Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

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


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.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2


  1. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL (2002) The cost of inbreeding in Arabidopsis. Nature 416:531–534

  2. Causton DR, Venus JC (1981) The biometry of plant growth. Edward Arnold, London

  3. Charlesworth D, Willis JH (2009) The genetics of inbreeding depression. Nat Rev Genet 10:783–796

  4. Chen ZJ, Pikaard CS (1997) Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev 11:2124–2136

  5. Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y et al (2000) Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12:1551–1567

  6. Hunt R (1982) Plant growth curves. The functional approach to plant growth analysis. Edward Arnold, London

  7. Ishizuka T, Tanabata T, Takano M, Shinomura T (2005) Kinetic measuring method of rice growth in tillering stage using auto digital imaging system. Environ Control Biol 43:83–96

  8. Jang I-C, Pahk Y-M, Song SI, Kwon HJ, Nahm BH, Kim J-K (2003) Structure and expression of the rice class-I type histone deacetylase genes OsHDAC1-3: OsHDAC1 overexpression in transgenic plants leads to increased growth rate and altered architecture. Plant J 33:531–541

  9. Jonckheere RA (1954a) A distribution-free k-sample test against ordered alternatives. Biometrika 41:133–145

  10. Jonckheere RA (1954b) A test of significance for the relation between m rankings and k ordered categories. Br J Statist Psychol 7:93–100

  11. Li Y, Butenko Y, Grafi G (2005) Histone deacetylation is required for progression through mitosis in tobacco cells. Plant J 41:346–352

  12. Liu B, Wendel JF (2003) Epigenetic phenomena and the evolution of plant allopolyploids. Mol Phylogenet Evol 29:365–379

  13. Loidl P (2004) A plant dialect of the histone language. Trends Plant Sci 9:84–90

  14. Lu J, Tang T, Tang H, Huang J, Shi S, Wu C-I (2006) The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet 22:126–131

  15. Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y et al (2009) Altered circadian rhythms regulate growth vigor in hybrids and allopolyploids. Nature 457:327–331

  16. Queitsch C, Sangster TA, Lindquist S (2002) Hsp90 as a capacitor of phenotypic variation. Nature 417:618–624

  17. Shaked H, Kasukush K, Ozkan H, Feldman M, Levy AA (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13:1749–1759

  18. Sollars V, Lu X, Xiao L, Wang X, Garfinkel MD, Ruden DM (2003) Evidence for an epigenetic mechanism by which Hsp90 acts as a capacitor for morphological evolution. Nat Genet 33:70–74

  19. Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, Schnable PS (2006) All possible models of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proc Natl Acad Sci USA 103:6805–6810

  20. Taddei A, Roche D, Bickmore WA, Almouzni G (2005) The effects of histone deacetylases inhibitors on heterochromatin: implications for anticancer therapy? EMBO Rep 6:520–524

  21. Tanabata T, Shimizu H, Shimnomura T, Takano M, Nakamura-Miyamura H, Saito T (2008) An image measurement system for phenotype analysis of rice seedlings growth. IEEJ Transact Electr Info Sys 128:962–969 (in Japanese with English abstract)

  22. True HL, Berlin I, Lindquist SL (2004) Epigenetic regulation of translation reveales hidden genetic variation to produce complex traits. Nature 431:184–187

  23. Wei G, Tao Y, Liu G, Chen C, Luo R, Xia H et al (2009) A transcriptomic analysis of superhybrid rice LYP9 and its parents. Proc Natl Acad Sci USA 106:7695–9701

Download references


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.).

Author information

Correspondence to Yoshiki Habu.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Tanabata, T., Taguchi-Shiobara, F., Kishimoto, N. et al. A phenomics approach detected differential epigenetic growth regulation between inbreds and their hybrid in Oryza sativa . Mol Breeding 26, 729–734 (2010). https://doi.org/10.1007/s11032-010-9484-3

Download citation


  • Epigenetics
  • Growth modeling
  • Histone deacetylase
  • Inbreeding depression
  • Oryza sativa