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Biologia Plantarum

, Volume 56, Issue 2, pp 269–275 | Cite as

Analysis of DNA methylation during the germination of wheat seeds

  • F. -R. Meng
  • Y. -C. Li
  • J. Yin
  • H. Liu
  • X. -J. Chen
  • Z. -F. Ni
  • Q. -X. Sun
Original Papers

Abstract

DNA methylation is known to play a crucial role in regulating plant development and organ or tissue differentiation. Here, we focused on the DNA methylation dynamics during the germination of wheat seeds using the adapted AFLP technique so called methylation-sensitive amplified polymorphism (MSAP). The MSAP profiles of genomic DNA in embryo and endosperm tissues of germinating seeds, as well as dry seeds were characterized and notable changes of cytosine methylation were detected. Comparisons of MSAP profiles in different tissues tested showed that the methylation level in dry seeds is the highest. The alteration analysis of cytosine methylation displayed that the number of demethylation events were three times higher than that of de novo methylation, which indicated that the demethylation was predominant in germinating wheat seeds, though the methylation events occurred as well. Sixteen differentially displayed DNA fragments in MSAP profiles were cloned and the sequencing analysis confirmed that nine of them contained CCGG sites. The further BLAST search showed that four of the cloned sequences were located in coding regions. Interestingly, three of the sixteen candidates were homologous to retrotransposons, which indicated that switches between DNA methylation and demethylation occurred in retrotransposon elements along with the germination of wheat seeds.

Additional key words

embryo endosperm cloning sequence analysis 

Abbreviations

MSAP

methylation-sensitive amplification polymorphism

AFLP

amplified fragment length polymorphism

PCR

polymerase chain reaction

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Notes

Acknowledgements

This research was supported by National Natural Science Foundation of China (30300195; 31071410).

