IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley

Abstract

The retrotransposon-based marker system, inter-retrotransposon amplified polymorphism (IRAP), and inter-simple sequence repeats (ISSRs) were used to detect somaclonal variation induced by tissue culture. IRAPs use a single primer designed to amplify out from the 5′ LTR sequence of the BARE-1 retrotransposon combined with a degenerate 3′ anchor, similar to that of ISSR primers. We analysed DNA polymorphisms in 147 primary regenerants and parental controls from three cultivars of barley (Hordeum vulgare). The ISSR marker system generated an average of 218 bands per primer, with 29 polymorphisms of which 12 were novel non-parental bands. In comparison, the IRAP system generated an average of 121 bands per primer, with 15 polymorphisms of which nine were novel non-parental bands. Polymorphism detected for IRAP and ISSR markers was more than twofold higher in Golden Promise than Mackay and Tallon cultivars. However, there was no significant difference in the frequency of novel non-parental bands. Cluster analysis revealed that the level of polymorphism and genetic variability detected was comparable between IRAP and ISSR markers. This suggests that retrotransposon-based marker systems, such as IRAP, based on retrotransposons such as BARE-1, are valuable tools for the detailed characterisation of mutation profiles that arise during tissue culture. Their use should improve our understanding of processes influencing mutation and somaclonal variation and allow for the design of methods that yield fewer genome changes in applications where maintaining clonal integrity is important.

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References

  1. Albani MC, Wilkinson MJ (1998) Inter simple sequence repeat polymerase chain reaction for the detection of somaclonal variation. Plant Breed 117:573–575

    Article  Google Scholar 

  2. Archak S, Gaikwad AB, Gautam D, Rao EVVB, Swamy KRM, Karihaloo JL (2003) Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India. Genome 46:362–369

    CAS  Article  PubMed  Google Scholar 

  3. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    CAS  PubMed  Google Scholar 

  4. Bregitzer P, Zhang S, Cho MJ, Lemaux PG (2002) Reduced somaclonal variation is associated with culturing highly differentiated, meristematic tissues. Crop Sci 42:1303–1308

    Article  Google Scholar 

  5. Cho MJ, Jiang W, Lemaux PG (1998) Transformation of recalcitrant barley cultivars through improvement of regenerability and decreased albinism. Plant Sci 138:229–244

    CAS  Article  Google Scholar 

  6. Damasco OP, Graham GC, Henry RJ, Adkins SW, Smith MK, Godwin ID (1996) Random amplified polymorphic DNA (RAPD) detection of dwarf off-types in micropropagated Cavendish bananas. Plant Cell Rep 16:118–123

    CAS  Article  Google Scholar 

  7. Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26:297–302

    Article  Google Scholar 

  8. Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992) Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher-plants. Nucl Acids Res 20:3639–3644

    CAS  Article  PubMed  Google Scholar 

  9. Godwin ID, Aitken EAB, Smith LW (1997a) Application of inter simple sequence repeat (ISSR) markers to plant genetics. Electrophoresis 18:1524–1528

    CAS  Article  PubMed  Google Scholar 

  10. Godwin ID, Sangduen N, Kunanuvatchaidach K, Piperidis G, Adkins SW (1997b) RAPD polymorphisms among variant and phenotypically normal rice (Oryza sativa var. indica) somaclonal progenies. Plant Cell Rep 16:320–324

    CAS  Google Scholar 

  11. Grandbastien MA (1992) Retroelements in higher plants. Trends Genet 8:103–108

    CAS  PubMed  Google Scholar 

  12. Grandbastien MA, Spielmann A, Caboche M (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant-cell genetics. Nature 337:376–380

    CAS  Article  PubMed  Google Scholar 

  13. Gribbon BM, Pearce SR, Kalendar R, Schulman AH, Paulin L, Jack P, Kumar A, Flavell AJ (1999) Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Mol Gen Genet 261:883–891

    CAS  Article  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  15. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93:7783–7788

    CAS  Article  PubMed  Google Scholar 

  16. IBSC (2009) http://www.public.iastate.edu/~imagefpc/IBSC%20Webpage/IBSC%20Template-home.html. Accessed 23 Sep 2009

  17. Jaaskelainen M, Mykkanen AH, Arna T, Vicient CM, Suoniemi A, Kalendar R, Savilahti H, Schulman AH (1999) Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells. Plant J 20:413–422

