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Maize DNA Methylation in Response to Drought Stress Is Involved in Target Gene Expression and Alternative Splicing. Int J Mol Sci 2021; 22:ijms22158285. [PMID: 34361051 PMCID: PMC8347047 DOI: 10.3390/ijms22158285] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 11/17/2022] Open
Abstract
DNA methylation is important for plant growth, development, and stress response. To understand DNA methylation dynamics in maize roots under water stress (WS), we reanalyzed DNA methylation sequencing data to profile DNA methylation and the gene expression landscape of two inbred lines with different drought sensitivities, as well as two of their derived recombination inbred lines (RILs). Combined with genotyping-by-sequencing, we found that the inheritance pattern of DNA methylation between RILs and parental lines was sequence-dependent. Increased DNA methylation levels were observed under WS and the methylome of drought-tolerant inbred lines were much more stable than that of the drought-sensitive inbred lines. Distinctive differentially methylated genes were found among diverse genetic backgrounds, suggesting that inbred lines with different drought sensitivities may have responded to stress in varying ways. Gene body DNA methylation showed a negative correlation with gene expression but a positive correlation with exon splicing events. Furthermore, a positive correlation of a varying extent was observed between small interfering RNA (siRNA) and DNA methylation, which at different genic regions. The response of siRNAs under WS was consistent with the differential DNA methylation. Taken together, our data can be useful in deciphering the roles of DNA methylation in plant drought-tolerance variations and in emphasizing its function in alternative splicing.
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Rodrigues JA, Hsieh PH, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proc Natl Acad Sci U S A 2021; 118:e2104445118. [PMID: 34272287 PMCID: PMC8307775 DOI: 10.1073/pnas.2104445118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Parent-of-origin-dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin-specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA-producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions-the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.
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Affiliation(s)
- Jessica A Rodrigues
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Ping-Hung Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Deling Ruan
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Toshiro Nishimura
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Manoj K Sharma
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Rita Sharma
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - XinYi Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Nicholas D Nguyen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Sukhranjan Nijjar
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Robert L Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
- Department of Cell and Developmental Biology, The John Innes Centre, Norwich NR4 7UH, United Kingdom
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Exploration of Epigenetics for Improvement of Drought and Other Stress Resistance in Crops: A Review. PLANTS 2021; 10:plants10061226. [PMID: 34208642 PMCID: PMC8235456 DOI: 10.3390/plants10061226] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 01/01/2023]
Abstract
Crop plants often have challenges of biotic and abiotic stresses, and they adapt sophisticated ways to acclimate and cope with these through the expression of specific genes. Changes in chromatin, histone, and DNA mostly serve the purpose of combating challenges and ensuring the survival of plants in stressful environments. Epigenetic changes, due to environmental stress, enable plants to remember a past stress event in order to deal with such challenges in the future. This heritable memory, called "plant stress memory", enables plants to respond against stresses in a better and efficient way, not only for the current plant in prevailing situations but also for future generations. Development of stress resistance in plants for increasing the yield potential and stability has always been a traditional objective of breeders for crop improvement through integrated breeding approaches. The application of epigenetics for improvements in complex traits in tetraploid and some other field crops has been unclear. An improved understanding of epigenetics and stress memory applications will contribute to the development of strategies to incorporate them into breeding for complex agronomic traits. The insight in the application of novel plant breeding techniques (NPBTs) has opened a new plethora of options among plant scientists to develop germplasms for stress tolerance. This review summarizes and discusses plant stress memory at the intergenerational and transgenerational levels, mechanisms involved in stress memory, exploitation of induced and natural epigenetic changes, and genome editing technologies with their future possible applications, in the breeding of crops for abiotic stress tolerance to increase the yield for zero hunger goals achievement on a sustainable basis in the changing climatic era.
