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Liu N, Hu Z, Zhang L, Yang Q, Deng L, Terzaghi W, Hua W, Yan M, Liu J, Zheng M. BAPID suppresses the inhibition of BRM on Di19-PR module in response to drought. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39166483 DOI: 10.1111/tpj.16984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/26/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Drought is one of the most important abiotic stresses, and seriously threatens plant development and productivity. Increasing evidence indicates that chromatin remodelers are pivotal for plant drought response. However, molecular mechanisms of chromatin remodelers-mediated plant drought responses remain obscure. In this study, we found a novel interactor of BRM called BRM-associated protein involved in drought response (BAPID), which interacted with SWI/SNF chromatin remodeler BRM and drought-induced transcription factor Di19. Our findings demonstrated that BAPID acted as a positive drought regulator since drought tolerance was increased in BAPID-overexpressing plants, but decreased in BAPID-deficient plants, and physically bound to PR1, PR2, and PR5 promoters to mediate expression of PR genes to defend against dehydration stress. Genetic approaches demonstrated that BRM acted epistatically to BAPID and Di19 in drought response in Arabidopsis. Furthermore, the BAPID protein-inhibited interaction between BRM and Di19, and suppressed the inhibition of BRM on the Di19-PR module by mediating the H3K27me3 deposition at PR loci, thus changing nucleosome accessibility of Di19 and activating transcription of PR genes in response to drought. Our results shed light on the molecular mechanism whereby the BAPID-BRM-Di19-PRs pathway mediates plant drought responses. We provide data improving our understanding of chromatin remodeler-mediated plant drought regulation network.
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Affiliation(s)
- Nian Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Zhiyong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Liang Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Qian Yang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Yuelushan Laboratory, Changsha, 410125, China
| | - Linbin Deng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, USA
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Yuelushan Laboratory, Changsha, 410125, China
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ming Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
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Geras'kin S. Plant adaptation to ionizing radiation: Mechanisms and patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170201. [PMID: 38246389 DOI: 10.1016/j.scitotenv.2024.170201] [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: 10/16/2023] [Revised: 12/21/2023] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
Adaptation to environmental stressors is an essential property of plants that allows them, despite an immobile lifestyle, to survive in a changeable environment. The chain of successive events culminating in the final radiobiological reaction begins with the absorption of energy of ionizing radiation in the cell. Starting from stochastic acts of molecular injury formation, radiation damage gradually acquires deterministic features, which are expressed in a limited number of phenomena that complete plant radiation damage. As plants undergo specialization, the differences between plants and animals become more pronounced, leading to distinct responses to radiation. Chronic radiation exposure may activate biological mechanisms resulting in increased radioresistance of the population. The higher the level of radiation exposure and the sensitivity of plants to radiation, the more intensive the selection. Depending on the circumstances, enhanced radioresistance of a population can be achieved in different ways or has not evolved at all. High dose rates of chronic irradiation leаd to selection for the efficiency of repair systems, while low dose rates activate epigenetic mechanisms that lead to the maintenance of oxidative balance, additional synthesis of chaperones, and control of TEs transposition. Due to huge differences in the radiosensitivity of organisms that make up the ecosystem, irradiation can result in disruption of connections between components of ecosystems which may lead to consequences that can differ drastically from those expected at the organismal and population levels. Therefore, the use of ecological knowledge is essential for understanding the responses of populations and ecosystems to radiation exposure.
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Affiliation(s)
- Stanislav Geras'kin
- Russian Institute of Radiology and Agroecology of NRC "Kurchatov Institute", Kievskoe shosse, 109 km, Obninsk, Kaluga Region 249032, Russia.
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3
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Miloro F, Kis A, Havelda Z, Dalmadi Á. Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation. PLANT CELL REPORTS 2024; 43:96. [PMID: 38480545 PMCID: PMC10937801 DOI: 10.1007/s00299-024-03177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
KEY MESSAGE Barley AGO4 proteins complement expressional changes of epigenetically regulated genes in Arabidopsis ago4-3 mutant and show a distinct affinity for the 5' terminal nucleotide of small RNAs, demonstrating functional conservation and divergence. The function of Argonaute 4 (AGO4) in Arabidopsis thaliana has been extensively characterized; however, its role in monocots, which have large genomes abundantly supplemented with transposable elements (TEs), remains elusive. The study of barley AGO4 proteins can provide insights into the conserved aspects of RNA-directed DNA methylation (RdDM) and could also have further applications in the field of epigenetics or crop improvement. Bioinformatic analysis of RNA sequencing data identified two active AGO4 genes in barley, HvAGO4a and HvAGO4b. These genes function similar to AtAGO4 in an Arabidopsis heterologous complementation system, primarily binding to 24-nucleotide long small RNAs (sRNAs) and triggering methylation at specific target loci. Like AtAGO4, HvAGO4B exhibits a preference for binding sRNAs with 5' adenine residue, while also accepting 5' guanine, uracil, and cytosine residues. In contrast, HvAGO4A selectively binds only sRNAs with a 5' adenine residue. The diverse binding capacity of barley AGO4 proteins is reflected in TE-derived sRNAs and in their varying abundance. Both barley AGO4 proteins effectively restore the levels of extrachromosomal DNA and transcript abundancy of the heat-activated ONSEN retrotransposon to those observed in wild-type Arabidopsis plants. Our study provides insight into the distinct binding specificities and involvement in TE regulation of barley AGO4 proteins in Arabidopsis by heterologous complementation.
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Affiliation(s)
- Fabio Miloro
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - András Kis
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Zoltán Havelda
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - Ágnes Dalmadi
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary.
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary.
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4
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Yolcu S, Skorupa M, Uras ME, Mazur J, Ozyiğit II. Genome-wide identification, phylogenetic classification of histone acetyltransferase genes, and their expression analysis in sugar beet (Beta vulgaris L.) under salt stress. PLANTA 2024; 259:85. [PMID: 38448714 PMCID: PMC10917867 DOI: 10.1007/s00425-024-04361-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
MAIN CONCLUSION This study identified seven histone acetyltransferase-encoding genes (HATs) from Beta vulgaris L. (sugar beet) genome through bioinformatics tools and analyzed their expression profiles under salt stress. Sugar beet HATs are phylogenetically divided into four families: GNAT, MYST, CBP, and TAFII250. The BvHAT genes were differentially transcribed in leaves, stems, and roots of B. vulgaris salt-resistant (Casino) and -sensitive (Bravo) cultivars under salt stress. Histone acetylation is regulated by histone acetyltransferases (HATs), which catalyze ɛ-amino bond formation between lysine residues and acetyl groups with a cofactor, acetyl-CoA. Even though the HATs are known to participate in stress response and development in model plants, little is known about the functions of HATs in crops. In sugar beet (Beta vulgaris L.), they have not yet been identified and characterized. Here, an in silico analysis of the HAT gene family in sugar beet was performed, and their expression patterns in leaves, stems, and roots of B. vulgaris were analyzed under salt stress. Salt-resistant (Casino) and -sensitive (Bravo) beet cultivars were used for gene expression assays. Seven HATs were identified from sugar beet genome, and named BvHAG1, BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2, and BvHAF1. The HAT proteins were divided into 4 groups including MYST, GNAT (GCN5, HAT1, ELP3), CBP and TAFII250. Analysis of cis-acting elements indicated that the BvHAT genes might be involved in hormonal regulation, light response, plant development, and abiotic stress response. The BvHAT genes were differentially expressed in leaves, stems, and roots under control and 300 mM NaCl. In roots of B. vulgaris cv. Bravo, the BvHAG1, BvHAG2, BvHAG4, BvHAF1, and BvHAC1 genes were dramatically expressed after 7 and 14 days of salt stress. Interestingly, the BvHAC2 gene was not expressed under both control and stress conditions. However, the expression of BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2 genes showed a significant increase in response to salt stress in the roots of cv. Casino. This study provides new insights into the potential roles of histone acetyltransferases in sugar beet.
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Affiliation(s)
- Seher Yolcu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Türkiye.
| | - Monika Skorupa
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100, Torun, Poland
| | - Mehmet Emin Uras
- Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Haliç University, 34060, Istanbul, Türkiye
| | - Justyna Mazur
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100, Torun, Poland
| | - Ibrahim Ilker Ozyiğit
- Faculty of Science, Department of Biology, Marmara University, 34722, Istanbul, Türkiye
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5
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Yu X, Yu K, Chen B, Liao Z, Liang J, Qin Z, Gao X. Metabolic and immune costs balance during natural acclimation of corals in fluctuating environments. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106284. [PMID: 38048660 DOI: 10.1016/j.marenvres.2023.106284] [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: 09/22/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023]
Abstract
Epigenetic modifications based on DNA methylation can rapidly improve the potential of corals to adapt to environmental pressures by increasing their phenotypic plasticity, a factor important for scleractinian corals to adapt to future global warming. However, the extent to which corals develop similar adaptive mechanisms and their specific adaptation processes remain unclear. Here, to reveal the regulatory mechanism by which DNA methylation improves thermal tolerance in Pocillopora damicornis under fluctuating environments, we analyzed genome-wide DNA methylation signatures in P. damicornis and compared the differences in the methylation and transcriptional responses of P. damicornis from fluctuating and stable environments using whole-genome bisulfite sequencing and nanopore-based RNA sequencingtranscriptome sequencing. We discovered low methylation levels in P. damicornis (average methylation 4.14%), with CpG accounting for 74.88%, CHH for 13.27%, and CHG for 11.85% of this methylation. However, methylation levels did not change between coral samples from the fluctuating and stable environments. The varied methylation levels in different regions of the gene revealed that the overall methylation level of the gene body was relatively high and showed a bimodal methylation pattern. Methylation occurs primarily in exons rather than introns within the gene body In P. damicornis, there was only a weak correlation between methylation and transcriptional changes at the individual gene level, and the methylation and gene expression levels generally exhibited a bell-shaped relationship, which we speculate may be due to the specificity of cnidarian species. Correlation analysis between methylation levels and the transcriptome revealed that the highest proportion of the top 20 enriched KEGG pathways was related to immunity. Additionally, P. damicornis collected from a high-temperature pool had a lower metabolic rate than those collected from a low-temperature pool. We hypothesize that the dynamic balance of energy-expenditure costs between immunity and metabolism is an important strategy for increasing P. damicornis tolerance. The fluctuating environment of high-temperature pools may increase the heat tolerance in corals by increasing their immunity and thus lowering their metabolism.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Xu Gao
- Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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6
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Gryzinska M, Kot B, Dudzinska E, Biernasiuk A, Jakubczak A, Malm A, Andraszek K. Changes in the Level of DNA Methylation in Candida albicans under the Influence of Physical and Chemical Factors. Int J Mol Sci 2023; 24:15873. [PMID: 37958861 PMCID: PMC10647513 DOI: 10.3390/ijms242115873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
The effects of physical factors such as radiation (electromagnetic, microwave, infrared, laser, UVC, and X-ray) and high temperature, as well as chemical factors (controlled atmosphere) on the level of global DNA cytosine methylation in C. albicans ATCC 10231 cells were investigated. Prolonged exposure to each type of radiation significantly increased the DNA methylation level. In addition, the global methylation level in C. albicans cells increased with the incubation temperature. An increase in the percentage of methylated DNA was also noted in C. albicans cells cultured in an atmosphere with reduced O2. In contrast, in an atmosphere containing more than 3% CO2 and in anaerobic conditions, the DNA methylation level decreased relative to the control. This study showed that prolonged exposure to various types of radiation and high temperature as well as reduced O2 in the atmosphere caused a significant increase in the global DNA methylation level. This is most likely a response protecting DNA against damage, which at the same time can lead to epigenetic disorders, and in consequence can adversely affect the functioning of the organism.
