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PMID: 20086188 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids.

The Plant cell ·Vol. 22 ·No. 1 ·2010-01-00 ·Pages 17-33

He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, Qi Y, Chen R, Deng XW

Abstract

The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here, we report highly integrated maps of the epigenome, mRNA, and small RNA transcriptomes of two rice (Oryza sativa) subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents, and more small RNAs were downregulated than upregulated in the reciprocal hybrids. Together, our data reveal a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses and provide a useful resource for the rice community.

MeSH Terms
Chimera Chromosome Mapping DNA Methylation Epigenesis, Genetic Gene Expression Profiling Gene Expression Regulation, Plant Gene Library Genome, Plant Histones/metabolism Oryza/genetics Polymorphism, Single Nucleotide RNA, Messenger/genetics RNA, Plant/genetics Transcription, Genetic
Chemicals
Histones RNA, Messenger RNA, Plant
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
He Guangming
Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.
Zhu Xiaopeng
Elling Axel A
Chen Liangbi
Wang Xiangfeng
Guo Lan
Liang Manzhong
He Hang
Zhang Huiyong
Chen Fangfang
Qi Yijun
Chen Runsheng
Deng Xing-Wang
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Article Info
Journal
The Plant cell
Abbr.
Plant Cell
ISSN
1532-298X
DOI
10.1105/tpc.109.072041
Published
2010-01-00
Epub
2010-00-19
Pages
17-33
Language
English
Region
England
NLM ID
9208688
PMCID
PMC2828707
Subset
IM
Grants
NIGMS NIH HHS · R01 GM047850 · United States
NIGMS NIH HHS · R37 GM047850 · United States
NIGMS NIH HHS · GM047850 · United States
External Links
PubMed source DOI: 10.1105/tpc.109.072041 PMC Full Text View journal details
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