Cereal Research Communications

, Volume 34, Issue 2–3, pp 879–886 | Cite as

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

  • Xinxin Zhao
  • Enji Jia
  • Weiguang Yang
  • Yingshan Dong
  • Bao LiuEmail author


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.

Index Words

Maize inbred lines DNA methylation polymorphism ISSR fingerprinting Molecular marker 


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  1. Ashikawa I (2001) Surveying CpG methylation at 5′-CCGG in the genomes of rice cultivars. Plant Molecular Biology 45: 31–39CrossRefGoogle 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: 543–552CrossRefGoogle Scholar
  3. Colot V, Rossignol JL (1999) Eukaryotic DNA methylation as an evolutionary device. Bioessays 21: 402–411CrossRefGoogle Scholar
  4. Gruenbaum Y, Naveh-Many T, Cedar H, Razin A (1981) Sequence specificity of methylation in higher plant DNA. Nature 292: 860–862CrossRefGoogle Scholar
  5. Hollick JB, Chandler VL (1998) Epigenetic allelic states of a maize transcriptional regulatory locus exhibit overdominant gene action. Genetics 150: 891–897PubMedPubMedCentralGoogle 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: 421–426CrossRefGoogle Scholar
  7. Keyte AL, Percifield R, Liu B, Wendel JF (2005) Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). Mol Genet Genomics (submitted)Google Scholar
  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.1–13Google Scholar
  9. Knox MR, Ellis THN (2001) Stability and inheritance of methylation states at Pst I sites in Pisum. Mol Genet Genomics 265: 497–507CrossRefGoogle 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: 301–306CrossRefGoogle Scholar
  11. Liu B, Wendel JF (2003) Epigenetic phenomena and the evolution of plant allopolyploids. Molecular Phylogenetics and Evolution 29: 365–379CrossRefGoogle 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: 3640–3659CrossRefGoogle 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: 753–770CrossRefGoogle Scholar
  14. Morgante M and Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotechnol. 14: 214–219CrossRefGoogle 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: 169–178CrossRefGoogle Scholar
  16. Richards EJ (1997) DNA methylation and plant development. Trends Genet. 13: 319–323CrossRefGoogle Scholar
  17. Riddle NC, Richards EJ (2002) The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162: 355–363PubMedPubMedCentralGoogle 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. 411–501Google Scholar
  20. Tariq M, Paszkowski J (2004) DNA and histone methylation in plants. Trends in Genetics 20: 244–251CrossRefGoogle 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: 658–66CrossRefGoogle Scholar
  22. Walbot V (2004) Genomic, chromosomal and allelic assessment of the amazing diversity of maize. Genome Biol. 5: 328CrossRefGoogle 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: 543–556PubMedGoogle 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: 439–46CrossRefGoogle 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: 8–9Google Scholar
  26. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20: 176–183CrossRefGoogle Scholar

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© Akadémiai Kiadó, Budapest 2006

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, 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.

Authors and Affiliations

  • Xinxin Zhao
    • 1
    • 2
  • Enji Jia
    • 2
  • Weiguang Yang
    • 2
  • Yingshan Dong
    • 3
  • Bao Liu
    • 1
    Email author
  1. 1.Laboratory of Molecular Epigenetics, Institute of Genetics & CytologyNortheast Normal UniversityChangchunChina
  2. 2.Department of AgronomyJilin Agricultural UniversityChangchunChina
  3. 3.The National Center of Transgenic Plant Research & CommercializationGongzulingChina

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