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Abdulraheem MI, Xiong Y, Moshood AY, Cadenas-Pliego G, Zhang H, Hu J. Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. PLANTS (BASEL, SWITZERLAND) 2024; 13:163. [PMID: 38256717 PMCID: PMC10820249 DOI: 10.3390/plants13020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.
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Affiliation(s)
- Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yani Xiong
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Abiodun Yusuff Moshood
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Gregorio Cadenas-Pliego
- Centro de Investigación en Química Aplicada, Blvd. Enrique Reyna 140, Saltillo 25294, Mexico;
| | - Hao Zhang
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
| | - Jiandong Hu
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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Pokharel BR, Sheri V, Kumar M, Zhang Z, Zhang B. The update and transport of aluminum nanoparticles in plants and their biochemical and molecular phototoxicity on plant growth and development: A systematic review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122875. [PMID: 37931678 DOI: 10.1016/j.envpol.2023.122875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
As aluminum nanoparticles (Al-NPs) are widely used in our daily life and various industries, Al-NPs has been becoming an emerging pollution in the environment. The impact of this NP has been attracting more and more attention from the scientific communities. In this review, we systematically summarized the interactions, uptake, and transport of Al-NPs in the plant system. Al-NPs can enter plants through different pathways and accumulate in various tissues, leading to alter plant growth and development. Al-NPs also affected root, shoot, and leaf characteristics as well as changing nutrient uptake and distribution and inducing oxidative stress via excess reactive radical generation, thereby impairing plant defense systems. Additionally, Al-NPs altered gene expression, which involved in various signaling pathways and metabolic processes in plants, that further altered plants susceptible or tolerant to stressors. The review also emphasized the effects of Al-NP size, surface charge, concentration, and exposure duration on plant growth and development. In the future, more research should be focused on mechanisms underlying Al-NPs phytotoxicity and potential risk to humans and off-target species.
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Affiliation(s)
| | - Vijay Sheri
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, 400019, India
| | - Zhiyong Zhang
- College of Life Sciences, Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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Rehman M, Kundu B, Regon P, Tanti B. Biochemical and molecular properties of Boro rice ( Oryza sativa L.) cultivars under abiotic stresses. 3 Biotech 2023; 13:422. [PMID: 38047036 PMCID: PMC10689613 DOI: 10.1007/s13205-023-03840-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023] Open
Abstract
The present investigation was conducted so as to unravel the various underlying antioxidant enzyme and non-enzyme defence mechanisms in some selected Boro rice cultivars that differ in temperature stress tolerance. Oxidative injury under heat and cold stress, H2O2 level showed a decline in roots and shoots of Boro in stressed condition whilst significant rise in the susceptible varieties was observed under both the stresses. However, susceptible varieties, such as Disang (shoots), Moricha (shoots) and China Boro (roots), showed a decreased H2O2 content at recovery. Under cold stress, roots and shoots of Boro and Laal Bihari showed a decreased level of lipid peroxidises and Boro and Kolong under heat stress. In contrast, significant enhancement of lipid peroxidase was revealed in the susceptible varieties. Remarkable increase in non-enzymatic antioxidants like proline, glutathione and ascorbate content was seen in the shoots of Boro in the treated and the recovery conditions. On the other hand, in enzymatic antioxidants like ascorbate peroxidase, guaiacol peroxidase, superoxide dismutase, catalase, and glutathione reductase activity, marked enhancement in ascorbate peroxidase activity was seen in the roots and the shoots of Boro and Kolong in treated and recovery samples and decreased in Swarnabh under heat stress. The guaiacol peroxidase activity of roots and shoots increased in Boro and Kolong under heat stress, and decreased in China boro and Swarnabh. The superoxide dismutase activity in the roots and shoot of Boro increased significantly under both the stress conditions in treated and recovery. Root and shoots of Swarnabh and Moricha showed decline in SOD activity in stressed conditions. The catalase activity in the case of Boro, showed a significant increase in both its roots and shoots under cold and heat stresses in the treated and the recovery samples. Moreover, under heat stress, the root and the shoots of Boro and Kolong showed the maximum glutathione activity, whilst Swarnabh and China Boro showed reduced glutathione activity at 96 h and recovery. On the other hand, the gene expression pattern of the cold-responsive genes (OsHAN1/OsCYP9B4 and FeSOD1) showed significant upregulation in the tolerant than the sensitive cultivars. Similarly, heat-responsive genes (OsTT1/OsPAB1 and OsHsfC1b) are also highly upregulated in the tolerant than the susceptible ones. Thus, the findings would provide a thorough insight into various non-enzymatic and enzymatic antioxidants and stress-responsive genes of Boro rice that could help in the future rice breeding programmes for cold and heat stresses.