    CAS  Article  PubMed  Google Scholar 

  18. Johns MA, Mottinger J, Freeling M (1985) A low copy number, copia -like transposon in maize. EMBO J 8:1093–1102

    Google Scholar 

  19. Kaeppler SM, Kaeppler HF, Rhee Y (2000) Epigenetic aspects of somaclonal variation in plants. Plant Mol Biol 43:179–188

    CAS  Article  PubMed  Google Scholar 

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

    CAS  Article  Google Scholar 

  21. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603–6607

    CAS  Article  PubMed  Google Scholar 

  22. Karp A (1994) Origins, causes, and uses of variation in plant tissue cultures. In: Vasil IK, Thorpe TA (eds) Plant cell and tissue culture. Kluwer, Dordrecht, pp 136–151

    Google Scholar 

  23. Kashkush K, Feldma M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33:102–106

    CAS  Article  PubMed  Google Scholar 

  24. Kumar A, Bennetzen J (1999) Plant retrotransposons. Annu Rev Genet 33:479–532

    CAS  Article  PubMed  Google Scholar 

  25. Kumekawa N, Ohtsubo H, Horiuchi T, Ohtsubo E (1999) Identification and characterization of novel retrotransposons of the gypsy type in rice. Mol Gen Genet 260:593–602

    CAS  Article  PubMed  Google Scholar 

  26. Kuznetsova OI, Ash OA, Hartina GA, Gostimskij SA (2005) RAPD and ISSR analyses of regenerated pea Pisum sativum L. plants. Russ J Genet 41:60–65

    CAS  Google Scholar 

  27. Larkin PJ, Scowcroft WR (1981) Somaclonal variation: a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60:197–214

    Article  Google Scholar 

  28. Lassner MW, Peterson P, Yoder JI (1989) Simultaneous amplification of multiple DNA fragment by polymerase chain reaction in the analysis of transgenic plants and their progeny. Plant Mol Biol Rep 7:116–128

    CAS  Article  Google Scholar 

  29. Laten HM, Majumdar A, Gaucher EA (1998) SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein. Proc Natl Acad Sci USA 95:6897–6902

    CAS  Article  PubMed  Google Scholar 

  30. Leprince AS, Grandbastien MA, Meyer C (2001) Retrotransposons of the Tnt1B family are mobile in Nicotiana plumbaginofolia and can induce alternative splicing of the host gene upon insertion. Plant Mol Biol 47:533–541

    CAS  Article  Google Scholar 

  31. Leroy XJ, Leon K, Hily JM, Chaumeil P, Branchard M (2001) Detection of in vitro culture-induced instability through inter-simple sequence repeat analysis. Theor Appl Genet 102:885–891

    CAS  Article  Google Scholar 

  32. Li A, Ge S (2001) Genetic variation and clonal diversity of Psammochloa villosa (Poaceae) detected by ISSR markers. Ann Bot (Lond) 87:585–590

    CAS  Article  Google Scholar 

  33. Li X, Yu X, Wang N, Feng Q, Dong Z, Liu L, Shen J, Liu B (2007) Genetic and epigenetic instabilities induced by tissue culture in wild barley (Hordeum brevisubulatum (Trin.) Link). Plant Cell Tiss Organ Cult 90:153–168

    Article  Google Scholar 

  34. Linacero R, Alves EF, Vazquez AM (2000) Hot spots of DNA instability revealed through the study of somaclonal variation in rye. Theor Appl Genet 100:506–511

    CAS  Article  Google Scholar 

  35. Manninen I, Schulman AH (1993) BARE-1, a copia-like retroelement in barley (Hordeum vulgare L). Plant Mol Biol 22:829–846

    CAS  Article  PubMed  Google Scholar 

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

    CAS  Article  Google Scholar 

  37. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

    CAS  Article  PubMed  Google Scholar 

  38. Olhoft PM, Phillips RL (1999) Genetic and epigenetic instabilities in tissue culture and regenerated progenies. In: Lerner HR (ed) Plant responses to environmental stresses: from phytohormones to genome reorganization. Marcel Dekker, New York, pp 111–148

    Google Scholar 

  39. Pearce SR, Knox M, Ellis THN, Flavell AJ, Kumar A (2000) Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum. Mol Gen Genet 263:898–907