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Affiliation(s)
- Magdalena Gryzinska
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland;
| | - Barbara Kot
- Institute of Biological Sciences, University of Siedlce, 08-110 Siedlce, Poland
| | - Ewa Dudzinska
- Department of Dietetics and Nutrition Education, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Anna Biernasiuk
- Chair and Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.M.)
| | - Andrzej Jakubczak
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland;
| | - Anna Malm
- Chair and Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.M.)
| | - Katarzyna Andraszek
- Institute of Animal Science and Fisheries, University of Siedlce, 08–110 Siedlce, Poland;
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7
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Zhu W, Yang C, Liu Q, Peng M, Li Q, Wang H, Chen X, Zhang B, Feng P, Chen T, Zeng D, Zhao Y. Integrated Analysis of DNA Methylome and Transcriptome Reveals Epigenetic Regulation of Cold Tolerance in Litopenaeus vannamei. Int J Mol Sci 2023; 24:11573. [PMID: 37511332 PMCID: PMC10380378 DOI: 10.3390/ijms241411573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
DNA methylation is an important epigenetic modification that has been shown to be associated with responses to non-biological stressors. However, there is currently no research on DNA methylation in response to environmental signals in shrimp. In this study, we conducted a comprehensive comparative analysis of DNA methylation profiles and differentially expressed genes between two strains of Litopenaeus vannamei with significantly different cold tolerance through whole genome bisulfite sequencing (WGBS) and transcriptome sequencing. Between Lv-C and Lv-T (constant temperature of 28 °C and low temperatures of 18 °C and 10 °C) under cytosine-guanine (CG) environments, 39,100 differentially methylated regions (DMRs) were identified, corresponding to 9302 DMR-related genes (DMRGs). The DMRs were mainly located in the gene body (exons and introns). Gene Ontology (GO) analysis showed that these DMRGs were significantly enriched in cell parts, catalytic activity, and metabolic processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed significant enrichment of these DMRGs in pathways such as proteasome (ko03050), oxidative phosphorylation (ko00190), mTOR signaling pathway (ko04150), fatty acid metabolism (ko01212), and fatty acid degradation (ko00071). The comprehensive results suggested that L. vannamei mainly regulates gene expression in response to low temperatures through hypermethylation or demethylation of some genes involved in thermogenesis, glycolysis, the autophagy pathway, the peroxisome, and drug metabolism pathways. These results provide important clues for studying DNA methylation patterns and identifying cold tolerance genes in shrimp.
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Affiliation(s)
- Weilin Zhu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery Huazhong Agricultural University, Wuhan 430070, China
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Bin Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Pengfei Feng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Tiancong Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
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8
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Dar AM, Touseef H, Nawaz K, Khan Y, Sahu PP. Editorial: Genomics in plant sciences: understanding and development of stress-tolerant plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1222818. [PMID: 37351219 PMCID: PMC10282997 DOI: 10.3389/fpls.2023.1222818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Affiliation(s)
- Ayaz Mahmood Dar
- Organic and Biomolecular Research, Department of Higher Education (GDC Sogam), University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Hussain Touseef
- Sevama AgriClinic and Laboratory, MatI Mate Agromart Pvt. Ltd., Bhavnagar, Gujarat, India
| | - Kashif Nawaz
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Köln, Germany
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Yusuf Khan
- Newborn Screening Department, University Hospital, Oslo, Norway
| | - Pranav Pankaj Sahu
- Laboratory of Ecological Plant Physiology, Global Change Research Institute of the Czech Academy of Sciences, Brno, Czechia
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9
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Laanen P, Cuypers A, Saenen E, Horemans N. Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:246-259. [PMID: 36731286 DOI: 10.1016/j.plaphy.2023.01.049] [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: 06/27/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.
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Affiliation(s)
- Pol Laanen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Ann Cuypers
- Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Eline Saenen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium.
| | - Nele Horemans
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
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10
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Tan JW, Shinde H, Tesfamicael K, Hu Y, Fruzangohar M, Tricker P, Baumann U, Edwards EJ, Rodríguez López CM. Global transcriptome and gene co-expression network analyses reveal regulatory and non-additive effects of drought and heat stress in grapevine. FRONTIERS IN PLANT SCIENCE 2023; 14:1096225. [PMID: 36818880 PMCID: PMC9932518 DOI: 10.3389/fpls.2023.1096225] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Despite frequent co-occurrence of drought and heat stress, the molecular mechanisms governing plant responses to these stresses in combination have not often been studied. This is particularly evident in non-model, perennial plants. We conducted large scale physiological and transcriptome analyses to identify genes and pathways associated with grapevine response to drought and/or heat stress during stress progression and recovery. We identified gene clusters with expression correlated to leaf temperature and water stress and five hub genes for the combined stress co-expression network. Several differentially expressed genes were common to the individual and combined stresses, but the majority were unique to the individual or combined stress treatments. These included heat-shock proteins, mitogen-activated kinases, sugar metabolizing enzymes, and transcription factors, while phenylpropanoid biosynthesis and histone modifying genes were unique to the combined stress treatment. Following physiological recovery, differentially expressed genes were found only in plants under heat stress, both alone and combined with drought. Taken collectively, our results suggest that the effect of the combined stress on physiology and gene expression is more severe than that of individual stresses, but not simply additive, and that epigenetic chromatin modifications may play an important role in grapevine responses to combined drought and heat stress.
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Affiliation(s)
- Jia W. Tan
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Harshraj Shinde
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Kiflu Tesfamicael
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
- School of Biological Science, The University of Adelaide, Adelaide, SA, Australia
| | - Yikang Hu
- School of Biological Science, The University of Adelaide, Adelaide, SA, Australia
| | - Mario Fruzangohar
- The Biometry Hub, School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Penny Tricker
- School of Agriculture, Food and Wine, The University of Adelaide, Hartley Grove, SA, Australia
- The New Zealand Institute for Plant and Food Research Limited, Plant & Food Research Canterbury Agriculture & Science Centre, Lincoln, New Zealand
| | - Ute Baumann
- School of Agriculture, Food and Wine, The University of Adelaide, Hartley Grove, SA, Australia
| | - Everard J. Edwards
- The Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture & Food, Glen Osmond, SA, Australia
| | - Carlos M. Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
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11
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Ferrari M, Muto A, Bruno L, Cozza R. DNA Methylation in Algae and Its Impact on Abiotic Stress Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:241. [PMID: 36678953 PMCID: PMC9861306 DOI: 10.3390/plants12020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites.
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12
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Vogt G. Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics. EPIGENOMES 2022; 7:1. [PMID: 36648862 PMCID: PMC9844400 DOI: 10.3390/epigenomes7010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
Organisms adapt to different environments by selection of the most suitable phenotypes from the standing genetic variation or by phenotypic plasticity, the ability of single genotypes to produce different phenotypes in different environments. Because of near genetic identity, asexually reproducing populations are particularly suitable for the investigation of the potential and molecular underpinning of the latter alternative in depth. Recent analyses on the whole-genome scale of differently adapted clonal animals and plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are among the molecular pathways supporting phenotypic plasticity and that epigenetic variation is used to stably adapt to different environments. Case studies revealed habitat-specific epigenetic fingerprints that were maintained over subsequent years pointing at the existence of epigenetic ecotypes. Environmentally induced epimutations and corresponding gene expression changes provide an ideal means for fast and directional adaptation to changing or new conditions, because they can synchronously alter phenotypes in many population members. Because microorganisms inclusive of human pathogens also exploit epigenetically mediated phenotypic variation for environmental adaptation, this phenomenon is considered a universal biological principle. The production of different phenotypes from the same DNA sequence in response to environmental cues by epigenetic mechanisms also provides a mechanistic explanation for the "general-purpose genotype hypothesis" and the "genetic paradox of invasions".
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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13
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Nunez-Vazquez R, Desvoyes B, Gutierrez C. Histone variants and modifications during abiotic stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:984702. [PMID: 36589114 PMCID: PMC9797984 DOI: 10.3389/fpls.2022.984702] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/28/2022] [Indexed: 06/17/2023]
Abstract
Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.
