Delineating the epigenetic regulation of heat and drought response in plants

Singh, Roshan Kumar; Prasad, Manoj

doi:10.1080/07388551.2021.1946004

Cited by 19 publications

(19 citation statements)

References 117 publications

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“…Nucleosome architectures are altered in response to epigenetic changes; however, this alteration does not involve the DNA sequence ( Zhao et al, 2021 ). Gene expression lowers or increases due to histone modification or DNA methylation ( Singh and Prasad, 2021 ). During developmental processes or under any stresses, epigenetic changes in chromatin structure are regular and extremely active ( Bhadouriya et al, 2021 ).…”

Section: Mechanismmentioning

confidence: 99%

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Moving Beyond DNA Sequence to Improve Plant Stress Responses

Saeed

Chaudhry²,

Bakhsh³

et al. 2022

Front. Genet.

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Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.

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Section: Mechanismmentioning

confidence: 99%

“…Patterns of DNA methylation are constant and particular to the exact cell type. These patterns are heritable and remain the same throughout life ( Singh and Prasad, 2021 ).…”

Section: Mechanismmentioning

confidence: 99%

Moving Beyond DNA Sequence to Improve Plant Stress Responses

Saeed

Chaudhry²,

Bakhsh³

et al. 2022

Front. Genet.

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“…Recently, epigenetics, which refers to the heritable and stable alterations in gene expression not attributable to DNA sequence changes or variation ( Peschansky and Wahlestedt, 2014 ), has emerged as a potential research avenue for exploitation in our endeavor to develop climate smart crops ( Crisp et al, 2021 ; Gogolev et al, 2021 ; Kakoulidou et al, 2021 ; Samantara et al, 2021 ). Such epigenetic modifications include DNA methylation, histone proteins/variants rearrangements, micro-RNA (mRNA) induced chromatin remodeling, histone acetylation, ATP-dependent nucleosome remodeling, among others ( McCoy et al, 2021 ; Singh and Prasad, 2021 ). These epigenetic modifications are instituted to modulate spatio-temporal gene expressions in response to external stimuli or specific developmental requirements ( Yuan et al, 2013 ; Singh and Prasad, 2021 ).…”

Section: Genomics and Pan-genomicsmentioning

confidence: 99%

“…Such epigenetic modifications include DNA methylation, histone proteins/variants rearrangements, micro-RNA (mRNA) induced chromatin remodeling, histone acetylation, ATP-dependent nucleosome remodeling, among others ( McCoy et al, 2021 ; Singh and Prasad, 2021 ). These epigenetic modifications are instituted to modulate spatio-temporal gene expressions in response to external stimuli or specific developmental requirements ( Yuan et al, 2013 ; Singh and Prasad, 2021 ). More crucially, these epigenetic alterations involve the development of internal memory marks which assist plants to adapt to several abiotic and biotic stresses via physiological regulation directed by plants‘ epigenetic history (reviewed in Samantara et al, 2021 ; Sun et al, 2021 ).…”

Section: Genomics and Pan-genomicsmentioning

confidence: 99%

“…A collection of examples of epigenetic studies for crop improvement are tabled in a more recent review by Kakoulidou et al, 2021 . Therefore enhancing our understanding of the epigenetic regulation induced gene expressions related to abiotic and biotic stress responses will create more avenues for crop improvement for climate resilience via molecular breeding and/or biotechnological approaches ( Chinnusamy et al, 2013 ; Singh and Prasad, 2021 ). Essentially, with the support of new genome analysis tools, epigenomics can be integrated with the investigation of non-coding RNA, cis-regulatory elements, and other non-genic variations controlling plant abiotic and biotic stress responses ( Crisp et al, 2021 ; Zenda et al, 2021 ), to facilitate epigenetics-assisted breeding of crops ( Gogolev et al, 2021 ).…”

Section: Genomics and Pan-genomicsmentioning

confidence: 99%

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Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

et al. 2021

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Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the “omics” technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

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Unveiling the epigenetic landscape of plants using flow cytometry approach

Jyoti,

Chandel,

Singh

2024

Cytometry Pt A

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Plants are sessile creatures that have to adapt constantly changing environmental circumstances. Plants are subjected to a range of abiotic stressors as a result of unpredictable climate change. Understanding how stress‐responsive genes are regulated can help us better understand how plants can adapt to changing environmental conditions. Epigenetic markers that dynamically change in response to stimuli, such as DNA methylation and histone modifications are known to regulate gene expression. Individual cells or particles' physical and/or chemical properties can be measured using the method known as flow cytometry. It may therefore be used to evaluate changes in DNA methylation, histone modifications, and other epigenetic markers, making it a potent tool for researching epigenetics in plants. We explore the use of flow cytometry as a technique for examining epigenetic traits in this thorough discussion. The separation of cell nuclei and their subsequent labeling with fluorescent antibodies, offering information on the epigenetic mechanisms in plants when utilizing flow cytometry. We also go through the use of high‐throughput data analysis methods to unravel the complex epigenetic processes occurring inside plant systems.

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Delineating the epigenetic regulation of heat and drought response in plants

Cited by 19 publications

References 117 publications

Moving Beyond DNA Sequence to Improve Plant Stress Responses

Moving Beyond DNA Sequence to Improve Plant Stress Responses

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Unveiling the epigenetic landscape of plants using flow cytometry approach

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