Skip to main content
SpringerLink
Log in

DNA methylation and tissue culture-induced variation in plants

  • Somatic Cell Genetics/Genetic Transformation
  • Published:
In Vitro Cellular & Developmental Biology - Plant Aims and scope Submit manuscript

Summary

Plant cells growing in an artificial culture environment make numerous genetic mistakes. These alterations are manifested as increased frequencies of single-gene mutations, chromosome breakages, transposable element activations, quantitative trait variations, and modifications of normal DNA methylation patterns. Evidence is presented that indicates a high frequency of DNA hypomethylation as the result of the tissue culture process. Fifteen percent of the methylation changes appear to have been homozygous in the original regenerated plants. A hypothesis is advanced that relates DNA methylation to the variety of genetic alterations found among maize tissue culture regenerants and their progenies. The epigenetic nature of DNA methylation raises questions concerning the stability of tissue culture-induced changes in self-pollinations and crosses.

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

Similar content being viewed by others

References

  • Antequera, F.; Bird, A. P. Unmethylated CpG islands associated with genes in higher plants. EMBO J. 7:2295–2299; 1989.

    Google Scholar 

  • Armstrong, C. L. Genetic and cytogenetic stability of maize tissue cultures: a comparative study of organogenic and embryogenic cultures. Minneapolis: Univ. of Minnesota; 1986. Thesis.

    Google Scholar 

  • Armstrong, C. L.; Phillips, R. L. Genetic and cytogenetic variation in plants regenerated from organogenic and friable, embryogenic tissue cultures of maize. Crop Sci. 28:363–369; 1988.

    Article  Google Scholar 

  • Baenziger, P. S.; Wesenberg, D. M.; Schaeffer, G. W., et al. Variation among anther culture derived doubled haploids of “Kitt” wheat. In: Sakamoto, S., ed. Proceedings of the Sixth International Wheat Genetics Symposium. Kyoto, Japan: Plant Germ-Plasm Inst. for Agric., Kyoto Univ.; 1983.

    Google Scholar 

  • Banks, J. A.; Masson, P.; Fedoroff, N. Molecular mechanisms in the developmental regulation of the maize suppressor-mutator transposable element. Genes Dev. 2:1364–1380; 1988.

    PubMed  CAS  Google Scholar 

  • Bayliss, M. W. Chromosomal variation in plant tissues in culture. Int. Rev. Cytol. Suppl. 11A:113–144; 1980.

    Google Scholar 

  • Benzion, G. Genetic and cytogenetic analysis of maize tissue cultures: a cell line pedigree analysis. Minneapolis: Univ. of Minnesota; 1984. Thesis.

    Google Scholar 

  • Benzion, G.; Phillips, R. L.; Rines, H. W. Case histories of genetic variabilityin vitro: oats and maize. In: Vasil, I. K., ed. Cell culture and somatic cell genetics of plants, vol. 3. New York: Academic Press; 1986:435–448.

    Google Scholar 

  • Bianchi, A.; Salamini, F.; Parlavecchio, R. On the origin of controlling elements in maize. Genet. Agrar. 22:335–344; 1969.

    Google Scholar 

  • Boyes, J.; Bird, A. DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell 64:1123–1134; 1991.

    Article  PubMed  CAS  Google Scholar 

  • Brettell, R. I. S.; Dennis, E. S. Reactivation of a silent Ac following tissue culture is associated with heritable alterations in its methylation pattern. Mol. Gen. Genet. 229:365–372; 1991.

    Article  PubMed  CAS  Google Scholar 

  • Brettell, R. I. S.; Dennis, E. S.; Scowcroft, W. R., et al. Molecular analysis of a somaclonal variant of alcohol dehydrogenase. Mol. Gen. Genet. 202:335–344; 1986.

    Article  Google Scholar 

  • Brown, P. T. H. DNA methylation in plants and its role in tissue culture. Genome 31:717–729; 1989.

    CAS  Google Scholar 

  • Brown, P. T. H.; Kyozuka, J.; Sukekiyo, Y., et al. Molecular changes in protoplast-derived rice plants. Mol. Gen. Genet. 223:324–328; 1990.

