefGoogle Scholar
  14. Hirochika H (1993) Activation of tobacco retrotransposons during tissue-culture. EMBO J 12:2521–2528PubMedGoogle Scholar
  15. Hosaka K, Sanetomo R (2009) Comparative differentiation in mitochondrial and chloroplast DNA among cultivated potatoes and closely related wild species. Genes Genet Syst 84:371–378PubMedCrossRefGoogle Scholar
  16. Huang SW, Xu X, Pan SK et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:U189–U194CrossRefGoogle Scholar
  17. Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270Google Scholar
  18. 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 8:145PubMedCrossRefGoogle Scholar
  19. 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 11:42PubMedCrossRefGoogle Scholar
  20. Jurka J, Kohany O, Pavlicek A, Kapitonov VV, Jurka MV (2005) Clustering, duplication and chromosomal distribution of mouse SINE retrotransposons. Cytogenet Genome Res 110:117–123PubMedCrossRefGoogle Scholar
  21. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711CrossRefGoogle Scholar
  22. Kalendar R, Antonius K, Smykal P, Schulman AH (2010) iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 121:1419–1430PubMedCrossRefGoogle Scholar
  23. 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 27:853–862PubMedCrossRefGoogle Scholar
  24. Kass DH, Batzer MA (1995) Inter-Alu polymerase chain reaction: advancements and applications. Anal Biochem 228:185–193PubMedCrossRefGoogle Scholar
  25. 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 84:37–45PubMedCrossRefGoogle Scholar
  26. Kramerov DA, Vassetzky NS (2005) Short retroposons in eukaryotic genomes. Int Rev Cytol 247:165–221PubMedCrossRefGoogle Scholar
  27. Kubis S, Schmidt T, Heslop-Harrison JS (1998) Repetitive DNA elements as a major component of plant genomes. Ann Bot 82:45–55CrossRefGoogle Scholar
  28. 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 100:205–217PubMedCrossRefGoogle Scholar
  29. Lara-Cabrera SI, Spooner DM (2004) Taxonomy of North and Central American diploid wild potato (Solanum sect. Petota) species: AFLP data. Plant Syst Evol 248:129–142CrossRefGoogle Scholar
  30. 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 104:199–205Google Scholar
  31. 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 18:2315–2322PubMedCrossRefGoogle Scholar
  32. 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 96:1121–1128CrossRefGoogle Scholar
  33. Lightbourn GJ, Jelesko JG, Veilleux RE (2007) Retrotransposon-based markers from potato monoploids used in somatic hybridization. Genome 50:492–501PubMedCrossRefGoogle Scholar
  34. 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 72:595–605PubMedCrossRefGoogle Scholar
  35. Ma JX, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410PubMedCrossRefGoogle Scholar
  36. 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 113:135–144CrossRefGoogle Scholar
  37. 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 48:191–200CrossRefGoogle Scholar
  38. 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 86:6686–6690PubMedCrossRefGoogle Scholar
  39. Nováková A, Šimáčková K, Bárta J, Čurn V (2009) Potato variety identification by molecular markers based on retrotransposon analyses. Czech J Genet Plant Breed 45:1–10Google Scholar
  40. Okada N (1991) SINEs. Curr Opin Genet Dev 1:498–504PubMedCrossRefGoogle Scholar
  41. Oliver KR, Greene WK (2009) Transposable elements: powerful facilitators of evolution. Bioessays 31:703–714PubMedCrossRefGoogle Scholar
  42. 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 165:107–155CrossRefGoogle Scholar
  43. Pieterse L, Hils U (2009) World Catalogue of Potato Varieties 2009/10 AgrimediaGoogle Scholar
  44. Reid A, Kerr EM (2007) A rapid simple sequence repeat (SSR)-based identification method for potato cultivars. Plant Genet Resour 5:7–13CrossRefGoogle Scholar
  45. 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 295–308Google Scholar
  46. 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 182:239–249CrossRefGoogle Scholar
  47. 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 81:8014–8018PubMedCrossRefGoogle Scholar
  48. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  49. Schmidt T (1999) LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol Biol 40:903–910PubMedCrossRefGoogle Scholar
  50. 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 79:177–181CrossRefGoogle Scholar
  51. 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 88:629–636CrossRefGoogle Scholar
  52. 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 145–174CrossRefGoogle Scholar
  53. Schwarzacher T, Heslop-Harrison P (2000) Practical in situ hybridization. BIOS Scientific Publishers Ltd, OxfordGoogle Scholar
  54. Scotti N, Cozzolino S, Cardi T (2007) Mitochondrial DNA variation in cultivated and wild potato species (Solanum spp.). Genome 50:706–713PubMedCrossRefGoogle Scholar
  55. 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 117–155Google Scholar
  56. Spooner DM, Hijmans RJ (2001) Potato systematics and germplasm collecting, 1989–2000. Am J Potato Res 78:237–268CrossRefGoogle Scholar
  57. 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 1–39Google Scholar
  58. 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 102:14694–14699PubMedCrossRefGoogle Scholar
  59. 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 110:1020–1026PubMedCrossRefGoogle Scholar
  60. 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 104:19398–19403PubMedCrossRefGoogle Scholar
  61. Sukhotu T, Hosaka K (2006) Origin and evolution of Andigena potatoes revealed by chloroplast and nuclear DNA markers. Genome 49:636–647PubMedCrossRefGoogle Scholar
  62. Sukhotu T, Kamijima O, Hosaka K (2004) Nuclear and chloroplast DNA differentiation in Andean potatoes. Genome 47:46–56PubMedCrossRefGoogle Scholar
  63. Van Berloo R, Hutten RCB, Van Eck HJ, Visser RGF (2007) An online potato pedigree database resource. Potato Res 50:45–57CrossRefGoogle Scholar
  64. 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 23:3117–3128PubMedCrossRefGoogle Scholar
  65. Wu F, Tanksley SD (2010) Chromosomal evolution in the plant family Solanaceae. BMC Genomics 11:182PubMedCrossRefGoogle Scholar
  66. 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 7:152PubMedCrossRefGoogle Scholar

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

Personalised recommendations