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Epigenomes 2018, 2(3), 14; https://doi.org/10.3390/epigenomes2030014

Dynamics of the Methylome and Transcriptome during the Regeneration of Rice

1
Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
2
Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
3
Transgenic Plant Core Facility, Academia Sinica, Taipei 11529, Taiwan
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 9 June 2018 / Revised: 29 June 2018 / Accepted: 17 July 2018 / Published: 21 July 2018
(This article belongs to the Special Issue Plant Epigenome Dynamics)
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Abstract

Oryza sativa indica (cv. IR64) and Oryza sativa japonica (cv. TNG67) vary in their regeneration efficiency. Such variation may occur in response to cultural environments that induce somaclonal variation. Somaclonal variations may arise from epigenetic factors, such as DNA methylation. We hypothesized that somaclonal variation may be associated with the differential regeneration efficiency between IR64 and TNG67 through changes in DNA methylation. We generated the stage-associated methylome and transcriptome profiles of the embryo, induced calli, sub-cultured calli, and regenerated calli (including both successful and failed regeneration) of IR64 and TNG67. We found that stage-associated changes are evident by the increase in the cytosine methylation of all contexts upon induction and decline upon regeneration. These changes in the methylome are largely random, but a few regions are consistently targeted at the later stages of culture. The expression profiles showed a dominant tissue-specific difference between the embryo and the calli. A prominent cultivar-associated divide in the global methylation pattern was observed, and a subset of cultivar-associated differentially methylated regions also showed stage-associated changes, implying a close association between differential methylation and the regeneration programs of these two rice cultivars. Based on these findings, we speculate that the differential epigenetic regulation of stress response and developmental pathways may be coupled with genetic differences, ultimately leading to differential regeneration efficiency. The present study elucidates the impact of tissue culture on callus formation and delineates the impact of stage and cultivar to determine the dynamics of the methylome and transcriptome in culture. View Full-Text
Keywords: DNA methylation; Oryza sativa; regeneration efficiency; RNA-Seq; somaclonal variation; tissue culture; WGBS DNA methylation; Oryza sativa; regeneration efficiency; RNA-Seq; somaclonal variation; tissue culture; WGBS
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Hsu, F.-M.; Gohain, M.; Allishe, A.; Huang, Y.-J.; Liao, J.-L.; Kuang, L.-Y.; Chen, P.-Y. Dynamics of the Methylome and Transcriptome during the Regeneration of Rice. Epigenomes 2018, 2, 14.

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