    Article  PubMed  CAS  Google Scholar 

  • Brown, P. T. H.; Gobel, E.; Lorz, H. RFLP analysis ofZea mays callus cultures and their regenerated plants. Theor. Appl. Genet. 81:227–232; 1991.

    Article  CAS  Google Scholar 

  • Cedar, H. DNA methylation and gene activity. Cell 53:3–4; 1988.

    Article  PubMed  CAS  Google Scholar 

  • Chandler, V. L.; Walbot, V. DNA modification of a maize transposable element correlates with loss of activity. Proc. Natl. Acad. Sci. USA 83:1767–1771; 1986.

    Article  PubMed  CAS  Google Scholar 

  • Chomet, P. S.; Wessler, S.; Dellaporta, S. Inactivation of the maize transposable element activator (Ac) is associated with its DNA modification. EMBO J. 6:295–302; 1987.

    PubMed  CAS  Google Scholar 

  • Culley, D. E. Evidence for activation of a cryptic transposable element Ac in maize endosperm cultures. In: VI Int. Congr. Plant Tiss. Cell Culture, Minneapolis, MN. 3–8 August, 1986. St. Paul, MN: Univ. of Minnesota. Abstracts p.220.

    Google Scholar 

  • Dahleen, L. S.; Stuthman, D. D.; Rines, H. W. Agronomic trait variation in oat lines derived from tissue culture. Crop Sci. 31:90–94; 1991.

    Article  Google Scholar 

  • D’Amato, F. Cytogenetics of differentiation in tissue and cell cultures. In: Reinert, J.; Bajaj, V. P. S., eds. Plant cell, tissue, and organ culture. New York: Springer-Verlag; 1977:343–357.

    Google Scholar 

  • D’Amato, F. Cytogenetics of plant cell and tissue cultures and their regenerates. CRC Crit. Rev. Plant Sci. 3:73–112; 1985.

    Google Scholar 

  • Dennis, E. S.; Brettell, R. I. S.; Peacock, W. J. A tissue culture inducedAdh1 null mutant of maize results from a single base change. Mol. Gen. Genet. 210:181–183; 1987.

    Article  CAS  Google Scholar 

  • Doerschug, E. B. Studies ofDotted, a regulatory element in maize. I. Induction ofDotted by chromatid breaks. II. Phase variation ofDotted. Theor. Appl. Genet. 43:182–189; 1973.

    Article  Google Scholar 

  • Earle, E. B.; Gracen, V. E. Somaclonal variation in progeny of plants from corn tissue culture. In: Henke, R.; Hughes, K.; Hollaender, A., eds. Propagation of higher plants through tissue culture. New York: Plenum Press; 1985.

    Google Scholar 

  • Edallo, S.; Zucchinali, C.; Perenzin, M., et al. Chromosomal variation and frequency of spontaneous mutation associated within vitro culture and plant regeneration of maize. Maydica 26:39–56; 1981.

    Google Scholar 

  • Ergle, D. R.; Katterman, F. R. H. Deoxyribonucleic acid of cotton. Plant Physiol. 36:811–815; 1961.

    PubMed  CAS  Google Scholar 

  • Evola, S. V.; Burr, F. A.; Burr, B. The nature of tissue culture-induced mutations in maize. Eleventh Annual Aharon Katzir-Katchalsky Conference, abstract.

  • Fedoroff, N.; Banks, J.; Masson, P. Molecular genetic analysis of the maize suppressor-mutator element’s epigenetic developmental regulatory mechanism. Genome 31:973–979; 1989.

    CAS  Google Scholar 

  • Fukui, K. Sequential occurrence of mutations in a growing rice callus. Theor. Appl. Genet. 65:225–230; 1983.

    Article  Google Scholar 

  • Groose, R. W.; Bingham, E. T. An unstable anthocyanin mutation recovered from tissue culture of alfalfa (Medicago sativa). 1. High frequency of reversion upon reculture. 2. Stable nonrevertants derived from reculture. Plant Cell Rep. 5:104–110; 1986.

    Article  CAS  Google Scholar 

  • Gruenbaum, Y.; Naveh-Many, T.; Cedar, H. Sequence specificity of methylation in higher plant DNA. Nature 292:860–862; 1981.

