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Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

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Title Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response
 
Creator Garg, Rohini
Chevala, VVS Narayana
Shankar, Rama
Jain, Mukesh
 
Subject Abiotic
Drought
 
Description Accepted date: 14 September 2015
DNA methylation is an epigenetic mechanism that play an important role in gene regulation in response to environmental conditions. The understanding of DNA methylation at the whole genome level can provide insights into the regulatory mechanisms underlying abiotic stress response/adaptation. We report DNA methylation patterns and their influence on transcription in three rice (Oryza sativa) cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant; Pokkali, salinity-tolerant) via an integrated analysis of whole genome bisulphite sequencing and RNA sequencing. We discovered extensive DNA methylation at single-base resolution in rice cultivars, identified the sequence context and extent of methylation at each site. Overall, methylation levels were significantly different in the three rice cultivars. Numerous differentially methylated regions (DMRs) among different cultivars were identified and many of which were associated with differential expression of genes important for abiotic stress response. Transposon-associated DMRs were found coupled to the transcript abundance of nearby protein-coding gene(s). Small RNA (smRNA) abundance was found to be positively correlated with hypermethylated regions. These results provide insights into interplay among DNA methylation, gene expression and smRNA abundance, and suggest a role in abiotic stress adaptation in rice.
This work was financially supported by the core grant of NIPGR and the Department of Biotechnology,
Government of India, New Delhi. RG acknowledges INSPIRE Faculty Award from the Department
of Science and Technology, Government of India, New Delhi. RS acknowledges the award of research
fellowship from the Department of Biotechnology, Government of India. We are thankful to Prof. Scott
Jackson, University of Georgia, for helpful suggestions.
 
Date 2016-01-04T06:20:26Z
2016-01-04T06:20:26Z
2015
 
Type Article
 
Identifier Scientific Reports, 5: 14922
2045-2322
http://172.16.0.77:8080/jspui/handle/123456789/502
http://www.nature.com/articles/srep14922
10.1038/srep14922
 
Language en_US
 
Publisher Nature Publishing Group