References

  1. Bitonti, M.B., Cozza, R., Chiappetta, A., Giannino, D., Ruffini Castiglione, M., Dewitte, W., Mariotti, D., Van Onckelen, H., Innocenti, A.M.: Distinct nuclear organization, DNA methylation pattern and cytokinin distribution mark juvenile, juvenile-like and adult vegetative apical meristems in peach (Prunus persica (L.) Batsch). — J. exp. Bot. 53: 1047–1054, 2002.PubMedCrossRefGoogle Scholar
  2. Burn, J.E., Bagnall, D.J., Metzger, J.D., Dennis, E.S., Peacock, W.J.: DNA methylation, vernalization, and the initiation of flowering. — Proc. nat. Acad. Sci. USA 90: 287–291, 1993.PubMedCrossRefGoogle Scholar
  3. Cantu, D., Vanzetti, L.S., Sumner, A., Dubcovsky, M., Matvienko, M., Distelfeld, A., Michelmore, R.W., Dubcovsky, J.: Small RNAs, DNA methylation and transposable elements in wheat. — BMC Genomics 11: 408, 2010.PubMedCrossRefGoogle Scholar
  4. Cervera, M.T., Ruiz-Garcia, L., Martinez-Zapater, J.M.: Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. — Mol. Genet Genomics 268: 543–552, 2002.PubMedCrossRefGoogle Scholar
  5. Cokus, S.J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C.D., Pradhan, S., Nelson, S.F., Pellegrini, M., Jacobsen, S.E.: Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. — Nature 452: 215–219, 2008.PubMedCrossRefGoogle Scholar
  6. Drozhdeniuk, A.P., Sulimova, G.E., Vaniushin, B.F.: [Changes in base composition and molecular population of wheat DNA on germination. ] — Mol. Biol. (Moskva) 10: 1378–1386, 1976. [In Russ. ]Google Scholar
  7. Fait, A., Angelovici, R., Less, H., Ohad, I., Urbanczyk-Wochniak, E., Fernie, A.R., Galili, G.: Arabidopsis seed development and germination is associated with temporally distinct metabolic switches. — Plant Physiol. 142: 839–854, 2006.PubMedCrossRefGoogle Scholar
  8. Fedoroff, N.: Transposons and genome evolution in plants. — Proc. nat. Acad. Sci. USA 97: 7002–7007, 2000.PubMedCrossRefGoogle Scholar
  9. Finnegan, E.J., Genger, R.K., Kovac, K., Peacock, W.J., Dennis, E.S.: DNA methylation and the promotion of flowering by vernalization. — Proc. nat. Acad. Sci. USA 95: 5824–5829, 1998a.PubMedCrossRefGoogle Scholar
  10. Finnegan, E.J., Genger, R.K., Peacock, W.J., Dennis, E.S.: DNA methylation in plants.— Annu. Rev. Plant Physiol. Plant mol. Biol 49: 223–247, 1998b.PubMedCrossRefGoogle Scholar
  11. Finnegan, E.J., Peacock, W.J., Dennis, E.S.: DNA methylation, a key regulator of plant development and other processes. — Curr. Opin. Genet. Dev. 10: 217–223, 2000.PubMedCrossRefGoogle Scholar
  12. Fraga, M.F., Canal, M.J., Rodriguez, R.: Phase-change related epigenetic and physiological changes in Pinus radiata D. Don. — Planta 215: 672–678, 2002.PubMedCrossRefGoogle Scholar
  13. Fulnecek, J., Matyasek, R., Kovarik, A.: Distribution of 5-methylcytosine residues in 5S rRNA genes in Arabidopsis thaliana and Secale cereale. — Mol. Genet. Genomics 268: 510–517, 2002.PubMedCrossRefGoogle Scholar
  14. Grunau, C., Renault, E., Rosenthal, A., Roizes, G.: MethDB — a public database for DNA methylation data. — Nucl. Acids Res. 29: 270–274, 2001.PubMedCrossRefGoogle Scholar
  15. Hafiz, I., Anjum, M., Grewal, A., Chaudhary, G.: DNA methylation — an essential mechanism in plant molecular biology. — Acta physiol. plant. 23: 491–499, 2001.CrossRefGoogle Scholar
  16. Kashkush, K., Feldman, M., Levy, A.A.: Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. —Nat. Genet. 33: 102–106, 2003.PubMedCrossRefGoogle Scholar
  17. Koornneef, M., Bentsink, L., Hilhorst, H.: Seed dormancy and germination. — Curr. Opin. Plant Biol. 5: 33–36, 2002.PubMedCrossRefGoogle Scholar
  18. Korch, C., Hagblom, P.: In-vivo-modified gonococcal plasmid pJD1. a model system for analysis of restriction enzyme sensitivity to DNA modifications. — Eur. J. Biochem. 161: 519–524, 1986.PubMedCrossRefGoogle Scholar
  19. Koukalova, B., Fojtova, M., Lim, K.Y., Fulnecek, J., Leitch, A.R., Kovarik, A.: Dedifferentiation of tobacco cells is associated with ribosomal RNA gene hypomethylation, increased transcription, and chromatin alterations. — Plant Physiol. 139: 275–286, 2005.PubMedCrossRefGoogle Scholar
  20. Kovarik, A., Van Houdt, H., Holy, A., Depicker, A.: Druginduced hypomethylation of a posttranscriptionally silenced transgene locus of tobacco leads to partial release of silencing. — FEBS Lett. 467: 47–51, 2000.PubMedCrossRefGoogle Scholar