    Article  PubMed  CAS  Google Scholar 

  • Hall, G.; Allen, G. C.; Loer, D. S., et al. Nuclear scaffolds and scaffold-attachment regions in higher plants. Proc. Natl. Acad. Sci. USA 88:9320–9324; 1991.

    Article  PubMed  CAS  Google Scholar 

  • Holliday, R. The inheritance of epigenetic defects. Science 238:163–170; 1987.

    Article  PubMed  CAS  Google Scholar 

  • Johnson, S. S.; Phillips, R. L.; Rines, H. W. Possible role of heterochromatin in chromosome breakage induced by tissue culture in oats (Avena sativa L.). Genome 29:439–446; 1987.

    Google Scholar 

  • Kaeppler, S. M. Molecular and genetic studies of tissue culture-induced variation in maize. St. Paul: Univ. Minnesota; 1992. Thesis.

    Google Scholar 

  • Klaas, M.; Amasino, R. DNA methylation is reduced in DNase1-sensitive regions of plant chromatin. Plant Physiol. 91:451–454; 1989.

    PubMed  CAS  Google Scholar 

  • Larkin, P. J. Somaclonal variation: history, method, and meaning. Iowa State J. Res. 61:393–434; 1987.

    Google Scholar 

  • Larkin, P. J.; Ryan, S. A.; Brettell, R. I. S., et al. Heritable somaclonal variation in wheat. Theor. Appl. Genet. 67:443–455; 1984.

    Article  CAS  Google Scholar 

  • Larkin, P. J.; Scowcroft, W. R. Somaclonal variation—a novel source of variability from cell cultures for plant improvement. Theor. Appl. Genet. 60:197–214; 1981.

    Article  Google Scholar 

  • Larkin, P.; Scowcroft, W. R. Somaclonal variation and crop improvement. In: Kosuge, T.; Meredith, C. P.; Hollander, A., eds. Genetic engineering of plants: an agricultural perspective. New York: Plenum Press; 1983:289–314.

    Google Scholar 

  • Lee, M. L.; Geadelmann, J. L.; Phillips, R. L. Agronomic evaluation of inbred lines derived from tissue cultures of maize. Theor. Appl. Genet. 75:841–849; 1988.

    Article  Google Scholar 

  • Lee, M. L.; Phillips, R. L. Genomic rearrangements in maize induced by tissue culture. Genome 29:122–128; 1987a.

    Google Scholar 

  • Lee, M. L.; Phillips, R. L. Genetic variability in progeny of regenerated maize (Zea mays L.) plants. Genome 29:344–355; 1987b.

    Google Scholar 

  • Lee, M. L.; Phillips, R. L. The chromosomal basis of somaclonal variation. Ann. Rev. Plant Physiol. Plant Mol. Biol. 39:413–437; 1988.

    Article  Google Scholar 

  • LoSchiavo, F.; Pitto, L.; Giuliano, G., et al. DNA methylation of embryogenic carrot cell cultures and its variations as caused by mutation, differentiation, hormones, and hypomethylating drugs. Theor. Appl. Genet. 77:325–331; 1989.

    Article  CAS  Google Scholar 

  • McClintock, B. The origin and behavior of mutable loci in maize. Proc. Natl. Acad. Sci. USA 36:344–355; 1950.

    Article  PubMed  CAS  Google Scholar 

  • McClintock, B. Mechanisms that rapidly reorganize the genome. Stadler Genet. Symp. 10:25–47; 1978.

    Google Scholar 

  • McClintock, B. The significance of responses of the genome to challenge. Science 226:792–801; 1984.

    Article  PubMed  CAS  Google Scholar 

  • McCoy, T. J.; Phillips, R. L.; Rines, H. W. Cytogenetic analysis of plants regenerated from oat (Avena sativa) tissue cultures; high frequency of partial chromsome loss. Can. J. Genet. Cytol. 24:37–50; 1982.

    Google Scholar 

  • McCoy, T. J.; Phillips, R. L. Chromosome stability in maize (Zea mays) tissue cultures and sectoring in some regenerated plants. Can. J. Genet. Cytol. 24:559–565; 1982.