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Affiliation(s)
- Mehzabin Rehman
- Department of Botany, Gauhati University, Guwahati, 781014 Assam India
- Department of Botany, University of Science and Technology, Meghalaya, Ri-Bhoi, Baridua, Meghalaya 793101 India
| | - Bikash Kundu
- Department of Botany, Gauhati University, Guwahati, 781014 Assam India
| | - Preetom Regon
- Department of Botany, Gauhati University, Guwahati, 781014 Assam India
| | - Bhaben Tanti
- Department of Botany, Gauhati University, Guwahati, 781014 Assam India
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Sharma M, Sidhu AK, Samota MK, Gupta M, Koli P, Choudhary M. Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants. Proteomes 2023; 11:38. [PMID: 38133152 PMCID: PMC10747722 DOI: 10.3390/proteomes11040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Abiotic stresses profoundly alter plant growth and development, resulting in yield losses. Plants have evolved adaptive mechanisms to combat these challenges, triggering intricate molecular responses to maintain tissue hydration and temperature stability during stress. A pivotal player in this defense is histone modification, governing gene expression in response to diverse environmental cues. Post-translational modifications (PTMs) of histone tails, including acetylation, phosphorylation, methylation, ubiquitination, and sumoylation, regulate transcription, DNA processes, and stress-related traits. This review comprehensively explores the world of PTMs of histones in plants and their vital role in imparting various abiotic stress tolerance in plants. Techniques, like chromatin immune precipitation (ChIP), ChIP-qPCR, mass spectrometry, and Cleavage Under Targets and Tag mentation, have unveiled the dynamic histone modification landscape within plant cells. The significance of PTMs in enhancing the plants' ability to cope with abiotic stresses has also been discussed. Recent advances in PTM research shed light on the molecular basis of stress tolerance in plants. Understanding the intricate proteome complexity due to various proteoforms/protein variants is a challenging task, but emerging single-cell resolution techniques may help to address such challenges. The review provides the future prospects aimed at harnessing the full potential of PTMs for improved plant responses under changing climate change.
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Affiliation(s)
- Madhvi Sharma
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Amanpreet K. Sidhu
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Mahesh Kumar Samota
- ICAR-Central Institute of Post-Harvest Engineering and Technology, Regional Station, Abohar 152116, India
| | - Mamta Gupta
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
| | - Pushpendra Koli
- Plant Animal Relationship Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi 284003, India;
- Post-Harvest Biosecurity, Murdoch University, Perth, WA 6150, Australia
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
- School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
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Li H, Tahir ul Qamar M, Yang L, Liang J, You J, Wang L. Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement. Int J Mol Sci 2023; 24:3105. [PMID: 36834516 PMCID: PMC9965044 DOI: 10.3390/ijms24043105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame has developed rapidly. Thus far, the genomes of five sesame accessions have been released, including white and black seed sesame. The genome studies reveal the function and structure of the sesame genome, and facilitate the exploitation of molecular markers, the construction of genetic maps and the study of pan-genomes. Methylomics focus on the study of the molecular level changes under different environmental conditions. Transcriptomics provide a powerful tool to study abiotic/biotic stress, organ development, and noncoding RNAs, and proteomics and metabonomics also provide some support in studying abiotic stress and important traits. In addition, the opportunities and challenges of multi-omics in sesame genetics breeding were also described. This review summarizes the current research status of sesame from the perspectives of multi-omics and hopes to provide help for further in-depth research on sesame.
