Molecular Breeding

, Volume 26, Issue 4, pp 729–734 | Cite as

A phenomics approach detected differential epigenetic growth regulation between inbreds and their hybrid in Oryza sativa

  • Takanari Tanabata
  • Fumio Taguchi-Shiobara
  • Naoki Kishimoto
  • Svetlana Chechetka
  • Tomoko Shinomura
  • Yoshiki Habu
Short Communication


Epigenetic changes in chromatin can be induced upon hybridization, but their contribution to phenotypic changes in F1 hybrids is not known. In this study, we examined the effect of genome-wide alteration of epigenetic chromatin status on the growth of inbreds and their F1 hybrid by large-scale fine-time-lapse growth monitoring of rice (Oryza sativa L.) under a controlled environment. This allowed us to dissect seedling growth of inbreds and their hybrid into separate growth parameters, and to analyze the effect of disturbance of inert chromatin states on these parameters. We found that superior growth parameters are generally more sensitive to global inhibition of the activities of histone deacetylases (HDACs), but this higher sensitivity is not directly correlated to heterosis in F1. Unexpectedly, however, the rate of the initial exponential growth of shoots is sensitive to HDAC inhibition only in inbreds, but not in F1, irrespective of phenotypic superiority. Our phenomics approach has detected an inbred-specific dependence of basic growth on the inert state of chromatin that is lost in F1 hybrids.


Epigenetics Growth modeling Histone deacetylase Inbreeding depression Oryza sativa 



We thank Keiko Hioki, Reiko Nigorikawa, Rie Takahashi, Kumiko Nissaka, Tomoko Watanabe and Hisayo Shimizu for technical assistance, and Helen Rothnie, Kentaro Ohigashi and Tetsuhisa Niwa for comments on the manuscript. This work was supported by the Ministry of Agriculture, Forestry and Fisheries of Japan (Integrated research project for plant, insect and animal using genome technology Japan, IP-1013 to Y.H. and IP-1006 T.S.; Genomics for Agricultural Innovation, NVR-0006 to Y.H.).

Supplementary material

11032_2010_9484_MOESM1_ESM.pdf (29 kb)
Supplementary Table 1 (PDF 30 kb)
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Supplementary Table 2 (PDF 26 kb)
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Supplementary Table 3 (PDF 22 kb)
11032_2010_9484_MOESM4_ESM.ppt (176 kb)
Supplementary Fig. 1 (PPT 172 kb)


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Takanari Tanabata
    • 1
    • 2
    • 3
  • Fumio Taguchi-Shiobara
    • 5
  • Naoki Kishimoto
    • 1
  • Svetlana Chechetka
    • 1
  • Tomoko Shinomura
    • 3
    • 4
  • Yoshiki Habu
    • 1
  1. 1.Division of Plant SciencesNational Institute of Agrobiological SciencesTsukubaJapan
  2. 2.QTL Genomics Research Center, National Institute of Agrobiological SciencesTsukubaJapan
  3. 3.Hitachi Central Research LaboratoryHatoyamaJapan
  4. 4.Department of BiosciencesTeikyo UniversityUtsunomiyaJapan
  5. 5.QTL Genomics Research Center, National Institute of Agrobiological SciencesTsukubaJapan

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