    CAS  Article  PubMed  Google Scholar 

  40. Phillips MH, Kaeppler SM, Olhoft P (1994) Genetic variability of plant tissue cultures: breakdown of normal control. Proc Natl Acad Sci USA 91:5222–5226

    CAS  Article  PubMed  Google Scholar 

  41. Polanco C, Ruiz ML (2002) AFLP analysis of somaclonal variation in Arabidopsis thaliana regenerated plants. Plant Sci 162:817–824

    CAS  Article  Google Scholar 

  42. Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112

    CAS  Article  Google Scholar 

  43. RI IPG (1994) Descriptors for barley (Hordeum vulgare L.). International Plant Genetic Resources Institute, Rome

    Google Scholar 

  44. Rogers SO, Bendich AJ (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant-tissues. Plant Mol Biol 5:69–76

    CAS  Article  Google Scholar 

  45. Rohlf FJ (2000) NTSYS-pc numerical taxonomy and multivariate analysis system version 2.1 manual. Applied Biostatistics, New York

    Google Scholar 

  46. Smykal P, Valledor L, Rodriguez R, Griga M (2007) Assessment of genetic and epigenetic stability in long-term in vitro shoot culture of pea (Pisum sativum L.). Plant Cell Rep 26:1985–1998

    CAS  Article  PubMed  Google Scholar 

  47. Sneath PHA, Sokal RR (1973) Numerical taxonomy. Freeman, San Francisco

    Google Scholar 

  48. Soleimani VD, Baum BR, Johnson DA (2005) Genetic diversity among barley cultivars assessed by sequence-specific amplification polymorphism. Theor Appl Genet 110:1290–1300

    CAS  Article  PubMed  Google Scholar 

  49. Suoniemi A, AnamthawatJonsson K, Arna T, Schulman AH (1996a) Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L) genome. Plant Mol Biol 30:321–1329

    Article  Google Scholar 

  50. Suoniemi A, Narvanto A, Schulman AH (1996b) The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol Biol 31:295–306

    CAS  Article  PubMed  Google Scholar 

  51. Suoniemi A, Schmidt D, Schulman AH (1997) BARE-1 insertion site preferences and evolutionary conservation of RNA and cDNA processing sites. Genetica 100:219–230

    CAS  Article  PubMed  Google Scholar 

  52. Suoniemi A, Tanskanen J, Pentikainen O, Johnson MS, Schulman AH (1998) The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution. Mol Biol Evol 15:1135–1144

    CAS  PubMed  Google Scholar 

  53. Tahara M, Aoki T, Suzuka S, Yamashita H, Tanaka M, Matsunaga S, Kokumai S (2004) Isolation of an active element from a high-copy-number family of retrotransposons in the sweet potato genome. Mol Genet Genomics 272:116–127

    CAS  Article  PubMed  Google Scholar 

  54. Tingay S, McElroy D, Kalla R, Fieg S, Wang M, Thornton S, Brettell R (1997) Agrobacterium tumefaciens-mediated barley transformation. Plant J 11:1369–1376

    CAS  Article  Google Scholar 

  55. Travella S, Ross SM, Harden J, Everett C, Snape JW, Harwood WA (2005) A comparison of transgenic barley lines produced by particle bombardment and Agrobacterium-mediated techniques. Plant Cell Rep 23:780–789

    CAS  Article  PubMed  Google Scholar 

  56. Vicient CM, Suoniemi A, Anamthawat-Jónsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11:1769–1784

    CAS  Article  PubMed  Google Scholar 

  57. Wan Y, Lemaux PG (1994) Generation of large numbers of independently transformed fertile barley plants. Plant Physiol 104:37–48

    CAS  PubMed  Google Scholar 

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Acknowledgments

We thank Dr Dipal Parh (DPI) and Mrs Sun Yue (University of Queensland) for helpful advice and assistance and Dr Hunter Laidlaw (University of Queensland) for his support in the editing process. This work was supported by the School of Land, Crop and Food Science, University of Queensland.

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Correspondence to Bradley C. Campbell.

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Campbell, B.C., LeMare, S., Piperidis, G. et al. IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Mol Breeding 27, 193–206 (2011). https://doi.org/10.1007/s11032-010-9422-4

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Keywords

  • Somaclonal variation
  • Retrotransposon
  • BARE-1
  • IRAP
  • ISSR
  • Hordeum vulgare