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Affiliation(s)
- Huan Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Junchao Liang
- Jiangxi Province Key Laboratory of Oil Crops Biology, Crop Research Institute, Nanchang Branch of National Center of Oil Crops Improvement, Jiangxi Academy of Agricultural Sciences, Nanchang 330000, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. Int J Genomics 2022; 2022:1092894. [PMID: 35747076 PMCID: PMC9213152 DOI: 10.1155/2022/1092894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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Azmat A, Tanveer Y, Yasmin H, Hassan MN, Shahzad A, Reddy M, Ahmad A. Coactive role of zinc oxide nanoparticles and plant growth promoting rhizobacteria for mitigation of synchronized effects of heat and drought stress in wheat plants. CHEMOSPHERE 2022; 297:133982. [PMID: 35181419 DOI: 10.1016/j.chemosphere.2022.133982] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/17/2022] [Accepted: 02/11/2022] [Indexed: 05/25/2023]
Abstract
This study intended to investigate the potential of the plant growth-promoting rhizobacteria (PGPR) and green synthesized zinc oxide nanoparticles (ZnO-NPs) (fruit extract of Papaya) against heat and drought stress in wheat. The characterization of green-synthesized ZnO-NPs was done through UV-vis spectrophotometry, Fourier-transform infrared spectrometry, X-ray diffraction and scanning electron microscopy. Individual and combination of PGPR (Pseudomonas sp.) and ZnO-NPs (10 ppm) amendments were tested in a pot experiment to upregulate wheat defence system under three stress groups (drought, heat and combined heat and drought stress). Drought and heat stress synergistically caused higher damage to wheat plants than individual heat and drought stress. This observation was confirmed with remarkable higher MDA and hydrogen peroxide (H2O2) content. Treated plants exposed to all stress groups showed an improved wheat growth and stress resistance through better biomass, photosynthetic pigments, nutrients, soluble sugars, protein and indole acetic acid content. Combination of ZnO-NPs and Pseudomonas sp. Protects the plants from all stress groups by producing higher proline, antioxidant enzymes i. e superoxide dismutase, peroxidase, catalase, ascorbate peroxidase, glutathione reductase and dehydroascorbate reductase, and abscisic acid. Moreover, higher stress alleviation by this treatment was manifested by marked reduced electrolyte leakage, MDA and H2O2. The findings of current study confirmed that the synergistic actions of PGPR and ZnO-NPs can rescue plants from both single and combined heat and drought stress.
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Affiliation(s)
- Ammar Azmat
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Yashfa Tanveer
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Humaira Yasmin
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan.
| | | | - Asim Shahzad
- Department of Botany, Mohi- Ud-Din Islamic University, Nerian Sharif, 12080, AJ&K, Pakistan
| | | | - Ajaz Ahmad
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
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Saeed F, Chaudhry UK, Bakhsh A, Raza A, Saeed Y, Bohra A, Varshney RK. Moving Beyond DNA Sequence to Improve Plant Stress Responses. Front Genet 2022; 13:874648. [PMID: 35518351 PMCID: PMC9061961 DOI: 10.3389/fgene.2022.874648] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023] Open
Abstract
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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Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Miao Y, Cong W, Mu J, Fu T, Zhuang T, Yan Y, Kang Y, Yu L, Zhao W, Li H, Lv Y, Zhang J, Rustgi S, Liu B, Ou X. Various potentially toxic element tolerances in different rice genotypes correlate with distinct physiological responses and alterations in DNA methylation. CHEMOSPHERE 2022; 292:133462. [PMID: 34973255 DOI: 10.1016/j.chemosphere.2021.133462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/12/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Potentially toxic elements (PTEs) are harmful to plant growth and reduce crop productivity. In this work, we studied three rice genotypes (T-35, RZ-1, and RZ-2) to quantify the diverse PTE effects and tolerances by examining morphology, physiology, and DNA methylation patterns. Morphological results showed that T-35 exhibits the highest tolerance to all studied PTE stressors (Cu, Cd, Cr). Physiological responses under PTE stresses confirmed earlier findings, where T-35 showed a higher potassium (K+) content and more peroxidase (POD) accumulation in the roots than the other two rice genotypes. The differences in PTE tolerance levels observed among the three rice genotypes were also associated with variations in the heavy metal transportation (HMT) gene expression level. Moreover, methylation-sensitive blotting analysis of the selected genes showed that the DNA methylation changes occurring due to PTE treatments are mainly CHG hypomethylation in T-35 but hypermethylation in RZ-1 and RZ-2. Our results demonstrate a tight relationship among physiological response, expression levels of the HMT genes, and DNA methylation pattern under PTEs stresses. It is also indicated that plants use generic mechanisms to tolerate stresses; however, different genotypes employ different combinations of such tactics to confer tolerance, which results in diverse PTE stress tolerances. These findings shed light on the PTE stresses tolerance mechanism and help direct future breeding activities in rice.
