DNA methylation polymorphism in a set of elite maize inbred lines revealed by methylation-sensitive ISSR analysis

Summary

DNA methylation polymorphism among nine elite maize inbred lines was assessed by inter-simple sequence repeat (ISSR) fingerprinting on intact DNA and DNA digested by either of a pair of methylation-sensitive isoschizomers, Hpa II and Msp I. It was found that, along with distinct genetic differentiation, extensive DNA methylation polymorphism exists among the nine inbred lines. The line-specific methylation patterns are homogeneous within each line, indicating their usefulness as molecular markers for cultivar identification. DNA sequences underlying the DNA methylation variations include a high proportion of coding genes. Cluster analysis, however, indicates the existence of incongruence between DNA methylation polymorphism and known-pedigree of the maize inbred lines.

References

  1. Ashikawa I (2001) Surveying CpG methylation at 5′-CCGG in the genomes of rice cultivars. Plant Molecular Biology 45: 31–39

    CAS  Article  Google Scholar 

  2. Cervera MT, Ruiz-Garcia L, Martinez-Zapater JM (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genomics 268: 543–552

    CAS  Article  Google Scholar 

  3. Colot V, Rossignol JL (1999) Eukaryotic DNA methylation as an evolutionary device. Bioessays 21: 402–411

    CAS  Article  Google Scholar 

  4. Gruenbaum Y, Naveh-Many T, Cedar H, Razin A (1981) Sequence specificity of methylation in higher plant DNA. Nature 292: 860–862

    CAS  Article  Google Scholar 

  5. Hollick JB, Chandler VL (1998) Epigenetic allelic states of a maize transcriptional regulatory locus exhibit overdominant gene action. Genetics 150: 891–897

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003) Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Current Biology 13: 421–426

    CAS  Article  Google Scholar 

  7. Keyte AL, Percifield R, Liu B, Wendel JF (2005) Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). Mol Genet Genomics (submitted)

  8. Kidwell KK, Osborn TC (1992) Simple plant DNA isolation procedures, In Plant genomes: Methods for Genetic and Physical Mapping, J. S. Beckman and T.C. Osborn, eds (Dordrecht, The Netherlands:Kluwer Academic Publishers), pp.1–13

    Google Scholar 

  9. Knox MR, Ellis THN (2001) Stability and inheritance of methylation states at Pst I sites in Pisum. Mol Genet Genomics 265: 497–507

    CAS  Article  Google Scholar 

  10. Kovarik A, Koukalová B, Bezdek M, Opatrn Z (1997) Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. Theor. Appl. Genet. 95: 301–306

    Article  Google Scholar 

  11. Liu B, Wendel JF (2003) Epigenetic phenomena and the evolution of plant allopolyploids. Molecular Phylogenetics and Evolution 29: 365–379

    CAS  Article  Google Scholar 

  12. McClelland M, Nelson M, Raschke E. (1994) Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res. 22: 3640–3659

    CAS  Article  Google Scholar 

  13. Messeguer R, Ganal MW, Stevens JC, Tanksley SD (1991) Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Molecular Biology 16: 753–770

    CAS  Article  Google Scholar 

  14. Morgante M and Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotechnol. 14: 214–219

    CAS  Article  Google Scholar 

  15. Portis E, Acquadro A, Comino C, Lanteri S (2003) Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). Plant Science 166: 169–178

    Article  Google Scholar 

  16. Richards EJ (1997) DNA methylation and plant development. Trends Genet. 13: 319–323

    CAS  Article  Google Scholar 

  17. Riddle NC, Richards EJ (2002) The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162: 355–363

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Rohlf FJ (1993) NTSYS-pc. Numerical taxonomy and multivariate analysis system. Exeter, Publishing Ltd., New York, USA.

    Google Scholar 

  19. Swofford DL, Olsen GJ (1990) Phylogenetic reconstruction. In: Molecular Systemics. Edited by DM Hillis & C Moritz. Sinauer Associations, Sunderland. pp. 411–501

    Google Scholar 

  20. Tariq M, Paszkowski J (2004) DNA and histone methylation in plants. Trends in Genetics 20: 244–251

    CAS  Article  Google Scholar 

  21. Wada Y, Miyamoto K, Kusano T, Sano H. (2004) Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants. Mol Genet Genomics. 271: 658–66

    CAS  Article  Google Scholar 

  22. Walbot V (2004) Genomic, chromosomal and allelic assessment of the amazing diversity of maize. Genome Biol. 5: 328

    Article  Google Scholar 

  23. Wang YM, Lin XY, Dong B, Wang YD, Liu B (2004) DNA methylation polymorphism in a set of elite rice cultivars and its possible contribution to inter-cultivar differential gene expression. Cell. Mol. Biol. Lett. 9: 543–556

    CAS  PubMed  Google Scholar 

  24. Xiong LZ, Xu CG, Maroof MAS, Zhang Q (1999) Patterns of cytosine methyaltion in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet 261: 439–46

    CAS  Article  Google Scholar 

  25. Zhao SH, Wang P, Li HH, Zhang JP and Li DM (2004) Evaluation of phylogenetic relationship among 28 maize inbred lines based on RAPD markers. Biotechnology 14: 8–9

    Google Scholar 

  26. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20: 176–183

    CAS  Article  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to Bao Liu.

Rights and permissions

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Reprints and Permissions

About this article

Cite this article

Zhao, X., Jia, E., Yang, W. et al. DNA methylation polymorphism in a set of elite maize inbred lines revealed by methylation-sensitive ISSR analysis. CEREAL RESEARCH COMMUNICATIONS 34, 879–886 (2006). https://doi.org/10.1556/CRC.34.2006.2-3.215

Download citation

Index Words

  • Maize inbred lines
  • DNA methylation polymorphism
  • ISSR fingerprinting
  • Molecular marker