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14
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Liu Y, Wang J, Liu B, Xu ZY. Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2252-2274. [PMID: 36149776 DOI: 10.1111/jipb.13368] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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15
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Sen MK, Hamouzová K, Košnarová P, Roy A, Soukup J. Herbicide resistance in grass weeds: Epigenetic regulation matters too. FRONTIERS IN PLANT SCIENCE 2022; 13:1040958. [PMID: 36438151 PMCID: PMC9685620 DOI: 10.3389/fpls.2022.1040958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Although herbicides have been successfully used for controlling weeds, their continuous use has developed in the evolution of resistance to all major herbicide modes of action worldwide. Reports suggest that the members of Poaceae family are more prone to developing herbicide resistance than other families. In plants, epigenetic mechanisms play critical roles by increasing their stress-adaptive potential in a rapidly changing environment. Epigenetic mechanisms involve alteration of the expression of genetic elements, but without any changes in the DNA sequence. Although the possible roles of epigenetic mechanisms in contributing to survival and fitness under various stresses are well documented in model plants and crops, their contribution to herbicide resistance in weeds is still in its infancy. A few studies with herbicides have shown differential expression of DNA methyltransferases, histone methyltransferases and DNA demethylases in response to the herbicides; however, no further studies were conducted. In the case of herbicide stress, exploring how these epigenetic processes affect the gene expression pattern in individual plants subjected to recurrent selection would be exciting. Hence, our mini-review will focus on the potential contributions of epigenetic mechanisms to the adaptive responses of grass-weedy species to herbicide stress. A better understanding of these epigenetic changes will add novel perceptions to our knowledge of herbicide resistance evolution in weeds enabling the development of herbicides with novel targets.
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Affiliation(s)
- Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Katerina Hamouzová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Pavlína Košnarová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Amit Roy
- Excellent Team for Mitigation (E.T.M.), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Praha, Czechia
| | - Josef Soukup
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
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16
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Jia L, Yang Y, Zhai H, He S, Xin G, Zhao N, Zhang H, Gao S, Liu Q. Production and characterization of a novel interspecific somatic hybrid combining drought tolerance and high quality of sweet potato and Ipomoea triloba L. PLANT CELL REPORTS 2022; 41:2159-2171. [PMID: 35943560 DOI: 10.1007/s00299-022-02912-8] [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: 04/19/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
A novel interspecific somatic hybrid combining drought tolerance and high quality of sweet potato and Ipomoea triloba L. was obtained and its genetic and epigenetic variations were studied. Somatic hybridization can be used to overcome the cross-incompatibility between sweet potato (Ipomoea batatas (L.) Lam.) and its wild relatives and transfer useful and desirable genes from wild relatives to cultivated plants. However, most of the interspecific somatic hybrids obtained to date cannot produce storage roots and do not exhibit agronomic characters. In the present study, a novel interspecific somatic hybrid, named XT1, was obtained through protoplast fusion between sweet potato cv. Xushu 18 and its wild relative I. triloba. This somatic hybrid produced storage roots and exhibited significantly higher drought tolerance and quality compared with its cultivated parent Xushu 18. Transcriptome and real-time quantitative PCR (qRT-PCR) analyses revealed that the well-known drought stress-responsive genes in XT1 and I. triloba were significantly up-regulated under drought stress. The genomic structural reconstructions between the two genomes of the fusion parents in XT1 were confirmed using genomic in situ hybridization (GISH) and specific nuclear and cytoplasmic DNA markers. The DNA methylation variations were characterized by methylation-sensitive amplified polymorphism (MSAP). This study not only reveals the significance of somatic hybridization in the genetic improvement of sweet potato but also provides valuable materials and knowledge for further investigating the mechanism of storage root formation in sweet potato.
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Affiliation(s)
- Licong Jia
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Yufeng Yang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Guosheng Xin
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China.
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17
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Shi M, Wang C, Wang P, Zhang M, Liao W. Methylation in DNA, histone, and RNA during flowering under stress condition: A review. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111431. [PMID: 36028071 DOI: 10.1016/j.plantsci.2022.111431] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/07/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Flowering is the most critical transition period in the whole lifecycle of plants, and it is a highly sensitive period to stress. New combinations of temperature, drought stress, carbon dioxide and other abiotic/biotic conditions resulting from contemporary climate change affect the flowering process. Plants have evolved several strategies to deal with environmental stresses, including epigenetic modifications. Numerous studies show that environmental stresses trigger methylation/demethylation during flowering to preserve/accelerate plant lifecycle. What's more, histone and DNA methylation can be induced to respond to stresses, resulting in changes of flowering gene expression and enhancing stress tolerance in plants. Furthermore, RNA methylation may influence stress-regulated flowering by regulating mRNA stability and antioxidant mechanism. Our review presents the involvement of methylation in stress-repressed and stress-induced flowering. The crosstalk between methylation and small RNAs, phytohormones and exogenous substances (such as salicylic acid, nitric oxide) during flowering under different stresses were discussed. The latest regulatory evidence of RNA methylation in stress-regulated flowering was collected for the first time. Meanwhile, the limited evidences of methylation in biotic stress-induced flowering were summarized. Thus, the review provides insights into understanding of methylation mechanism in stress-regulated flowering and makes use for the development of regulating plant flowering at epigenetic level in the future.
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Affiliation(s)
- Meimei Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Peng Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Meiling Zhang
- College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China.
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18
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Yang Z, Yan H, Wang J, Nie G, Feng G, Xu X, Li D, Huang L, Zhang X. DNA hypermethylation promotes the flowering of orchardgrass during vernalization. PLANT PHYSIOLOGY 2022; 190:1490-1505. [PMID: 35861426 PMCID: PMC9516772 DOI: 10.1093/plphys/kiac335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Vernalization, influenced by environmental factors, is an essential process associated with the productivity of temperate crops, during which epigenetic regulation of gene expression plays an important role. Although DNA methylation is one of the major epigenetic mechanisms associated with the control of gene expression, global changes in DNA methylation in the regulation of gene expression during vernalization-induced flowering of temperate plants remain largely undetermined. To characterize vernalization-associated DNA methylation dynamics, we performed whole-genome bisulfite-treated sequencing and transcriptome sequencing in orchardgrass (Dactylis glomerata) during vernalization. The results revealed that increased levels of genome DNA methylation during the early vernalization of orchardgrass were associated with transcriptional changes in DNA methyltransferase and demethylase genes. Upregulated expression of vernalization-related genes during early vernalization was attributable to an increase in mCHH in the promoter regions of these genes. Application of an exogenous DNA methylation accelerator or overexpression of orchardgrass NUCLEAR POLY(A) POLYMERASE (DgPAPS4) promoted earlier flowering, indicating that DNA hypermethylation plays an important role in vernalization-induced flowering. Collectively, our findings revealed that vernalization-induced hypermethylation is responsible for floral primordium initiation and development. These observations provide a theoretical foundation for further studies on the molecular mechanisms underlying the control of vernalization in temperate grasses.
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Affiliation(s)
| | | | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, Florida 32611, USA
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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19
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Müller LM, Bahn M. Drought legacies and ecosystem responses to subsequent drought. GLOBAL CHANGE BIOLOGY 2022; 28:5086-5103. [PMID: 35607942 PMCID: PMC9542112 DOI: 10.1111/gcb.16270] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 05/19/2023]
Abstract
Climate change is expected to increase the frequency and severity of droughts. These events, which can cause significant perturbations of terrestrial ecosystems and potentially long-term impacts on ecosystem structure and functioning after the drought has subsided are often called 'drought legacies'. While the immediate effects of drought on ecosystems have been comparatively well characterized, our broader understanding of drought legacies is just emerging. Drought legacies can relate to all aspects of ecosystem structure and functioning, involving changes at the species and the community scale as well as alterations of soil properties. This has consequences for ecosystem responses to subsequent drought. Here, we synthesize current knowledge on drought legacies and the underlying mechanisms. We highlight the relevance of legacy duration to different ecosystem processes using examples of carbon cycling and community composition. We present hypotheses characterizing how intrinsic (i.e. biotic and abiotic properties and processes) and extrinsic (i.e. drought timing, severity, and frequency) factors could alter resilience trajectories under scenarios of recurrent drought events. We propose ways for improving our understanding of drought legacies and their implications for subsequent drought events, needed to assess the longer-term consequences of droughts on ecosystem structure and functioning.
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Affiliation(s)
- Lena M. Müller
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Michael Bahn
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
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20
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Molecular and epigenetic basis of heat stress responses and acclimatization in plants. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00400-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Wang N, Lin Y, Qi F, Xiaoyang C, Peng Z, Yu Y, Liu Y, Zhang J, Qi X, Deyholos M, Zhang J. Comprehensive Analysis of Differentially Expressed Genes and Epigenetic Modification-Related Expression Variation Induced by Saline Stress at Seedling Stage in Fiber and Oil Flax, Linum usitatissimum L. PLANTS (BASEL, SWITZERLAND) 2022; 11:2053. [PMID: 35956530 PMCID: PMC9370232 DOI: 10.3390/plants11152053] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/23/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The ability of different germplasm to adapt to a saline-alkali environment is critical to learning about the tolerance mechanism of saline-alkali stress in plants. Flax is an important oil and fiber crop in many countries. However, its molecular tolerance mechanism under saline stress is still not clear. In this study, we studied morphological, physiological characteristics, and gene expression variation in the root and leaf in oil and fiber flax types under saline stress, respectively. Abundant differentially expressed genes (DEGs) induced by saline stress, tissue/organ specificity, and different genotypes involved in plant hormones synthesis and metabolism and transcription factors and epigenetic modifications were detected. The present report provides useful information about the mechanism of flax response to saline stress and could lead to the future elucidation of the specific functions of these genes and help to breed suitable flax varieties for saline/alkaline soil conditions.
