Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars

Rajkumar, Mohan Singh; Shankar, Rama; Garg, Rohini; Jain, Mukesh

doi:10.1016/j.ygeno.2020.04.005

Cited by 55 publications

(42 citation statements)

References 55 publications

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“…Since CpG islands are predicted targets for methylation, it would be good to examine their relevance using global analysis approach. There is a positive correlation between DNA methylation and gene expression under stress in rice (Rajkumar et al ., 2020), which suggests the relevance of DNA methylation in abiotic stress responses. This study provided only a lead and indicated the need for exploring the importance of CpG islands in the promoter region in regulating DRGs especially under severe stress.…”

Section: Discussionmentioning

confidence: 99%

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

Sapna¹,

Ashwini²,

Ramesh³

et al. 2020

Plant Genet. Resour.

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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.

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Section: Discussionmentioning

confidence: 99%

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

Sapna¹,

Ashwini²,

Ramesh³

et al. 2020

Plant Genet. Resour.

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“…In addition, accumulating epigenomic data in various crops will facilitate the identification of additional candidate targets. For example, genome-wide changes in DNA methylation in response to environmental stress conditions were described in rice [ 304 , 305 ], maize [ 306 ], foxtail millet [ 307 ], and sesame [ 308 ]. These and additional surveys of comparative DNA methylation patterns in response to environmental conditions reveal many possible targets for which causality should be assessed.…”

Section: Gaps In Knowledge and Future Challengesmentioning

confidence: 99%

Epigenetics for Crop Improvement in Times of Global Change

Kakoulidou

Avramidou²,

Baránek

et al. 2021

Biology

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Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity—naturally, genetically, chemically, or environmentally induced—can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.

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“…The interplay between the altered expression profile of water-deficit responsive genes and methylation changes was noted [ 295 ]. Rajkumar et al [ 296 ] studied the methylome of various rice cultivars (desiccation-tolerant: Nagina 22, salinity tolerant: Pokkali and sensitive: IR64) and observed that methylation in the CHH context was most dynamic under desiccation and/or salinity stress conditions in these rice cultivars. Further, they found that hypomethylation in the CHH context was correlated with higher gene expression under desiccation stress in Nagina 22.…”

Section: Plant Epigenetics and Epigenomics: Omics Studies (Methylome By Wgbs And Histone Modifications By Chip-seq)mentioning

confidence: 99%

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

Gogolev

Ahmar

Akpınar³

et al. 2021

Plants

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The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.

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Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars

Cited by 55 publications

References 55 publications

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

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

Epigenetics for Crop Improvement in Times of Global Change

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

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