Molecular Breeding

, Volume 31, Issue 4, pp 815–827

Epigenetic changes and transposon reactivation in Thai rice hybrids

  • Laksana Kantama
  • Supaporn Junbuathong
  • Janejira Sakulkoo
  • Hans de Jong
  • Somsak Apisitwanich

DOI: 10.1007/s11032-013-9836-x

Cite this article as:
Kantama, L., Junbuathong, S., Sakulkoo, J. et al. Mol Breeding (2013) 31: 815. doi:10.1007/s11032-013-9836-x


Inter- or intraspecific hybridization is the first step in transferring exogenous traits to the germplasm of a recipient crop. One of the complicating factors is the occurrence of epigenetic modifications of the hybrids, which in turn can change their gene expression and phenotype. In this study we present an analysis of epigenome changes in rice hybrids that were obtained by crossing rice cultivars, most of them of indica type and Thai origin. Comparing amplified fragment length polymorphism (AFLP) fingerprints of twenty-four cultivars, we calculated Nei’s indexes for measuring genetic relationships. Epigenetic changes in their hybrids were established using methylation-sensitive AFLP fingerprinting and transposon display of the rice transposable elements (TEs) Stowaway Os-1 and Mashu, leading to the question whether the relationship between parental genomes is a predictor of epigenome changes, TE reactivation and changes in TE methylation. Our study now reveals that the genetic relationship between the parents and DNA methylation changes in their hybrids is not significantly correlated. Moreover, genetic distance correlates only weakly with Mashu reactivation, whereas it does not correlate with Stowaway Os-1 reactivation. Our observations also suggest that epigenome changes in the hybrids are localized events affecting specific chromosomal regions and transposons rather than affecting the genomic methylation landscape as a whole. The weak correlation between genetic distance and Mashu methylation and reactivation points at only limited influence of genetic background on the epigenetic status of the transposon. Our study further demonstrates that hybridizations between and among specific japonica and indica cultivars induce both genomic DNA methylation and reactivation/methylation change in the Stowaway Os-1 and Mashu transposons. The observed epigenetic changes seem to affect the transposons in a clear manner, partly driven by stochastic processes, which may account for a broader phenotypic plasticity of the hybrids. A better understanding of the epigenome changes leading to such transposon activation can lead to the development of novel tools for more variability in future rice breeding.


Oryza sativa Intraspecific hybridization DNA methylation Transposon Epigenetics 



Amplified fragment length polymorphism


Hexadecyl trimethyl-ammonium bromide


Ethylene diamine tetra-acetic acid


Rice accession from IRRI, Philippines


Miniature inverted-repeat transposable element


Methylation-sensitive amplified polymorphism


Rice department accession number


Transposon display


Tris-EDTA buffer


Transposon methylation display


Unweighted pair group method with arithmetic mean

Supplementary material

11032_2013_9836_MOESM1_ESM.docx (26 kb)
Supplementary material 1 (DOCX 26 kb)
11032_2013_9836_MOESM2_ESM.eps (1.5 mb)
Supplementary material 2 (EPS 1520 kb)
11032_2013_9836_MOESM3_ESM.eps (1.6 mb)
Supplementary material 3 (EPS 1612 kb)

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Laksana Kantama
    • 1
  • Supaporn Junbuathong
    • 2
  • Janejira Sakulkoo
    • 3
  • Hans de Jong
    • 5
  • Somsak Apisitwanich
    • 3
    • 4
  1. 1.Faculty of Liberal Arts and ScienceKasetsart UniversityNakorn PathomThailand
  2. 2.Pathumthani Rice Research Centre, Bureau of the Research and Development, Rice DepartmentMinister of Agriculture and CooperationPathum ThaniThailand
  3. 3.Department of Genetics, Faculty of ScienceKasetsart UniversityBangkokThailand
  4. 4.Center of Advanced studies for Tropical Natural ResourcesKasetsart UniversityBangkokThailand
  5. 5.Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands

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