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Affiliation(s)
- Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Yujie Lin
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Chunxiao Xiaoyang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun 130000, China
| | - Ying Yu
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Yingnan Liu
- Institute of Natural Resource and Ecology, Heilongjiang Academy of Science, Harbin 150040, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Xin Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
| | - Michael Deyholos
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC V1V 1V7, Canada
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22
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Chandana BS, Mahto RK, Singh RK, Ford R, Vaghefi N, Gupta SK, Yadav HK, Manohar M, Kumar R. Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea. Front Genet 2022; 13:900253. [PMID: 35937986 PMCID: PMC9355295 DOI: 10.3389/fgene.2022.900253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.
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Affiliation(s)
- B. S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | | | - Rebecca Ford
- Center for Planetary Health and Food Security, Griffith University, Brisbane, QLD, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | | | | | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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23
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Plant DNA Methylation Responds to Nutrient Stress. Genes (Basel) 2022; 13:genes13060992. [PMID: 35741754 PMCID: PMC9222553 DOI: 10.3390/genes13060992] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 12/16/2022] Open
Abstract
Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification that can effectively regulate genome stability. Exploring DNA methylation responses to nutrient stress could lay the foundation for improving plant tolerance to nutrient stress. This article summarizes the plant DNA methylation patterns, the effects of nutrient stress, such as nitrogen, phosphorus, iron, zinc and sulfur stress, on plant DNA methylation and research techniques for plant DNA methylation, etc. Our discussion provides insight for further research on epigenetics response to nutrient stress in the future.
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24
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Kumari P, Khan S, Wani IA, Gupta R, Verma S, Alam P, Alaklabi A. Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal. Front Genet 2022; 13:819941. [PMID: 35664328 PMCID: PMC9157814 DOI: 10.3389/fgene.2022.819941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression patterns which occur without altering DNA sequence. These changes are reversible and do not change the sequence of the DNA but can alter the way in which the DNA sequences are read. Epigenetic modifications are induced by DNA methylation, histone modification, and RNA-mediated mechanisms which alter the gene expression, primarily at the transcriptional level. Such alterations do control genome activity through transcriptional silencing of transposable elements thereby contributing toward genome stability. Plants being sessile in nature are highly susceptible to the extremes of changing environmental conditions. This increases the likelihood of epigenetic modifications within the composite network of genes that affect the developmental changes of a plant species. Genetic and epigenetic reprogramming enhances the growth and development, imparts phenotypic plasticity, and also ensures flowering under stress conditions without changing the genotype for several generations. Epigenetic modifications hold an immense significance during the development of male and female gametophytes, fertilization, embryogenesis, fruit formation, and seed germination. In this review, we focus on the mechanism of epigenetic modifications and their dynamic role in maintaining the genomic integrity during plant development and reproduction.
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Affiliation(s)
- Priyanka Kumari
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajid Khan
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ishfaq Ahmad Wani
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Renu Gupta
- Division of Soil Sciences & Agricultural Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha, India
| | - Susheel Verma
- Department of Botany, University of Jammu, Jammu, India
- *Correspondence: Susheel Verma,
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University (PSAU), Alkharj, Saudi Arabia
| | - Abdullah Alaklabi
- Department of Biology, College of Science, University of Bisha, Bisha, Saudi Arabia
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Tomczyk PP, Kiedrzyński M, Forma E, Zielińska KM, Kiedrzyńska E. Changes in global DNA methylation under climatic stress in two related grasses suggest a possible role of epigenetics in the ecological success of polyploids. Sci Rep 2022; 12:8322. [PMID: 35585117 PMCID: PMC9117213 DOI: 10.1038/s41598-022-12125-4] [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: 07/11/2021] [Accepted: 04/29/2022] [Indexed: 11/23/2022] Open
Abstract
Polyploidization drives the evolution of grasses and can result in epigenetic changes, which may have a role in the creation of new evolutionary lineages and ecological speciation. As such changes may be inherited, they can also influence adaptation to the environment. Populations from different regions and climates may also differ epigenetically; however, this phenomenon is poorly understood. The present study analyzes the effect of climatic stress on global DNA methylation based on a garden collection of two related mountain grasses (the narrow endemic diploid Festuca tatrae and the more widely distributed mixed-ploidy F. amethystina) with different geographic ranges and ecological niches. A lower level of DNA methylation was observed for F. tatrae, while a higher mean level was obtained for the diploid and tetraploid of F. amethystina; with the tetraploids having a higher level of global methylated DNA than the diploids. The weather conditions (especially insolation) measured 24 h prior to sampling appeared to have a closer relationship with global DNA methylation level than those observed seven days before sampling. Our findings suggest that the level of methylation during stress conditions (drought, high temperature and high insolation) may be significantly influenced by the ploidy level and bioclimatic provenance of specimens; however an important role may also be played by the intensity of stress conditions in a given year.
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Affiliation(s)
- Przemysław P Tomczyk
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237, Lodz, Poland. .,The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland.
| | - Marcin Kiedrzyński
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237, Lodz, Poland
| | - Ewa Forma
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Katarzyna M Zielińska
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237, Lodz, Poland
| | - Edyta Kiedrzyńska
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90-364, Lodz, Poland.,UNESCO Chair On Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
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Cui C, Wang Z, Su Y, Wang T. Antioxidant Regulation and DNA Methylation Dynamics During Mikania micrantha Seed Germination Under Cold Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:856527. [PMID: 35463422 PMCID: PMC9024368 DOI: 10.3389/fpls.2022.856527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
As a primary goal, adaptation to cold climate could expand an invasion range of exotic plants. Here, we aimed to explore the regulation strategy of M. micrantha seed development under cold stress through molecular physiology and multi-omics analysis. Significant increase of hydrogen peroxide, malondialdehyde, and electrolyte leakage observed under cold stress revealed that oxidative damage within M. micrantha seed cells was induced in the initial germination phase. Proteomic data underscored an activation of antioxidant activity to maintain redox homeostasis, with a cluster of antioxidant proteins identified. Genomic-wide transcriptome, in combination with time-series whole-genome bisulfite sequencing mining, elucidated that seven candidate genes, which were the target of DNA demethylation-dependent ROS scavenging, were possibly associated with an M. micrantha germ break. Progressive gain of CHH context DNA methylation identified in an early germination phrase suggested a role of a DNA methylation pathway, while an active DNA demethylation pathway was also initiated during late seed development, which was in line with the expression trend of methylation and demethylation-related genes verified through qRT-PCR. These data pointed out that cold-dependent DNA demethylation and an antioxidant regulatory were involved together in restoring seed germination. The expression level of total 441 genes presented an opposite trend to the methylation divergence, while the expression of total 395 genes was proved to be negatively associated with their methylation levels. These data provided new insights into molecular reprograming events during M. micrantha seed development.
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Affiliation(s)
- Can Cui
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Ting Wang
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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Miryeganeh M, Marlétaz F, Gavriouchkina D, Saze H. De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza. THE NEW PHYTOLOGIST 2022; 233:2094-2110. [PMID: 34532854 PMCID: PMC9293310 DOI: 10.1111/nph.17738] [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: 06/27/2021] [Accepted: 09/02/2021] [Indexed: 05/27/2023]
Abstract
Mangroves are adapted to harsh environments, such as high ultraviolet (UV) light, low nutrition, and fluctuating salinity in coastal zones. However, little is known about the transcriptomic and epigenomic basis of the resilience of mangroves due to limited available genome resources. We performed a de novo genome assembly and in natura epigenome analyses of the mangrove Bruguiera gymnorhiza, one of the dominant mangrove species. We also performed the first genome-guided transcriptome assembly for mangrove species. The 309 Mb of the genome is predicted to encode 34 403 genes and has a repeat content of 48%. Depending on its growing environment, the natural B. gymnorhiza population showed drastic morphological changes associated with expression changes in thousands of genes. Moreover, high-salinity environments induced genome-wide DNA hypermethylation of transposable elements (TEs) in the B. gymnorhiza. DNA hypermethylation was concurrent with the transcriptional regulation of chromatin modifier genes, suggesting robust epigenome regulation of TEs in the B. gymnorhiza genome under high-salinity environments. The genome and epigenome data in this study provide novel insights into the epigenome regulation of mangroves and a better understanding of the adaptation of plants to fluctuating, harsh natural environments.
