Skip to main content
SpringerLink
Log in

Detection of DNA methylation pattern in thidiazuron-induced blueberry callus using methylation-sensitive amplification polymorphism

  • Original paper
  • Published:
Biologia Plantarum

Abstract

During the normal developmental process, programmed gene expression is an essential phenomenon in all organisms. In eukaryotes, DNA methylation plays an important role in the regulation of gene expression. The extent of cytosine methylation polymorphism was evaluated in leaf tissues collected from the greenhouse grown plants and in in vitro-derived callus of three lowbush and one hybrid blueberry genotypes, using methylation-sensitive amplification polymorphism (MSAP) technique. Callus formation started from the leaf segments after 4 weeks of culture on a thidiazuron (TDZ) containing medium. Maximum callus formation (98 %) was observed in the hybrid blueberry at 1.0 mg dm-3 TDZ. Although noticeable changes in cytosine methylation pattern were detected within the MSAP profiles of both leaf and callus tissues, methylation events were more polymorphic in calli than in leaf tissues. The number of methylated CCGG sites varied significantly within the genotypes ranging from 75 to 100 in leaf tissues and from 215 to 258 in callus tissues. Differences in the methylation pattern were observed not only in a tissue-specific manner but also within the genotype in a treatment specific manner. These results demonstrated the unique effect of TDZ and the tissue culture process on DNA methylation during callus development.

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

Abbreviations

AFLP:

amplified fragment length polymorphism

BM:

basal medium

MSAP:

methylation-sensitive amplification polymorphism

PPFD:

photosynthetic photon flux density

TDZ:

thidiazuron

References

  • Arnholdt-Schmitt, B., Herterich, S., Neumann, K.H.: Physiological aspects of genome variability in tissue culture. I. Growth phase-dependent differential DNA methylation of the carrot genome (Daucus carota L.) during primary culture. — Theor. appl. Genet. 91: 809–815, 1995.

    CAS  PubMed  Google Scholar 

  • Bassam, B.J., Caetano-Anollés, G., Gresshoff, P.M.: Fast and sensitive silver staining of DNA in polyacrylamide gels. — Anal. Biochem. 196: 80–83, 1991.

    Article  CAS  PubMed  Google Scholar 

  • Bell, D.J., Rowland, L.J., Zhang, D., Drummond, F.A.: The spatial genetic structure of lowbush blueberry, Vaccinium angustifolium, in four fields in Maine. — Botany 87: 932–946, 2009.

    Article  CAS  Google Scholar 

  • Chakrabarty, D., Yu, K.W., Paek, K.Y.: Detection of DNA methylation changes during somatic embryogenesis of Siberian ginseng (Eleuterococcus senticosus). — Plant Sci. 165: 61–68, 2003.

    Article  CAS  Google Scholar 

  • Debnath, S.C.: A two-step procedure for adventitious shoot regeneration on excised leaves of lowbush blueberry. — In Vitro cell. dev. Biol. Plant 45: 122–128, 2009.

    Article  Google Scholar 

  • Debnath, S.C.: Structured diversity using EST-PCR and ESTSSR markers in a set of wild blueberry clones and cultivars. — Biochem. Syst. Ecol. 54: 337–347, 2014.

    Article  CAS  Google Scholar 

  • Debnath, S.C., McRae, K.B.: In vitro culture of lingonberry (Vaccinium vitis-idaea L.) the influence of cytokinins and media types on propagation. — Small Fruits Rev. 1: 3–19, 2001.

    Article  CAS  Google Scholar 

  • Duncan, D.B.: Multiple range and multiple F tests. — Biometrics 11: 1–42, 1955.

    Article  Google Scholar 

  • Duncun, R.R.: Tissue culture induced variation in crop improvement. - In: Sparks, D.L. (ed.): Advances in Agronomy. Vol. 58. Pp. 201–240. Academic Press, New York 1997.

    Google Scholar 

  • Finnegan, E.J., Peacock, W.J., Dennis, E.S.: Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. — Proc. nat. Acad. Sci. USA 93: 8449–8454, 1996.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Finnegan, E.J., Genger, R., Peacock, W.J. Dennis, E.: DNA methylation in plants. — Annu. Rev. Plant Biol. 49: 223–247, 1998.

    Article  CAS  Google Scholar 

  • Fu, Y., Luo, G.Z., Chen, K., Deng, X., Yu, M., Han, D., Hao, Z., Liu, J., Lu, X., Dore, L.C., Weng, X., Ji, Q., Mets, L., He, C.: N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. — Cell 161: 879–892, 2015.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fulneček, J., Kovařík, A.: How to interpret methylation sensitive amplified polymorphism (MSAP) profiles? — BMC Gen. 15: 2, 2014.

    Article  Google Scholar 

  • Ghosh, A., Hossain, M.M., Sharma, M.: Mass propagation of Cymbidium giganteum Wall. ex Lindl. using in vitro seedlings. — Indian J. exp. Biol. 52: 905–911, 2014.

    PubMed  Google Scholar 

  • Goyali, J.C., Igamberdiev, A.U., Debnath, S.C.: Propagation methods affect fruit morphology and antioxidant properties but maintain clonal fidelity in lowbush blueberry. — HortScience 50: 888–896, 2015.

