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Assessment of DNA methylation pattern under drought stress using methylation-sensitive randomly amplified polymorphism analysis in rice

Published online by Cambridge University Press:  24 August 2020

Harihar Sapna Open the ORCID record for Harihar Sapna [Opens in a new window] ,
Narasimha Ashwini ,
Sampangiramareddy Ramesh Open the ORCID record for Sampangiramareddy Ramesh [Opens in a new window]  and
Karaba N. Nataraja
Harihar Sapna
Affiliation:
Department of Crop Physiology, University of Agricultural Sciences, Gandhi Krishi Vigyan Kendra, Bengaluru560065, India
Narasimha Ashwini
Affiliation:
Department of Crop Physiology, University of Agricultural Sciences, Gandhi Krishi Vigyan Kendra, Bengaluru560065, India
Sampangiramareddy Ramesh
Affiliation:
Department of Genetics and Plant Breeding, University of Agricultural Sciences, Gandhi Krishi Vigyan Kendra, Bengaluru560065, India
Karaba N. Nataraja*
Affiliation:
Department of Crop Physiology, University of Agricultural Sciences, Gandhi Krishi Vigyan Kendra, Bengaluru560065, India
*
*Corresponding author. E-mail: nataraja_karaba@yahoo.com
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Abstract

DNA methylation is known to regulate gene expression when plants are exposed to abiotic stress such as drought. Therefore, insight into DNA methylation pattern would be useful for a better understanding of the expression profile of genes associated with drought adaptation. In the present study, we attempted to analyse the DNA methylation pattern at the whole-genome level and the expression of a few drought-responsive genes in rice under different regimes of soil water status, i.e. puddled, 100 and 60% field capacities (FC). The methylation-sensitive randomly amplified polymorphic DNA analysis was employed to identify DNA methylation pattern. We observed an increase in DNA methylation at 60% FC, and reduced methylation under 100% FC compared to puddled condition. The genes such as protein phosphatases (PP2C) and phenylalanine ammonia-lyase (PAL) having CpG islands in their promoter region had lower expression level under 100 and 60% FC compared to puddled conditions. Heat shock protein 70 (HSP70) and RNA helicase 25 (RH25), with no CpG islands in their promoter region, exhibited enhanced expression compared to puddled plants. In rice, increased DNA methylation seems to be an important mechanism associated with drought responses, which probably regulates the methylation-sensitive gene expression. The drought-induced changes in DNA methylation would contribute for epigenetic mechanism. The study provided evidence to argue that drought-induced increased methylation might be one of the major mechanisms associated with acclimation responses in field crops like rice.

Keywords

CpG islandDNA methylationdrought stressgene expressionMS-RAPDrice
Type
Research Article
Information
Plant Genetic Resources , Volume 18 , Issue 4 , August 2020 , pp. 222 - 230
Copyright
Copyright © NIAB 2020

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