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Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
| | - Ferdinand Marlétaz
- Department of Genetics, Evolution and Environment (GEE)University College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Daria Gavriouchkina
- Molecular Genetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
| | - Hidetoshi Saze
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
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Kumar S, Seem K, Kumar S, Vinod KK, Chinnusamy V, Mohapatra T. Pup1 QTL Regulates Gene Expression Through Epigenetic Modification of DNA Under Phosphate Starvation Stress in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:871890. [PMID: 35712593 PMCID: PMC9195100 DOI: 10.3389/fpls.2022.871890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/29/2022] [Indexed: 05/03/2023]
Abstract
Cytosine methylation, epigenetic DNA modification, is well known to regulate gene expression. Among the epigenetic modifications, 5-methylcytosine (5-mC) has been one of the extensively studied epigenetic changes responsible for regulating gene expression in animals and plants. Though a dramatic change in 5-mC content is observed at the genome level, the variation in gene expression is generally less than that it is expected. Only less is understood about the significance of 5-mC in gene regulation under P-starvation stress in plants. Using whole-genome bisulfite sequencing of a pair of rice [Pusa-44 and its near-isogenic line (NIL)-23 harboring Pup1 QTL] genotypes, we could decipher the role of Pup1 on DNA (de)methylation-mediated regulation of gene expression under P-starvation stress. We observed 13-15% of total cytosines to be methylated in the rice genome, which increased significantly under the stress. The number of differentially methylated regions (DMRs) for hypomethylation (6,068) was higher than those (5,279) for hypermethylated DMRs under the stress, particularly in root of NIL-23. Hypomethylation in CHH context caused upregulated expression of 489 genes in shoot and 382 genes in root of NIL-23 under the stress, wherein 387 genes in shoot and 240 genes in root were upregulated exclusively in NIL-23. Many of the genes for DNA methylation, a few for DNA demethylation, and RNA-directed DNA methylation were upregulated in root of NIL-23 under the stress. Methylation or demethylation of DNA in genic regions differentially affected gene expression. Correlation analysis for the distribution of DMRs and gene expression indicated the regulation of gene mainly through (de)methylation of promoter. Many of the P-responsive genes were hypomethylated or upregulated in roots of NIL-23 under the stress. Hypermethylation of gene body in CG, CHG, and CHH contexts caused up- or downregulated expression of transcription factors (TFs), P transporters, phosphoesterases, retrotransposon proteins, and other proteins. Our integrated transcriptome and methylome analyses revealed an important role of the Pup1 QTL in epigenetic regulation of the genes for transporters, TFs, phosphatases, carbohydrate metabolism, hormone-signaling, and chromatin architecture or epigenetic modifications in P-starvation tolerance. This provides insights into the molecular function of Pup1 in modulating gene expression through DNA (de)methylation, which might be useful in improving P-use efficiency or productivity of rice in P-deficient soil.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Suresh Kumar ; ; orcid.org/0000-0002-7127-3079
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - K. K. Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Saradadevi GP, Das D, Mangrauthia SK, Mohapatra S, Chikkaputtaiah C, Roorkiwal M, Solanki M, Sundaram RM, Chirravuri NN, Sakhare AS, Kota S, Varshney RK, Mohannath G. Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review. BIOLOGY 2021; 10:biology10121255. [PMID: 34943170 PMCID: PMC8698797 DOI: 10.3390/biology10121255] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022]
Abstract
Simple Summary Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses. Abstract Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.
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Affiliation(s)
- Gargi Prasad Saradadevi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Satendra K. Mangrauthia
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Sridev Mohapatra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Manish Solanki
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Raman Meenakshi Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Neeraja N. Chirravuri
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Akshay S. Sakhare
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Suneetha Kota
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
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Zhu F, Li M, Yan M, Qiao F, Jiang X. Integrated Transcriptome Analysis and Single-Base Resolution Methylomes of Watermelon ( Citrullus lanatus) Reveal Epigenome Modifications in Response to Osmotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:769712. [PMID: 34912359 PMCID: PMC8667863 DOI: 10.3389/fpls.2021.769712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
DNA methylation plays an important role against adverse environment by reshaping transcriptional profile in plants. To better understand the molecular mechanisms of watermelon response to osmotic stress, the suspension cultured watermelon cells were treated with 100mM mannitol, and then a methylated cytosines map was generated by whole genome bisulfite sequencing (WGBS). Combined with transcriptome sequencing, the effects of osmotic stress on differentially methylated expressed genes (DMEGs) were assessed. It was found that genes related to plant hormone synthesis, signal transduction, osmoregulatory substance-related and reactive oxygen species scavenging-related enzyme could rapidly respond to osmotic stress. The overall methylation level of watermelon decreased after osmotic stress treatment, and demethylation occurred in CG, CHG, and CHH contexts. Moreover, differentially methylated expressed genes (DMEGs) were significantly enriched in RNA transport, starch and sucrose metabolism, plant hormone signal transduction and biosynthesis of secondary metabolites, especially in biosynthesis of osmolytes synthase genes. Interestingly, demethylation of a key enzyme gene Cla014489 in biosynthesis of inositol upregulated its expression and promoted accumulation of inositol, which could alleviate the inhibition of cell growth caused by osmotic stress. Meanwhile, a recombinant plasmid pET28a-Cla014489 was constructed and transferred into Escherichia coli BL21 for prokaryotic expression and the expression of ClMIPS protein could improve the tolerance of E. coli to osmotic stress. The effect of methylation level on the expression properties of inositol and its related genes was further confirmed by application of DNA methylation inhibitor 5-azacytidine. These results provide a preliminary insight into the altered methylation levels of watermelon cells in response to osmotic stress and suggest a new mechanism that how watermelon cells adapt to osmotic stress.
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Affiliation(s)
- Fangming Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University (HNU), Haikou, China
- Key Laboratory of Tropical Agritourism in Greenhouse of Haikou, College of Horticulture, Hainan University (HNU), Haikou, China
| | - Mingyan Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University (HNU), Haikou, China
- Key Laboratory of Tropical Agritourism in Greenhouse of Haikou, College of Horticulture, Hainan University (HNU), Haikou, China
| | - Manwen Yan
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University (HNU), Haikou, China
| | - Fei Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Xuefei Jiang
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University (HNU), Haikou, China
- Key Laboratory of Tropical Agritourism in Greenhouse of Haikou, College of Horticulture, Hainan University (HNU), Haikou, China
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Rui C, Zhang Y, Fan Y, Han M, Dai M, Wang Q, Chen X, Lu X, Wang D, Wang S, Gao W, Yu JZ, Ye W. Insight Between the Epigenetics and Transcription Responding of Cotton Hypocotyl Cellular Elongation Under Salt-Alkaline Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:772123. [PMID: 34868171 PMCID: PMC8632653 DOI: 10.3389/fpls.2021.772123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Gossypium barbadense is a cultivated cotton not only known for producing superior fiber but also for its salt and alkaline resistance. Here, we used Whole Genome Bisulfite Sequencing (WGBS) technology to map the cytosine methylation of the whole genome of the G. barbadense hypocotyl at single base resolution. The methylation sequencing results showed that the mapping rates of the three samples were 75.32, 77.54, and 77.94%, respectively. In addition, the Bisulfite Sequence (BS) conversion rate was 99.78%. Approximately 71.03, 53.87, and 6.26% of the cytosine were methylated at CG, CHG, and CHH sequence contexts, respectively. A comprehensive analysis of DNA methylation and transcriptome data showed that the methylation level of the promoter region was a positive correlation in the CHH context. Saline-alkaline stress was related to the methylation changes of many genes, transcription factors (TFs) and transposable elements (TEs), respectively. We explored the regulatory mechanism of DNA methylation in response to salt and alkaline stress during cotton hypocotyl elongation. Our data shed light into the relationship of methylation regulation at the germination stage of G. barbadense hypocotyl cell elongation and salt-alkali treatment. The results of this research help understand the early growth regulation mechanism of G. barbadense in response to abiotic stress.
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Affiliation(s)
- Cun Rui
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Yuexin Zhang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
| | - Yapeng Fan
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
| | - Mingge Han
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
| | - Maohua Dai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
| | - Qinqin Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
| | - Xiugui Chen
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
| | - Xuke Lu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
| | - Delong Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
| | - Shuai Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
| | - Wenwei Gao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - John Z. Yu
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University/Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, China
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
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Dubas E, Żur I, Moravčiková J, Fodor J, Krzewska M, Surówka E, Nowicka A, Gerši Z. Proteins, Small Peptides and Other Signaling Molecules Identified as Inconspicuous but Possibly Important Players in Microspores Reprogramming Toward Embryogenesis. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.745865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this review, we describe and integrate the latest knowledge on the signaling role of proteins and peptides in the stress-induced microspore embryogenesis (ME) in some crop plants with agricultural importance (i.e., oilseed rape, tobacco, barley, wheat, rice, triticale, rye). Based on the results received from the most advanced omix analyses, we have selected some inconspicuous but possibly important players in microspores reprogramming toward embryogenic development. We provide an overview of the roles and downstream effect of stress-related proteins (e.g., β-1,3-glucanases, chitinases) and small signaling peptides, especially cysteine—(e.g., glutathione, γ-thionins, rapid alkalinization factor, lipid transfer, phytosulfokine) and glycine-rich peptides and other proteins (e.g., fasciclin-like arabinogalactan protein) on acclimation ability of microspores and the cell wall reconstruction in a context of ME induction and haploids/doubled haploids (DHs) production. Application of these molecules, stimulating the induction and proper development of embryo-like structures and green plant regeneration, brings significant improvement of the effectiveness of DHs procedures and could result in its wider incorporation on a commercial scale. Recent advances in the design and construction of synthetic peptides–mainly cysteine-rich peptides and their derivatives–have accelerated the development of new DNA-free genome-editing techniques. These new systems are evolving incredibly fast and soon will find application in many areas of plant science and breeding.
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Cai S, Shen Q, Huang Y, Han Z, Wu D, Chen Z, Nevo E, Zhang G. Multi-Omics Analysis Reveals the Mechanism Underlying the Edaphic Adaptation in Wild Barley at Evolution Slope (Tabigha). ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101374. [PMID: 34390227 PMCID: PMC8529432 DOI: 10.1002/advs.202101374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/27/2021] [Indexed: 06/13/2023]
Abstract
At the microsite "Evolution Slope", Tabigha, Israel, wild barley (Hordeum spontaneum) populations adapted to dry Terra Rossa soil, and its derivative abutting wild barley population adapted to moist and fungi-rich Basalt soil. However, the mechanisms underlying the edaphic adaptation remain elusive. Accordingly, whole genome bisulfite sequencing, RNA-sequencing, and metabolome analysis are performed on ten wild barley accessions inhabiting Terra Rossa and Basalt soil. A total of 121 433 differentially methylated regions (DMRs) and 10 478 DMR-genes are identified between the two wild barley populations. DMR-genes in CG context (CG-DMR-genes) are enriched in the pathways related with the fundamental processes, and DMR-genes in CHH context (CHH-DMR-genes) are mainly associated with defense response. Transcriptome and metabolome analysis reveal that the primary and secondary metabolisms are more active in Terra Rossa and Basalt wild barley populations, respectively. Multi-omics analysis indicate that sugar metabolism facilitates the adaptation of wild barley to dry Terra Rossa soil, whereas the enhancement of phenylpropanoid/phenolamide biosynthesis is beneficial for wild barley to inhabit moist and fungi pathogen-rich Basalt soil. The current results make a deep insight into edaphic adaptation of wild barley and provide elite genetic and epigenetic resources for developing barley with high abiotic stress tolerance.
