Ecological Research

, Volume 23, Issue 5, pp 927–930

Utility of the methylation-sensitive amplified polymorphism (MSAP) marker for detection of DNA methylation polymorphism and epigenetic population structure in a wild barley species (Hordeum brevisubulatum)

  • Yidan Li
  • Xiaohui Shan
  • Xiaoming Liu
  • Lanjuan Hu
  • Wanli Guo
  • Bao Liu
Note and Comment

Abstract

We report here that by using a modified scoring criterion, the methylation-sensitive amplified polymorphism or MSAP marker can be used effectively to detect polymorphism in DNA methylation patterns within and among populations of a perennial wild barley species, Hordeum brevisubulatum. Twenty-four selected individual genotypes representing four natural populations of H. brevisubulatum distributed in the Songnen Prairie in northeastern China were studied. The utility of MSAP was evidenced by its detection of high levels of polymorphism in DNA methylation patterns between individuals within a given population, and the clear inter-population differentiation in methylation patterns (methylation-based epigenetic population structure) revealed among the four populations. The resolving power of MSAP to detect DNA methylation polymorphism was found to be comparable with that of a retrotransposon-based sequence-specific amplified polymorphism marker, or SSAP, to detect genetic polymorphism in the same set of plants, suggesting that MSAP with a modified scoring criterion can be used efficiently to detect DNA methylation polymorphism and assess epigenetic population structure in natural plant populations.

Keywords

DNA methylation polymorphism Epigenetic population structure MSAP Hordeum brevisubulatum 

Supplementary material

11284_2007_459_MOESM1_ESM.doc (2.2 mb)
Supplementary Fig. S1 (DOC 2,228 kb)
11284_2007_459_MOESM2_ESM.doc (64 kb)
Supplementary Tables S1, S2 (DOC 64 kb)

References

  1. Ashikawa I (2001) Surveying CpG methylation at 5′-CCGG in the genomes of rice cultivars. Plant Mol Biol 45:31–39PubMedCrossRefGoogle 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 268:543–552PubMedCrossRefGoogle Scholar
  3. Grant-Downton RT, Dickinson HG (2005) Epigenetics and its implications for plant biology. 1. The epigenetic network in plants. Ann Bot (Lond) 96:1143–64CrossRefGoogle Scholar
  4. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603–6607PubMedCrossRefGoogle Scholar
  5. Kalisz S, Purugganan MD (2004) Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol Evol 19:309–314PubMedCrossRefGoogle Scholar
  6. Keyte AL, Kercifield R, Liu B, Wendel JF (2006) Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). Heredity 97:444–450CrossRefGoogle Scholar
  7. Lippman Z, May B, Yordan C, Singer T, Martienssen R (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol 1:E67PubMedCrossRefGoogle Scholar
  8. Liu B, Brubaker CL, Mergeai GR, Cronn RC, Wendel JF (2001) Polyploid formation in cotton is not accompanied by rapid genetic changes. Genome 44:321–330PubMedCrossRefGoogle Scholar
  9. Liu ZL, Han FP, Tan M, Shan XH, Dong YZ, Wang XZ, Fedak G, Hao S, Liu B (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theor Appl Genet 109:200–209PubMedCrossRefGoogle Scholar
  10. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323PubMedCrossRefGoogle Scholar
  11. Rangwala SH, Richards EJ (2004) The value-added genome: building and maintaining genomic cytosine methylation landscapes. Curr Opin Genet Dev 14:686–691PubMedCrossRefGoogle Scholar
  12. Rapp RA, Wendel JF (2005) Epigenetics and plant evolution. New Phytol 168:81–91PubMedCrossRefGoogle Scholar
  13. Reina-López GR, Simpson J, Ruiz-Herrera J (1997) Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphism. Mol Genet Genomics 253:703–710Google Scholar
  14. Rohlf FJ (2000) NTSYS-pc, numerical taxonomy and multivariate analysis system. Version 2.1. Exeter Publications, New YorkGoogle Scholar
  15. Salmon A, Ainouche ML, Wendel JF (2005) Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14:1163–1175PubMedCrossRefGoogle Scholar
  16. Selker EU (1997) Epigenetic phenomena in filamentous fungi: useful paradigms or repeat-induced confusion? Trends Genet 13:296–301PubMedCrossRefGoogle Scholar
  17. Sneath PHA, Sokal RR (1973) Numerical taxonomy. Freeman, San Francisco, 573 ppGoogle Scholar
  18. Vaughn MW, Tanurdžić M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A, Colot V, Doerge RW, Martienssen RA (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol 5:1617–1629CrossRefGoogle Scholar
  19. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M (1995) AFLP, a new technique for DNA fingerprinting. Nucleic Acids Res 23:3307–3314CrossRefGoogle Scholar
  20. Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence specific amplification polymorphisms (SSAP). Mol Genet Genomics 253:687–694CrossRefGoogle Scholar
  21. Yeh FC, Yang RC, Boyle TBJ, Ye ZH, Mao JX (1997) POPGENE, the user-friendly shareware for population genetic analysis. Version 1.21. Molecular biology and biotechnology, Centre University of Alberta CanadaGoogle Scholar

Copyright information

© The Ecological Society of Japan 2008

Authors and Affiliations

  • Yidan Li
    • 1
  • Xiaohui Shan
    • 1
  • Xiaoming Liu
    • 1
  • Lanjuan Hu
    • 1
  • Wanli Guo
    • 1
  • Bao Liu
    • 1
  1. 1.Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and CytologyNortheast Normal UniversityChangchunPeople’s Republic of China

Personalised recommendations