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Rabara RC, Msanne J, Basu S, Ferrer MC, Roychoudhury A. Coping with inclement weather conditions due to high temperature and water deficit in rice: An insight from genetic and biochemical perspectives. PHYSIOLOGIA PLANTARUM 2021; 172:487-504. [PMID: 33179306 DOI: 10.1111/ppl.13272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Climatic fluctuations, temperature extremes, and water scarcity are becoming increasingly unpredictable with the passage of time. Such environmental atrocities have been the scourge of agriculture over the ages, bringing with them poor harvests and threat of famine. Rice production, owing to its high-water requirement for cultivation, is highly vulnerable to the threat of changing climate, particularly prolonged drought and high temperature, individually or in combination. Amidst all the abiotic stresses, heat and drought are considered as the most important concurrent stressors, largely affecting rice yield and productivity under the current scenario. Such threats heighten the need for new breeding and cultivation strategies in generating abiotic stress-resilient rice varieties with better yield potential. Responses of rice to these stresses can be categorized at the morphological, physiological and biochemical levels. This review examines the physiological and molecular mechanism, in the form of up regulation of several defense machineries of rice varieties to cope with drought stress (DS), high temperature stress (HTS), and their combination (DS-HTS). Genotypic differences among rice varieties in their tolerance ability have also been addressed. The review also appraises research studies conducted in rice regarding various phenotypic traits, genetic loci and response mechanisms to stress conditions to help craft new breeding strategies for improved tolerance to DS and HTS, singly or in combination. The review also encompasses the gene regulatory networks and transcription factors, and their cross-talks in mediating tolerance to such stresses. Understanding the epigenetic regulation, involving DNA methylation and histone modification during such hostile situations, will also play a crucial role in our comprehensive understanding of combinatorial stress responses. Taken together, this review consolidates current research and available information on promising rice cultivars with desirable traits as well as advocates synergistic and complementary approaches in molecular and systems biology to develop new rice breeds that favorably respond to DS-HTS-induced abiotic stress.
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Affiliation(s)
- Roel C Rabara
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Joseph Msanne
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Supratim Basu
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Marilyn C Ferrer
- Genetic Resources Division, Philippine Rice Research Institute, Science City of Muñoz, Nueva Ecija, Philippines
| | - Aryadeep Roychoudhury
- Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, West Bengal, India
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In Response to Abiotic Stress, DNA Methylation Confers EpiGenetic Changes in Plants. PLANTS 2021; 10:plants10061096. [PMID: 34070712 PMCID: PMC8227271 DOI: 10.3390/plants10061096] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023]
Abstract
Epigenetics involves the heritable changes in patterns of gene expression determined by developmental and abiotic stresses, i.e., drought, cold, salinity, trace metals, and heat. Gene expression is driven by changes in DNA bases, histone proteins, the biogenesis of ncRNA, and changes in the nucleotide sequence. To cope with abiotic stresses, plants adopt certain changes driven by a sophisticated biological system. DNA methylation is a primary mechanism for epigenetic variation, which can induce phenotypic alterations in plants under stress. Some of the stress-driven changes in plants are temporary, while some modifications may be stable and inheritable to the next generations to allow them to cope with such extreme stress challenges in the future. In this review, we discuss the pivotal role of epigenetically developed phenotypic characteristics in plants as an evolutionary process participating in adaptation and tolerance responses to abiotic and biotic stresses that alter their growth and development. We emphasize the molecular process underlying changes in DNA methylation, differential variation for different species, the roles of non-coding RNAs in epigenetic modification, techniques for studying DNA methylation, and its role in crop improvement in tolerance to abiotic stress (drought, salinity, and heat). We summarize DNA methylation as a significant future research priority for tailoring crops according to various challenging environmental issues.
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Skorupa M, Szczepanek J, Mazur J, Domagalski K, Tretyn A, Tyburski J. Salt stress and salt shock differently affect DNA methylation in salt-responsive genes in sugar beet and its wild, halophytic ancestor. PLoS One 2021; 16:e0251675. [PMID: 34043649 PMCID: PMC8158878 DOI: 10.1371/journal.pone.0251675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/29/2021] [Indexed: 01/19/2023] Open
Abstract
Here we determined the impact of salt shock and salt stress on the level of DNA methylation in selected CpG islands localized in promoters or first exons of sixteen salt-responsive genes in beets. Two subspecies differing in salt tolerance were subjected for analysis, a moderately salt-tolerant sugar beet Beta vulgaris ssp. vulgaris cv. Huzar and a halophytic beet, Beta vulgaris ssp. maritima. The CpG island methylation status was determined. All target sequences were hyper- or hypomethylated under salt shock and/or salt stress in one or both beet subspecies. It was revealed that the genomic regions analyzed were highly methylated in both, the salt treated plants and untreated controls. Methylation of the target sequences changed in a salt-dependent manner, being affected by either one or both treatments. Under both shock and stress, the hypomethylation was a predominant response in sugar beet. In Beta vulgaris ssp. maritima, the hypermethylation occurred with higher frequency than hypomethylation, especially under salt stress and in the promoter-located CpG sites. Conversely, the hypomethylation of the promoter-located CpG sites predominated in sugar beet plants subjected to salt stress. This findings suggest that DNA methylation may be involved in salt-tolerance and transcriptomic response to salinity in beets.