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Affiliation(s)
- Shengguan Cai
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Qiufang Shen
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Yuqing Huang
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- Institute of Crop ScienceHangzhou Academy of Agricultural SciencesHangzhou310024China
| | - Zhigang Han
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Dezhi Wu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Zhong‐Hua Chen
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaMount CarmelHaifa34988384Israel
| | - Guoping Zhang
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
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Jacques C, Salon C, Barnard RL, Vernoud V, Prudent M. Drought Stress Memory at the Plant Cycle Level: A Review. PLANTS (BASEL, SWITZERLAND) 2021; 10:1873. [PMID: 34579406 PMCID: PMC8466371 DOI: 10.3390/plants10091873] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/07/2021] [Accepted: 09/07/2021] [Indexed: 05/25/2023]
Abstract
Plants are sessile organisms whose survival depends on their strategy to cope with dynamic, stressful conditions. It is urgent to improve the ability of crops to adapt to recurrent stresses in order to alleviate the negative impacts on their productivity. Although our knowledge of plant adaptation to drought has been extensively enhanced during the last decades, recent studies have tackled plant responses to recurrent stresses. The present review synthesizes the major findings from studies addressing plant responses to multiple drought events, and demonstrates the ability of plants to memorize drought stress. Stress memory is described as a priming effect allowing a different response to a reiterated stress when compared to a single stress event. Here, by specifically focusing on water stress memory at the plant cycle level, we describe the different underlying processes at the molecular, physiological and morphological levels in crops as well as in the model species Arabidopsis thaliana. Moreover, a conceptual analysis framework is proposed to study drought stress memory. Finally, the essential role of interactions between plants and soil microorganisms is emphasized during reiterated stresses because their plasticity can play a key role in supporting overall plant resilience.
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Affiliation(s)
| | | | | | | | - Marion Prudent
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, F-21000 Dijon, France; (C.J.); (C.S.); (R.L.B.); (V.V.)
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Carballo J, Zappacosta D, Selva JP, Caccamo M, Echenique V. Eragrostis curvula, a Model Species for Diplosporous Apomixis. PLANTS (BASEL, SWITZERLAND) 2021; 10:1818. [PMID: 34579351 PMCID: PMC8472828 DOI: 10.3390/plants10091818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
Eragrostis curvula (Schrad.) Ness is a grass with a particular apomictic embryo sac development called Eragrostis type. Apomixis is a type of asexual reproduction that produces seeds without fertilization in which the resulting progeny is genetically identical to the mother plant and with the potential to fix the hybrid vigour from more than one generation, among other advantages. The absence of meiosis and the occurrence of only two rounds of mitosis instead of three during embryo sac development make this model unique and suitable to be transferred to economically important crops. Throughout this review, we highlight the advances in the knowledge of apomixis in E. curvula using different techniques such as cytoembryology, DNA methylation analyses, small-RNA-seq, RNA-seq, genome assembly, and genotyping by sequencing. The main bulk of evidence points out that apomixis is inherited as a single Mendelian factor, and it is regulated by genetic and epigenetic mechanisms controlled by a complex network. With all this information, we propose a model of the mechanisms involved in diplosporous apomixis in this grass. All the genetic and epigenetic resources generated in E. curvula to study the reproductive mode changed its status from an orphan to a well-characterised species.
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Affiliation(s)
- Jose Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, Bahía Blanca 8000, Argentina; (J.C.); (J.P.S.); (V.E.)
| | - Diego Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, Bahía Blanca 8000, Argentina; (J.C.); (J.P.S.); (V.E.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, Bahía Blanca 8000, Argentina
| | - Juan Pablo Selva
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, Bahía Blanca 8000, Argentina; (J.C.); (J.P.S.); (V.E.)
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), San Juan 670, Bahía Blanca 8000, Argentina
| | - Mario Caccamo
- NIAB, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK;
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, Bahía Blanca 8000, Argentina; (J.C.); (J.P.S.); (V.E.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, Bahía Blanca 8000, Argentina
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S Alotaibi S, El-Shehawi AM, M Elseehy M. Heat Shock Proteins Expression Is Regulated by Promoter CpG Methylation/demethylation under Heat Stress in Wheat Varieties. Pak J Biol Sci 2021; 23:1310-1320. [PMID: 32981265 DOI: 10.3923/pjbs.2020.1310.1320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Heat shock proteins are induced by high temperature and other environmental stimuli to protect cellular proteins. Despite extensive research on the molecular response to heat stress, the effect of high temperatures on genes and pathways remains unclear. This study investigated the expression of the HSP17 gene in nine Egyptian wheat varieties and the role of HSP17 promoter CpG methylation in the regulation of HSP17 under high temperature. MATERIALS AND METHODS The HSP17 expression was investigated by using semi-quantitative PCR analysis. Methylation at the HSP17 promoter proximal region was analyzed using bisulphite sequencing and CpG viewer software. RESULTS Under normal conditions, HSP17 and methyltransferase 3 (MET3) exhibited similar expression levels in the 9 studied varieties. After exposure to high temperature, the expression level of HSP17 in Giza155 was barely detected. Among the nine varieties, the expression level of HSP17 was highest in Giza168 (11.3 folds of Giza155). Analysis of methylation of 14 CpG islands at the HSP17 proximal promoter sequence showed that methylation of 10 CpG islands differed only by 10-20%, whereas methylation at the other 4 CpGs differed by 56.7-60%. The high expression of HSP17 in Giza168 in response to high temperature was associated with low methylation of four CpGs and low MET3 expression, whereas low expression of HSP17 in Giza155 was associated with high methylation and high MET3 expression. CONCLUSION The results can aid the development of next-generation approaches to the evaluation of commercial wheat varieties and the development of next-generation approaches to plant breeding employing epiallele integration.
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Singh RK, Prasad M. Delineating the epigenetic regulation of heat and drought response in plants. Crit Rev Biotechnol 2021; 42:548-561. [PMID: 34289772 DOI: 10.1080/07388551.2021.1946004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Being sessile in nature, plants cannot overlook the incursion of unfavorable environmental conditions, including heat and drought. Heat and drought severely affect plant growth, development, reproduction and therefore productivity which poses a severe threat to global food security. Plants respond to these hostile environmental circumstances by rearranging their genomic and molecular architecture. One such modification commonly known as epigenetic changes involves the perishable to inheritable changes in DNA or DNA-binding histone proteins leading to modified chromatin organization. Reversible epigenetic modifications include DNA methylation, exchange of histone variants, histone methylation, histone acetylation, ATP-dependent nucleosome remodeling, and others. These modifications are employed to regulate the spatial and temporal expression of genes in response to external stimuli or specific developmental requirements. Understanding the epigenetic regulation of stress-related gene expression in response to heat and drought would commence manifold avenues for crop improvement through molecular breeding or biotechnological approaches.
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Affiliation(s)
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
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Girón-Calva PS, Pérez-Fons L, Sandmann G, Fraser PD, Christou P. Nitrogen inputs influence vegetative metabolism in maize engineered with a seed-specific carotenoid pathway. PLANT CELL REPORTS 2021; 40:899-911. [PMID: 33787959 DOI: 10.1007/s00299-021-02689-2] [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: 02/15/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Metabolomic profiling of a maize line engineered with an endosperm-specific carotenogenic pathway revealed unexpected metabolic readjustments of primary metabolism in leaves and roots. High-carotenoid (HC) maize was engineered to accumulate high levels of carotenoids in the endosperm. The metabolic interventions influenced the flux through non-target pathways in tissues that were not affected by the targeted intervention. HC maize at the vegetative stage also showed a reduced susceptibility to insect feeding. It is unknown, however, whether the metabolic history of the embryo has any impact on the metabolite composition in vegetative tissues. We, therefore, compared HC maize and its isogenic counterpart (M37W) to test the hypothesis that boosting the carotenoid content in the endosperm triggers compensatory effects in core metabolism in vegetative tissues. Specifically, we investigated whether the metabolite composition of leaves and roots at the V6 stage differs between HC and M37W, and whether N inputs further alter the core metabolism of HC compared to M37W. We found an increase in the abundance of organic acids from the tricarboxylic acid (TCA) cycle in HC even under restricted N conditions. In contrast, low levels of carotenoids and chlorophyll were measured regardless of N levels. Sugars were also significantly depleted in HC under low N. We propose a model explaining the observed genotype-dependent and input-dependent effects, in which organic acids derived from the TCA cycle accumulate during vegetative growth and contribute to the increased demand for pyruvate and/or acetyl-CoA in the endosperm and embryo. This response may in part reflect the transgenerational priming of vegetative tissues in the embryo induced by the increased demand for metabolic precursors during seed development in the previous generation.
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Affiliation(s)
- Patricia S Girón-Calva
- Department of Plant Production and Forestry Sciences, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Laura Pérez-Fons
- Department of Biological Sciences, Royal Holloway, University London, Egham, Surrey, UK
| | - Gerhard Sandmann
- Institute of Molecular Bioscience, J. W. Goethe University, Frankfurt am Main, Germany
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway, University London, Egham, Surrey, UK.
| | - Paul Christou
- Department of Plant Production and Forestry Sciences, University of Lleida-Agrotecnio Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
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Morán-Diez ME, Martínez de Alba ÁE, Rubio MB, Hermosa R, Monte E. Trichoderma and the Plant Heritable Priming Responses. J Fungi (Basel) 2021; 7:jof7040318. [PMID: 33921806 PMCID: PMC8072925 DOI: 10.3390/jof7040318] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 01/08/2023] Open
Abstract
There is no doubt that Trichoderma is an inhabitant of the rhizosphere that plays an important role in how plants interact with the environment. Beyond the production of cell wall degrading enzymes and metabolites, Trichoderma spp. can protect plants by inducing faster and stronger immune responses, a mechanism known as priming, which involves enhanced accumulation of dormant cellular proteins that function in intracellular signal amplification. One example of these proteins is the mitogen-activated protein kinases (MAPK) that are triggered by the rise of cytosolic calcium levels and cellular redox changes following a stressful challenge. Transcription factors such as WRKYs, MYBs, and MYCs, play important roles in priming as they act as regulatory nodes in the transcriptional network of systemic defence after stress recognition. In terms of long-lasting priming, Trichoderma spp. may be involved in plants epigenetic regulation through histone modifications and replacements, DNA (hypo)methylation, and RNA-directed DNA methylation (RdDM). Inheritance of these epigenetic marks for enhanced resistance and growth promotion, without compromising the level of resistance of the plant’s offspring to abiotic or biotic stresses, seems to be an interesting path to be fully explored.