    Google Scholar 

  • Messenguer, R.; Ganal, M. W.; Steffens, J. C., et al. Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Mol. Biol. 16:753–770; 1991.

    Article  Google Scholar 

  • Monk, M. Changes in DNA methylation during mouse embryonic development in relation to X-chromosome activity and imprinting. Philos. Trans. R. Soc. Lond. B Biol. Sci. 326:299–312; 1990.

    PubMed  CAS  Google Scholar 

  • Müller, E.; Brown, P. T. H.; Hartke, S., et al. DNA variation in tissue culture-derived rice plants. Theor. Appl. Genet. 80:673–679; 1990.

    Google Scholar 

  • Neuffer, M. G. Stability of the suppressor element in two mutator systems of theA1 locus in maize. Genetics 53:541–549; 1966.

    PubMed  CAS  Google Scholar 

  • Oono, K.In vitro methods applied to rice. In: Thorpe, T. A., ed. Plant tissue culture. New York: Academic Press; 1981:273–298.

    Google Scholar 

  • Oono, K. Putative homozygous mutants in regenerated plants of rice. Mol. Gen. Genet. 198:377–384; 1985.

    Article  Google Scholar 

  • Orton, T. J. Genetic variation in somatic tissues: Method or madness? Adv. Plant Pathol. 2:153–189; 1984.

    Google Scholar 

  • Pardue, M. L. Dynamic instability of chromosomes and genomes. Cell 66:427–431; 1991.

    Article  PubMed  CAS  Google Scholar 

  • Pavlica, M.; Nagy, B.; Papes, D. 2,4-D causes chromosome and chromatin abnormalities in plant cells and mutation in cultured mammalian cells. Mutat. Res. 263:77–82; 1991.

    Article  PubMed  CAS  Google Scholar 

  • Peschke, V. M.; Phillips, R. L. Activation of the maize transposable elementSuppressor-mutator (Spm) in tissue culture. Theor. Appl. Genet. 81:90–97; 1991.

    Article  Google Scholar 

  • Peschke, V. M.; Phillips, R. L.; Gengenbach, B. G. Discovery of transposable element activity among progeny of tissue culture-derived maize plants. Science 238:804–807; 1987.

    Article  PubMed  CAS  Google Scholar 

  • Peschke, V. M.; Phillips, R. L.; Gengenbach, B. G. Genetic and molecular analysis of tissue culture-derivedAc elements. Theor. Appl. Genet. 82:121–129; 1991.

    Article  CAS  Google Scholar 

  • Peschke, V. M.; Phillips, R. L. Genetic implications of somaclonal variation in plants. Adv. Genet. 30:41–75; 1992.

    Article  CAS  Google Scholar 

  • Peterson, P. A. A mutable plae green locus in maize. Genetics 38:682–683; 1953.

    Google Scholar 

  • Phillips, R. L. Somaclonal and gametoclonal variation. Genome 31:1119–1120; 1989.

    Google Scholar 

  • Phillips, R. L.; Kaeppler, S. M.; Peschke, V. M. Do we understand somaclonal variation? In: Nijkamp, H. J. J.; VanDerPlas, L. H. W.; Van Aartrijk, J., eds. Progress in plant cellular and molecular biology. Dordrecht: Kluwer Academic Publishing; 1990:131–141.

    Google Scholar 

  • Pryor, A.; Faulker, K.; Rhoades, M. M., et al. Asynchronous replication of heterochromatin in maize. Proc. Natl. Acad. Sci. USA 77:6705–6709; 1980.

    Article  PubMed  CAS  Google Scholar 

  • Quemeda, H.; Roth, E. J.; Lark, K. G. Changes in methylation of tissue cultured soybean cells detected by digestion with the restriction enzymesHpall andMspI. Plant Cell Rep. 6:63–66; 1987.

    Article  Google Scholar 

  • Rhoades, M. M.; Dempsey, E. On the mechanism of chromatin loss induced by the B chromosome of maize. Genetics 71:73–96; 1972.