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Affiliation(s)
- Monika Skorupa
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
- * E-mail:
| | - Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Justyna Mazur
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Domagalski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Department of Immunology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Andrzej Tretyn
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Jarosław Tyburski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
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Tyczewska A, Gracz-Bernaciak J, Szymkowiak J, Twardowski T. Herbicide stress-induced DNA methylation changes in two Zea mays inbred lines differing in Roundup® resistance. J Appl Genet 2021; 62:235-248. [PMID: 33512663 PMCID: PMC8032638 DOI: 10.1007/s13353-021-00609-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/29/2020] [Accepted: 01/03/2021] [Indexed: 01/18/2023]
Abstract
DNA methylation plays a crucial role in the regulation of gene expression, activity of transposable elements, defense against foreign DNA, and inheritance of specific gene expression patterns. The link between stress exposure and sequence-specific changes in DNA methylation was hypothetical until it was shown that stresses can induce changes in the gene expression through hypomethylation or hypermethylation of DNA. To detect changes in DNA methylation under herbicide stress in two local Zea mays inbred lines exhibiting differential susceptibility to Roundup®, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation levels were determined at approximately 60% for both tested lines. The most significant changes were observed for the more sensitive Z. mays line, where 6 h after the herbicide application, a large increase in the level of DNA methylation (attributed to the increase in fully methylated bands (18.65%)) was noted. DNA sequencing revealed that changes in DNA methylation profiles occurred in genes encoding heat shock proteins, membrane proteins, transporters, kinases, lipases, methyltransferases, zinc-finger proteins, cytochromes, and transposons. Herbicide stress-induced changes depended on the Z. mays variety, and the large increase in DNA methylation level in the sensitive line resulted in a lower ability to cope with stress conditions.
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Affiliation(s)
- Agata Tyczewska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznań, Poland
| | | | - Jakub Szymkowiak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznań, Poland
| | - Tomasz Twardowski
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznań, Poland
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Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response. Int J Mol Sci 2021; 22:ijms22042013. [PMID: 33670556 PMCID: PMC7922328 DOI: 10.3390/ijms22042013] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/06/2023] Open
Abstract
Sessile plants are exposed throughout their existence to environmental abiotic and biotic stress factors, such as cold, heat, salinity, drought, dehydration, submergence, waterlogging, and pathogen infection. Chromatin organization affects genome stability, and its dynamics are crucial in plant stress responses. Chromatin dynamics are epigenetically regulated and are required for stress-induced transcriptional regulation or reprogramming. Epigenetic regulators facilitate the phenotypic plasticity of development and the survival and reproduction of plants in unfavorable environments, and they are highly diversified, including histone and DNA modifiers, histone variants, chromatin remodelers, and regulatory non-coding RNAs. They contribute to chromatin modifications, remodeling and dynamics, and constitute a multilayered and multifaceted circuitry for sophisticated and robust epigenetic regulation of plant stress responses. However, this complicated epigenetic regulatory circuitry creates challenges for elucidating the common or differential roles of chromatin modifications for transcriptional regulation or reprogramming in different plant stress responses. Particularly, interacting chromatin modifications and heritable stress memories are difficult to identify in the aspect of chromatin-based epigenetic regulation of transcriptional reprogramming and memory. Therefore, this review discusses the recent updates from the three perspectives—stress specificity or dependence of transcriptional reprogramming, the interplay of chromatin modifications, and transcriptional stress memory in plants. This helps solidify our knowledge on chromatin-based transcriptional reprogramming for plant stress response and memory.