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40
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Wang G, Li X, Li Y, Ye N, Li H, Zhang J. Comprehensive epigenome and transcriptome analysis of carbon reserve remobilization in indica and japonica rice stems under moderate soil drying. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1384-1398. [PMID: 33130853 DOI: 10.1093/jxb/eraa502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Moderate soil drying (MD) imposed at the post-anthesis stage significantly improves carbon reserve remobilization in rice stems, increasing grain yield. However, the methylome and transcriptome profiles of carbon reserve remobilization under MD are obscure in indica and japonica rice stems. Here, we generated whole-genome single-base resolution maps of the DNA methylome in indica and japonica rice stems. DNA methylation levels were higher in indica than in japonica and positively correlated with genome size. MD treatment had a weak impact on the changes in methylation levels in indica. Moreover, the number of differentially methylated regions was much lower in indica, indicating the existence of cultivar-specific methylation patterns in response to MD during grain filling. The gene encoding β-glucosidase 1, involved in the starch degradation process, was hypomethylated and up-regulated in indica, resulting in improved starch to sucrose conversion under MD treatment. Additionally, increased expression of MYBS1 transactivated the expression of AMYC2/OsAMY2A in both indica and japonica, leading to enhanced starch degradation under MD. In contrast, down-regulated expression of MYB30 resulted in increased expression of BMY5 in both cultivars. Our findings decode the dynamics of DNA methylation in indica and japonica rice stems and propose candidate genes for improving carbon reserve remobilization.
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Affiliation(s)
- Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Xiaozheng Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yongqiang Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
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Kumar S, Mohapatra T. Dynamics of DNA Methylation and Its Functions in Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:596236. [PMID: 34093600 PMCID: PMC8175986 DOI: 10.3389/fpls.2021.596236] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/19/2021] [Indexed: 05/20/2023]
Abstract
Epigenetic modifications in DNA bases and histone proteins play important roles in the regulation of gene expression and genome stability. Chemical modification of DNA base (e.g., addition of a methyl group at the fifth carbon of cytosine residue) switches on/off the gene expression during developmental process and environmental stresses. The dynamics of DNA base methylation depends mainly on the activities of the writer/eraser guided by non-coding RNA (ncRNA) and regulated by the developmental/environmental cues. De novo DNA methylation and active demethylation activities control the methylation level and regulate the gene expression. Identification of ncRNA involved in de novo DNA methylation, increased DNA methylation proteins guiding DNA demethylase, and methylation monitoring sequence that helps maintaining a balance between DNA methylation and demethylation is the recent developments that may resolve some of the enigmas. Such discoveries provide a better understanding of the dynamics/functions of DNA base methylation and epigenetic regulation of growth, development, and stress tolerance in crop plants. Identification of epigenetic pathways in animals, their existence/orthologs in plants, and functional validation might improve future strategies for epigenome editing toward climate-resilient, sustainable agriculture in this era of global climate change. The present review discusses the dynamics of DNA methylation (cytosine/adenine) in plants, its functions in regulating gene expression under abiotic/biotic stresses, developmental processes, and genome stability.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Suresh Kumar, ; , orcid.org/0000-0002-7127-3079
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Laanen P, Saenen E, Mysara M, Van de Walle J, Van Hees M, Nauts R, Van Nieuwerburgh F, Voorspoels S, Jacobs G, Cuypers A, Horemans N. Changes in DNA Methylation in Arabidopsis thaliana Plants Exposed Over Multiple Generations to Gamma Radiation. FRONTIERS IN PLANT SCIENCE 2021; 12:611783. [PMID: 33868326 PMCID: PMC8044457 DOI: 10.3389/fpls.2021.611783] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/09/2021] [Indexed: 05/05/2023]
Abstract
Previous studies have found indications that exposure to ionising radiation (IR) results in DNA methylation changes in plants. However, this phenomenon is yet to be studied across multiple generations. Furthermore, the exact role of these changes in the IR-induced plant response is still far from understood. Here, we study the effect of gamma radiation on DNA methylation and its effect across generations in young Arabidopsis plants. A multigenerational set-up was used in which three generations (Parent, generation 1, and generation 2) of 7-day old Arabidopsis thaliana plants were exposed to either of the different radiation treatments (30, 60, 110, or 430 mGy/h) or to natural background radiation (control condition) for 14 days. The parental generation consisted of previously non-exposed plants, whereas generation 1 and generation 2 plants had already received a similar irradiation in the previous one or two generations, respectively. Directly after exposure the entire methylomes were analysed with UPLC-MS/MS to measure whole genome methylation levels. Whole genome bisulfite sequencing was used to identify differentially methylated regions (DMRs), including their methylation context in the three generations and this for three different radiation conditions (control, 30 mGy/h, and 110 mGy/h). Both intra- and intergenerational comparisons of the genes and transposable elements associated with the DMRs were made. Taking the methylation context into account, the highest number of changes were found for cytosines followed directly by guanine (CG methylation), whereas only limited changes in CHG methylation occurred and no changes in CHH methylation were observed. A clear increase in IR-induced DMRs was seen over the three generations that were exposed to the lowest dose rate, where generation 2 had a markedly higher number of DMRs than the previous two generations (Parent and generation 1). Counterintuitively, we did not see significant differences in the plants exposed to the highest dose rate. A large number of DMRs associated with transposable elements were found, the majority of them being hypermethylated, likely leading to more genetic stability. Next to that, a significant number of DMRs were associated with genes (either in their promoter-associated region or gene body). A functional analysis of these genes showed an enrichment for genes related to development as well as various stress responses, including DNA repair, RNA splicing, and (a)biotic stress responses. These observations indicate a role of DNA methylation in the regulation of these genes in response to IR exposure and shows a possible role for epigenetics in plant adaptation to IR over multiple generations.
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Affiliation(s)
- Pol Laanen
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
| | - Eline Saenen
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mohamed Mysara
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Jorden Van de Walle
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
| | - May Van Hees
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Robin Nauts
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
- NXTGNT, Ghent University, Ghent, Belgium
| | | | - Griet Jacobs
- Vlaamse Instelling voor Technologisch Onderzoek, VITO, Mol, Belgium
| | - Ann Cuypers
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
| | - Nele Horemans
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
- *Correspondence: Nele Horemans,
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Song Y, Jia Z, Hou Y, Ma X, Li L, Jin X, An L. Roles of DNA Methylation in Cold Priming in Tartary Buckwheat. FRONTIERS IN PLANT SCIENCE 2020; 11:608540. [PMID: 33365044 PMCID: PMC7750358 DOI: 10.3389/fpls.2020.608540] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/23/2020] [Indexed: 05/04/2023]
Abstract
Plants experience a wide array of environmental stimuli, some of which are frequent occurrences of cold weather, which have priming effects on agricultural production and agronomic traits. DNA methylation may act as an epigenetic regulator for the cold response of Tartary buckwheat (Fagopyrum tataricum). Combined with long-term field observation and laboratory experiments, comparative phenome, methylome, and transcriptome analyses were performed to investigate the potential epigenetic contributions for the cold priming of Tartary buckwheat variety Dingku1. Tartary buckwheat cv. Dingku1 exhibited low-temperature resistance. Single-base resolution maps of the DNA methylome were generated, and a global loss of DNA methylation was observed during cold responding in Dingku1. These sites with differential methylation levels were predominant in the intergenic regions. Several hundred genes had different DNA methylation patterns and expressions in different cold treatments (cold memory and cold shock), such as CuAO, RPB1, and DHE1. The application of a DNA methylation inhibitor caused a change of the free lysine content, suggesting that DNA methylation can affect metabolite accumulation for Tartary buckwheat cold responses. The results of the present study suggest important roles of DNA methylation in regulating cold response and forming agronomic traits in Tartary buckwheat.
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Affiliation(s)
- Yuan Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhifeng Jia
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Yukang Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiang Ma
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Lizhen Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xing Jin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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44
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Chen P, Xiao WF, Pan MH, Xiao JS, Feng YJ, Dong ZQ, Zou BX, Zhou L, Zhang YH, Lu C. Comparative genome-wide DNA methylation analysis reveals epigenomic differences in response to heat-humidity stress in Bombyx mori. Int J Biol Macromol 2020; 164:3771-3779. [PMID: 32891645 DOI: 10.1016/j.ijbiomac.2020.08.251] [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: 07/22/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 11/26/2022]
Abstract
DNA methylation is an important epigenetic modification and has been shown to be involved in the response to abiotic stress. However, there are few studies on DNA methylation in insect response to environmental signals. In this study, we conducted a comprehensive comparative analysis of DNA methylation profiles between two silkworm strains with significantly different resistance to heat and humidity by whole-genome bisulfite sequencing (WGBS). We identified, in total, 2934 differentially methylated regions (DMRs) between RT_48h (resistant strain with high-temperature/humidity treatment for 48 h) and ST_48h (sensitive strain with high-temperature/humidity treatment for 48 h) under cytosine context (CG), which corresponded to 1230 DMR-related genes (DMGs), and the DMRs were primarily located in the gene body (exon and intron) region. Gene ontology (GO) and KEGG analysis showed that these DMGs were most significantly enriched in binding, cellular metabolic process, and RNA transport pathways. Moreover, 10 DMGs have been revealed to be involved in the heat-humidity stress response in the silkworm. The results of this study indicated that DNA methylation plays crucial roles in silkworm response to environmental stressors and provides important clues to identify key resistance genes in silkworm under high-temperature/humidity stress response.