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Affiliation(s)
- Yiling Miao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Weixuan Cong
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jingyao Mu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Tiansi Fu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Tingting Zhuang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China; Changchun Institute of Applied Chemistry Chinese Academy of Sciences, Changchun, 130024, China
| | - Yujia Yan
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Ying Kang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Lina Yu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Wenhao Zhao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Hebing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Yinhe Lv
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jiayu Zhang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC, 29506, USA.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China.
| | - Xiufang Ou
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China.
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Guarino F, Heinze B, Castiglione S, Cicatelli A. Epigenetic Analysis through MSAP-NGS Coupled Technology: The Case Study of White Poplar Monoclonal Populations/Stands. Int J Mol Sci 2020; 21:ijms21197393. [PMID: 33036388 PMCID: PMC7582538 DOI: 10.3390/ijms21197393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 12/19/2022] Open
Abstract
Over the last several decades, several lines of evidence have shown that epigenetic modifications modulate phenotype and mediate an organism’s response to environmental stimuli. Plant DNA is normally highly methylated, although notable differences exist between species. Many biomolecular techniques based on PCR have been developed to analyse DNA methylation status, however a qualitative leap was made with the advent of next-generation sequencing (NGS). In the case of large, repetitive, or not-yet-sequenced genomes characterised by a high level of DNA methylation, the NGS analysis of bisulphite pre-treated DNA is expensive and time consuming, and moreover, in some cases data analysis is a major challenge. Methylation-sensitive amplification polymorphism (MSAP) analysis is a highly effective method to study DNA methylation. The method is based on the comparison of double DNA digestion profiles (EcoRI-HpaII and EcoRI-MspI) to reveal methylation pattern variations. These are often attributable to pedoclimatic and stress conditions which affect all organisms during their lifetime. In our study, five white poplar (Populus alba L.) specimens were collected from different monoclonal stands in the Maltese archipelago, and their DNA was processed by means of an innovative approach where MSAP analysis was followed by NGS. This allowed us to identify genes that were differentially methylated among the different specimens and link them to specific biochemical pathways. Many differentially methylated genes were found to encode transfer RNAs (tRNAs) related to photosynthesis or light reaction pathways. Our results clearly demonstrate that this combinatorial method is suitable for epigenetic studies of unsequenced genomes like P. alba (at the time of study), and to identify epigenetic variations related to stress, probably caused by different and changing pedoclimatic conditions, to which the poplar stands have been exposed.
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Affiliation(s)
- Francesco Guarino
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy; (F.G.); (A.C.)
| | - Berthold Heinze
- Department of Forest Genetics, Austrian Federal Research Centre for Forests, 1131 Vienna, Austria;
| | - Stefano Castiglione
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy; (F.G.); (A.C.)
- Correspondence:
| | - Angela Cicatelli
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy; (F.G.); (A.C.)
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