    CAS  Google Scholar 

  • Harrison, R.E., Luby, J.J., Ascher, P.D.: Genetic characteristics of self fertility in highbush and half-high blueberries. — Euphytica 67: 79–88, 1993.

    Article  Google Scholar 

  • Hsieh, C.L.: In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b. — Mol. cell. Biol. 19: 8211–8218, 1999.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang, H., Han, S.S., Wang, Y., Zhang, X.Z. and Han, Z.H.: Variations in leaf morphology and DNA methylation following in vitro culture of Malus xiaojinensis. — Plant Cell Tissue Organ Cult. 111: 153–161, 2012.

    Article  CAS  Google Scholar 

  • Ikeuchi, M., Sugimoto, K., Iwase, A.: Plant callus: mechanisms of induction and repression. — Plant Cell 25: 3159–3173, 2013.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaeppler, S.M., Kaeppler, H.F., Rhee, Y.: Epigenetic aspects of somaclonal variation in plants. — Plant mol. Biol. 43: 179–188, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Karp, A.: Somaclonal variation as a tool for crop improvement. — Euphytica 85: 295–302, 1995.

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Lin, C., Wang, R., Jauh, G.: Enhancement of callus formation on grape single bud cuttings by thidiazuron. — Acta Hort. 239: 129–132, 1989.

    Article  Google Scholar 

  • LoSchiavo, F., Pitto, L., Giuliano, G., Torti, G., Nuti-Ronchi, V., Marazziti, D., Vergara, R., Orselli, S., Terzi, M.: 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  PubMed  Google Scholar 

  • Murthy, B.N.S., Murch, S.J., Saxena P.K.: Thidiazuron: a potent regulator of in vitro plant morphogenesis. — In Vitro cell. dev. Biol. Plant. 34: 267–275, 1998.

    Article  CAS  Google Scholar 

  • Niederhuth, C.E., Schmitz, R.J.: Covering your bases: Inheritance of DNA methylation in plant genomes. — Mol. Plant. 7: 472–480, 2014.

    Article  CAS  PubMed  Google Scholar 

  • Park, S.Y., Murthy, H.N., Chakrabarthy, D., Paek, K.Y.: Detection of epigenetic variation in tissue-culture-derived plants of Doritaenopsis by methylation-sensitive amplification polymorphism (MSAP) analysis. — In Vitro cell. dev. Biol. Plant. 45: 104–108, 2009.

    Article  CAS  Google Scholar 

  • Peraza-Echeverria, S., Herrera-Valencia, V.A., Kay, A.J.: Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP). — Plant Sci. 161: 359–367, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Qureshi, J.A., Hucl, P., Kartha, K.K.: Is somaclonal variation a reliable tool for spring wheat improvement? — Euphytica 60: 221–228, 1992.

    Google Scholar 

  • Reyna-López, G.E., Simpson, J., Ruiz-Herrera, J.: Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. — Mol. gen. Genet. 253: 703–710, 1997.

    Article  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Tardy-Planechaud, S., Fujimoto, J., Lin, S.S., Sowers, L.C.: Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)- cytosine. — Nucl. Acids Res. 25: 553–558, 1997. Vander

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kloet, S.P.: Systematics, distribution, and nomenclature of the polymorphic Vaccinium angustifolium. — Rhodora 80: 358–376, 1978.

    Google Scholar 

  • Von Arnold, S., Sabala, I., Bozhkov, P., Dyachok, J., Filonova, L.: Developmental pathways of somatic embryogenesis. — Plant Cell Tissue Organ Cult. 69: 233–249, 2002.

    Article  Google Scholar 

  • Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van de Lee, T., Hornes, M., Friters, A., Pot, J., Paleman, J., Kuiper, M.: AFLP: a new technique for DNA fingerprinting. — Nucl. Acids Res. 23: 4407–4414, 1995.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wion, D., Casadesús, J.: N6-methyl-adenine: an epigenetic signal for DNA-protein interactions. — Nat. Rev. Microbiol. 4: 183–192, 2006.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiong, L., Xu, C., Maroof, M.S., Zhang, Q.: Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. — Mol. gen. Genet. 261: 439–446, 1999.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biology, Memorial University of Newfoundland, St. John’s, A1B 3X9, Canada

    A. Ghosh & A. U. Igamberdiev

  2. St. John’s Research and Development Centre, Agriculture and Agri-Food Canada, St. John’s, A1B 0B2, Canada

    A. Ghosh & S. C. Debnath

Authors
  1. A. Ghosh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. U. Igamberdiev
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. C. Debnath
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to S. C. Debnath.

Additional information

Acknowledgements: The authors are thankful to Darryl Martin, Sarah Leonard, Glenn Chubbs, Juran Goyali, and Dhrumit Bhatt for their excellent technical help.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ghosh, A., Igamberdiev, A.U. & Debnath, S.C. Detection of DNA methylation pattern in thidiazuron-induced blueberry callus using methylation-sensitive amplification polymorphism. Biol Plant 61, 511–519 (2017). https://doi.org/10.1007/s10535-016-0678-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10535-016-0678-3

Additional key words

Search

Navigation