    PubMed  CAS  Google Scholar 

  • Rhoades, M. M.; Dempsey, E. Chromatin elimination induced by the B chromosome of maize. J. Hered. 64:12–18; 1973.

    Google Scholar 

  • Rhodes, C. A.; Phillips, R. L.; Green, C. E. Cytogenetic stability of aneuploid maize tissue cultures. Can. J. Genet. Cytol. 28:374–384; 1986.

    Google Scholar 

  • Rice, T. B. Tissue culture induced genetic variation in regenerated maize inbreds. In: Proc. 37th Annu. Corn and Sorghum Research Conference. Chicago, IL, December, 1982. Washington, DC: Amer. Seed Assoc.; 1982:148–162.

    Google Scholar 

  • Schaeffer, G. W. Recovery of heritable variability in anther-derived doubled-haploid rice. Crop Sci. 22:1160–1164; 1982.

    Article  Google Scholar 

  • Schwartz, D. Gene-controlled cytosine demethylation in the promoter region of theAc transposable element in maize. Proc. Natl. Acad. Sci. USA 86:2789–2793; 1989.

    Article  PubMed  CAS  Google Scholar 

  • Schwartz, D.; Dennis, E. Transposase activity of theAc controlling element in maize is regulated by its degree of methylation. Mol. Gen. Genet. 205:476–482; 1986.

    Article  CAS  Google Scholar 

  • Silva, A. J.; White, R. Inheritance of allelic blueprints for methylation patterns. Cell 54:145–152; 1988.

    Article  PubMed  CAS  Google Scholar 

  • Sun, Z. X.; Zheng, K. L. Somaclonal variation in rice. In: Bajaj, Y. P. S., ed. Biotechnology in agriculture and forestry, vol. 3. Berlin: Springer-Verlag; 1990:288–325.

    Google Scholar 

  • Sunderland, N. Nuclear cytology. In: Street, H. E., ed. Plant tissue and cell culture, 2nd ed. Oxford: Blackwell; 1973:177–205.

    Google Scholar 

  • Vergara, R.; Verde, F.; Pitto, L., et al. Reversible variations in the methylation pattern of carrot DNA during somatic embryogenesis. Plant Cell Rep. 8:697–700; 1990.

    Article  CAS  Google Scholar 

  • Vincent, A.; Heitz, D.; Petit, C., et al. Abnormal methylation pattern detected in fragile-X patients by pulsed field gel electrophoresis. Nature 349:624–626; 1991.

    Article  PubMed  CAS  Google Scholar 

  • Walbot, V. Reactivation of theMutator transposable element system following gamma irradiation of seed. Mol. Gen. Genet. 212:259–264; 1988.

    Article  CAS  Google Scholar 

  • Woodman, J. C.; Kramer, D. A. The recovery of somaclonal variants from tissue cultures of B73, an elite inbred line of maize. In: VI Intl. Congr. Plant Tissue Cell Culture, Minneapolis, MN, 3–8 August, 1986. St. Paul, MN: Univ. of Minnesota. Abstracts, p. 215.

    Google Scholar 

  • Zehr, B. E.; Williams, M. E.; Duncan, D. R., et al. Somaclonal variation among the progeny of plants regenerated from callus cultures of seven inbred lines of maize. Can. J. Bot. 61:491–499; 1987.

    Article  Google Scholar 

Download references

Author information

Author notes

  1. S. M. Kaeppler

    Present address: Department of Agronomy, University of Nebraska, Lincoln, NE

Authors and Affiliations

  1. Department of Agronomy and Plant Genetics and Plant Molecular Genetics Institute, University of Minnesota, 55108, St. Paul, Minnesota

    S. M. Kaeppler & R. L. Phillips

Authors
  1. S. M. Kaeppler
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. L. Phillips
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

Presented in the Session-in-Depth Exploitation of Plant Cell Culture Variants at the 1992 World Congress on Cell and Tissue Culture, Washington, DC, June 20–25, 1992.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kaeppler, S.M., Phillips, R.L. DNA methylation and tissue culture-induced variation in plants. In Vitro Cell Dev Biol - Plant 29, 125–130 (1993). https://doi.org/10.1007/BF02632283

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02632283

Key words

Search

Navigation