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Affiliation(s)
- Peng Chen
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Wen-Fu Xiao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China; Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Min-Hui Pan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Jin-Shu Xiao
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Yu-Jie Feng
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Zhan-Qi Dong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Bang-Xing Zou
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Li Zhou
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - You-Hong Zhang
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China.
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China.
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da Silva MF, Gonçalves MC, Brito MDS, Medeiros CN, Harakava R, Landell MGDA, Pinto LR. Sugarcane mosaic virus mediated changes in cytosine methylation pattern and differentially transcribed fragments in resistance-contrasting sugarcane genotypes. PLoS One 2020; 15:e0241493. [PMID: 33166323 PMCID: PMC7652275 DOI: 10.1371/journal.pone.0241493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022] Open
Abstract
Sugarcane mosaic virus (SCMV) is the causal agent of sugarcane mosaic disease (SMD) in Brazil; it is mainly controlled by using resistant cultivars. Studies on the changes in sugarcane transcriptome provided the first insights about the molecular basis underlying the genetic resistance to SMD; nonetheless, epigenetic modifications such as cytosine methylation is also informative, considering its roles in gene expression regulation. In our previous study, differentially transcribed fragments (DTFs) were obtained using cDNA-amplified fragment length polymorphism by comparing mock- and SCMV-inoculated plants from two sugarcane cultivars with contrasting responses to SMD. In this study, the identification of unexplored DTFs was continued while the same leaf samples were used to evaluate SCMV-mediated changes in the cytosine methylation pattern by using methylation-sensitive amplification polymorphism. This analysis revealed minor changes in cytosine methylation in response to SCMV infection, but distinct changes between the cultivars with contrasting responses to SMD, with higher hypomethylation events 24 and 72 h post-inoculation in the resistant cultivar. The differentially methylated fragments (DMFs) aligned with transcripts, putative promoters, and genomic regions, with a preponderant distribution within CpG islands. The transcripts found were associated with plant immunity and other stress responses, epigenetic changes, and transposable elements. The DTFs aligned with transcripts assigned to stress responses, epigenetic changes, photosynthesis, lipid transport, and oxidoreductases, in which the transcriptional start site is located in proximity with CpG islands and tandem repeats. Real-time quantitative polymerase chain reaction results revealed significant upregulation in the resistant cultivar of aspartyl protease and VQ protein, respectively, selected from DMF and DTF alignments, suggesting their roles in genetic resistance to SMD and supporting the influence of cytosine methylation in gene expression. Thus, we identified new candidate genes for further validation and showed that the changes in cytosine methylation may regulate important mechanisms underlying the genetic resistance to SMD.
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Affiliation(s)
- Marcel Fernando da Silva
- Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias (FCAV) Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, São Paulo, Brazil
| | | | - Michael dos Santos Brito
- Departamento de Ciência e Tecnologia, Instituto de Ciência e Tecnologia da Universidade Federal de São Paulo, São José dos Campos, São Paulo, Brazil
| | | | - Ricardo Harakava
- Crop Protection Research Centre, Instituto Biológico, São Paulo, Brazil
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Chu S, Zhang X, Yu K, Lv L, Sun C, Liu X, Zhang J, Jiao Y, Zhang D. Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress. Int J Mol Sci 2020; 21:E6817. [PMID: 32957498 PMCID: PMC7555642 DOI: 10.3390/ijms21186817] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 01/23/2023] Open
Abstract
Low-phosphorus (low-P) stress has a significant limiting effect on crop yield and quality. Although the molecular mechanisms of the transcriptional level responsible for the low-P stress response have been studied in detail, the underlying epigenetic mechanisms in gene regulation remain largely unknown. In this study, we evaluated the changes in DNA methylation, gene expression and small interfering RNAs (siRNAs) abundance genome-wide in response to low-P stress in two representative soybean genotypes with different P-efficiencies. The DNA methylation levels were slightly higher under low-P stress in both genotypes. Integrative methylation and transcription analysis suggested a complex regulatory relationship between DNA methylation and gene expression that may be associated with the type, region, and extent of methylation. Association analysis of low-P-induced differential methylation and gene expression showed that transcriptional alterations of a small part of genes were associated with methylation changes. Dynamic methylation alterations in transposable element (TE) regions in the CHH methylation context correspond with changes in the amount of siRNA under low-P conditions, indicating an important role of siRNAs in modulating TE activity by guiding CHH methylation in TE regions. Together, these results could help to elucidate the epigenetic regulation mechanisms governing the responses of plants to abiotic stresses.
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Affiliation(s)
- Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Xiangqian Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Kaiye Yu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Lingling Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Jinyu Zhang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China;
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
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Jerome Jeyakumar JM, Ali A, Wang WM, Thiruvengadam M. Characterizing the Role of the miR156-SPL Network in Plant Development and Stress Response. PLANTS 2020; 9:plants9091206. [PMID: 32942558 PMCID: PMC7570127 DOI: 10.3390/plants9091206] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/27/2020] [Accepted: 09/11/2020] [Indexed: 01/22/2023]
Abstract
MicroRNA (miRNA) is a short, single-stranded, non-coding RNA found in eukaryotic cells that can regulate the expression of many genes at the post-transcriptional level. Among various plant miRNAs with diverse functions, miR156 plays a key role in biological processes, including developmental regulation, immune response, metabolic regulation, and abiotic stress. MiRNAs have become the regulatory center for plant growth and development. MicroRNA156 (miR156) is a highly conserved and emerging tool for the improvement of plant traits, including crop productivity and stress tolerance. Fine-tuning of squamosa promoter biding-like (SPL) gene expression might be a useful strategy for crop improvement. Here, we studied the regulation of the miR156 module and its interaction with SPL factors to understand the developmental transition of various plant species. Furthermore, this review provides a strong background for plant biotechnology and is an important source of information for further molecular breeding to optimize farming productivity.
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Affiliation(s)
- John Martin Jerome Jeyakumar
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Asif Ali
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Wen-Ming Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
- Correspondence:
| | - Muthu Thiruvengadam
- Department of Applied Bioscience, College of Life and Environmental Sciences, Konkuk University, Seoul 05029, Korea;
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Rehman M, Tanti B. Understanding epigenetic modifications in response to abiotic stresses in plants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Summanwar A, Basu U, Rahman H, Kav NNV. Non-coding RNAs as emerging targets for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110521. [PMID: 32563460 DOI: 10.1016/j.plantsci.2020.110521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 05/23/2023]
Abstract
Food security is affected by climate change, population growth, as well as abiotic and biotic stresses. Conventional and molecular marker assisted breeding and genetic engineering techniques have been employed extensively for improving resistance to biotic stress in crop plants. Advances in next-generation sequencing technologies have permitted the exploration and identification of parts of the genome that extend beyond the regions with protein coding potential. These non-coding regions of the genome are transcribed to generate many types of non-coding RNAs (ncRNAs). These ncRNAs are involved in the regulation of growth, development, and response to stresses at transcriptional and translational levels. ncRNAs, including long ncRNAs (lncRNAs), small RNAs and circular RNAs have been recognized as important regulators of gene expression in plants and have been suggested to play important roles in plant immunity and adaptation to abiotic and biotic stresses. In this article, we have reviewed the current state of knowledge with respect to lncRNAs and their mechanism(s) of action as well as their regulatory functions, specifically within the context of biotic stresses. Additionally, we have provided insights into how our increased knowledge about lncRNAs may be used to improve crop tolerance to these devastating biotic stresses.
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Affiliation(s)
- Aarohi Summanwar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
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The assessment of epigenetic diversity, differentiation, and structure in the 'Fuji' mutation line implicates roles of epigenetic modification in the occurrence of different mutant groups as well as spontaneous mutants. PLoS One 2020; 15:e0235073. [PMID: 32584862 PMCID: PMC7316255 DOI: 10.1371/journal.pone.0235073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/07/2020] [Indexed: 01/01/2023] Open
Abstract
The ‘Fuji’ line includes many varieties with a similar genetic background and consistent inducement factors with epigenetic occurrence, thus it may be considered an ideal candidate for epigenetic research. In this study, 91 bud mutations of ‘Fuji’ apple were used as the test materials. Using the genetic variation within ‘Fuji’ as the control, the characteristics of epigenetic variation at different levels in both varieties and mutant groups were examined. The results showed that: (1) the global genomic DNA methylation level of the 91 bud mutants of ‘Fuji’ ranged from 29.120%-45.084%, with an average of 35.910%. Internal cytosine methylation was the main DNA methylation pattern. Regarding the variation of methylation patterns of ‘Fuji’ mutants, the vast majority of loci maintained the original methylation pattern existed in ‘Fuji’. CHG methylation variation was the main type of variation; (2) the variation in methylation patterns between the mutant groups was greater than that of methylation levels. Among these patterns, the variation in CHG methylation patterns (including CHG hypermethylation and CHG demethylation) was expected to be dominant. The observed variation in methylation levels was more important in the Color mutant group; however, the variation in methylation patterns was more obvious in both the early maturation and Spur mutant groups. Moreover, the range of variation in the Early-maturation group was much wider than that in the Spur mutant group; (3) epigenetic diversity and genetic diversity were both low between the mutant groups. In the ‘Fuji’ mutant groups, there was few correlation between genetic and epigenetic variation, and epigenetic differentiation resulted in more loci with moderate or greater differentiation; (4) the purifying selection seemed to play a major role in the differentiation of different groups of ‘Fuji’ mutants (65.618%), but epigenetic diversity selection still occurred at nearly 35% of loci. Sixteen epigenetic outlier loci were detected.
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