  21. Kumar, A., Bennetzen, J.L.: Plant retrotransposons. — Annu. Rev. Genet. 33: 479–532, 1999.PubMedCrossRefGoogle Scholar
  22. Lu, G., Wu, X., Chen, B., Gao, G., Xu, K., Li, X.: Detection of DNA methylation changes during seed germination in rapeseed (Brassica napus). — Chin. Sci. Bull. 51: 182–190, 2006.CrossRefGoogle Scholar
  23. Martienssen, R.A., Colot, V.: DNA methylation and epigenetic inheritance in plants and filamentous fungi. — Science 293: 1070–1074, 2001.PubMedCrossRefGoogle Scholar
  24. Matassi, G., Melis, R., Kuo, K.C., Macaya, G., Gehrke, C.W., Bernardi, G.: Large-scale methylation patterns in the nuclear genomes of plants. — Gene 122: 239–245, 1992.PubMedCrossRefGoogle Scholar
  25. McClelland, M., Nelson, M., Raschke, E.: Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. — Nucl. Acids Res. 22: 3640–3659, 1994.PubMedCrossRefGoogle Scholar
  26. Messeguer, R., Ganal, M.W., Steffens, J.C., Tanksley, S.D.: Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. — Plant mol. Biol. 16: 753–770, 1991.PubMedCrossRefGoogle Scholar
  27. Meyer, P., Niedenhof, I., Ten Lohuis, M.: Evidence for cytosine methylation of non-symmetrical sequences in transgenic Petunia hybrida. — EMBO J. 13: 2084–2088, 1994.PubMedGoogle Scholar
  28. Paszkowski, J., Whitham, S.A.: Gene silencing and DNA methylation processes. — Curr. Opin. Plant Biol. 4: 123–129, 2001.PubMedCrossRefGoogle Scholar
  29. Petit, M., Guidat, C., Daniel, J., Denis, E., Montoriol, E., Bui, Q.T., Lim, K.Y., Kovarik, A., Leitch, A.R., Grandbastien, M.A., Mhiri, C.: Mobilization of retrotransposons in synthetic allotetraploid tobacco. — New Phytol. 186: 135–147, 2010.PubMedCrossRefGoogle Scholar
  30. Portis, E., Acquadro, A., Comino, C., Lanteri, S.: Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). — Plant Sci. 166: 169–178, 2004.CrossRefGoogle Scholar
  31. Riddle, N.C., Richards, E.J.: The control of natural variation in cytosine methylation in Arabidopsis. — Genetics 162: 355–363, 2002.PubMedGoogle Scholar
  32. Ruiz-García, L., Cervera, M., Martínez-Zapater, J.: DNA methylation increases throughout Arabidopsis development. — Planta 222: 301–306, 2005.PubMedCrossRefGoogle Scholar
  33. Sherman, J.D., Talbert, L.E.: Vernalization-induced changes of the DNA methylation pattern in winter wheat. — Genome 45: 253–260, 2002.PubMedCrossRefGoogle Scholar
  34. Siroky, J., Castiglione, M.R., Vyskot, B.: DNA methylation patterns of Melandrium album chromosomes. — Chromosome Res. 6: 441–446, 1998.PubMedCrossRefGoogle Scholar
  35. Slotkin, R.K., Martienssen, R.: Transposable elements and the epigenetic regulation of the genome. —Nat. Rev. Genet. 8: 272–285, 2007.PubMedCrossRefGoogle Scholar
  36. Sulimova, G.E., Dokhiem, M., Vaniushin, B.F.: [Character of the methylation and reassociation of wheat DNA fractions differing in their nucleotide composition.] — Mol. Biol. (Moskva) 12: 845–852, 1978. [In Russ. ]Google Scholar
  37. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M.: AFLP: a new technique for DNA fingerprinting. — Nucl. Acids Res. 23: 4407–4414, 1995.PubMedCrossRefGoogle Scholar
  38. Wendel, J.F., Wessler, S.R.: Retrotransposon-mediated genome evolution on a local ecological scale. — Proc. nat. Acad. Sci. USA 97: 6250–6252, 2000.PubMedCrossRefGoogle Scholar
  39. Xiong, L.Z., Xu, C.G., Saghai Maroof, M.A., 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.PubMedCrossRefGoogle Scholar
  40. Zluvova, J., Janousek, B., Vyskot, B.: Immunohistochemical study of DNA methylation dynamics during plant development. — J. exp. Bot. 52: 2265–2273, 2001.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • F. -R. Meng
    • 1
  • Y. -C. Li
    • 2
    • 3
  • J. Yin
    • 2
    • 3
  • H. Liu
    • 1
  • X. -J. Chen
    • 1
  • Z. -F. Ni
    • 4
  • Q. -X. Sun
    • 4
  1. 1.College of Life ScienceHenan Agricultural UniversityZhengzhouP.R. China
  2. 2.National Engineering Research Centre for WheatHenan Agricultural UniversityZhengzhouP.R. China
  3. 3.State Key Laboratory Cultivation Base of Crop Physiological Ecology and Genetic Improvement in Henan ProvinceHenan Agricultural UniversityZhengzhouP.R. China
  4. 4.Department of Plant Genetics and Breeding, State Key Lab for Agro-BiotechnologyChina Agricultural UniversityBeijingP.R. China

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