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Korotko U, Chwiałkowska K, Sańko-Sawczenko I, Kwasniewski M. DNA Demethylation in Response to Heat Stress in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22041555. [PMID: 33557095 PMCID: PMC7913789 DOI: 10.3390/ijms22041555] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental stress is one of the most important factors affecting plant growth and development. Recent studies have shown that epigenetic mechanisms, such as DNA methylation, play a key role in adapting plants to stress conditions. Here, we analyzed the dynamics of changes in the level of DNA methylation in Arabidopsis thaliana (L.) Heynh. (Brassicaceae) under the influence of heat stress. For this purpose, whole-genome sequencing of sodium bisulfite-treated DNA was performed. The analysis was performed at seven time points, taking into account the control conditions, heat stress, and recovery to control conditions after the stress treatment was discontinued. In our study we observed decrease in the level of DNA methylation under the influence of heat stress, especially after returning to control conditions. Analysis of the gene ontology enrichment and regulatory pathways showed that genes characterized by differential DNA methylation are mainly associated with stress response, including heat stress. These are the genes encoding heat shock proteins and genes associated with translation regulation. A decrease in the level of DNA methylation in such specific sites suggests that under the influence of heat stress we observe active demethylation phenomenon rather than passive demethylation, which is not locus specific.
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Affiliation(s)
- Urszula Korotko
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
- Department of Genetics, University of Silesia in Katowice, 40-007 Katowice, Poland
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
| | - Izabela Sańko-Sawczenko
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warszawa, Poland;
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
- Correspondence:
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Shi Y, Zhang X, Chang X, Yan M, Zhao H, Qin Y, Wang H. Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple. BMC PLANT BIOLOGY 2021; 21:19. [PMID: 33407144 PMCID: PMC7789485 DOI: 10.1186/s12870-020-02814-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/22/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood. RESULTS Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH. CONCLUSIONS Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.
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Affiliation(s)
- Yan Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xiaojun Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Maokai Yan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Heming Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Haifeng Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
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Transcriptome skimming of lentil (Lens culinaris Medikus) cultivars with contrast reaction to salt stress. Funct Integr Genomics 2021; 21:139-156. [PMID: 33389259 DOI: 10.1007/s10142-020-00766-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
Extensive transcriptomic skimming was conducted to decipher molecular, morphological, physiological, and biochemical responses in salt-tolerant (PDL-1) and salt-sensitive (L-4076) cultivars under control (0 mM NaCl) and salinity stress (120 mM NaCl) conditions at seedling stage. Morphological, physiological, and biochemical studies revealed that PDL-1 exhibited no salt injury and had higher K+/Na+ ratio, relative water content (RWC), chlorophyll, glycine betaine, and soluble sugars in leaves while lower H2O2 induced fluorescence signals in roots as compared to L-4076. Transcriptomic profile revealed a total of 17,433 significant differentially expressed genes (DEGs) under different treatments and cultivar combinations that include 2557 upregulated and 1533 downregulated transcripts between contrasting cultivars under salt stress. Accuracy of transcriptomic analysis was validated through quantification of 10 DEGs via quantitative real-time polymerase chain reaction (qRT-PCR). DEGs were functionally characterized by Gene Ontology (GO) analysis and assigned to various metabolic pathways using MapMan. DEGs were found to be significantly associated with phytohormone-mediated signal transduction, cellular redox homoeostasis, secondary metabolism, nitrogen metabolism, and cellular stress signaling. The present study revealed putative molecular mechanism of salinity tolerance in lentil together with identification of 5643 simple sequence repeats (SSRs) and 176,433 single nucleotide polymorphisms (SNPs) which can be utilized to enhance linkage maps density along with detection of quantitative trait loci (QTLs) associated with traits of interests. Stress-related pathways identified in this study divulged plant functioning that can be targeted to improve salinity stress tolerance in crop species.
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Gouda G, Gupta MK, Donde R, Sabarinathan S, Vadde R, Behera L, Mohapatra T. Computational Epigenetics in Rice Research. APPLICATIONS OF BIOINFORMATICS IN RICE RESEARCH 2021:113-140. [DOI: 10.1007/978-981-16-3997-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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63
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Wyler M, Stritt C, Walser JC, Baroux C, Roulin AC. Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon. Genome Biol Evol 2020; 12:1994-2001. [PMID: 32853352 PMCID: PMC7643609 DOI: 10.1093/gbe/evaa180] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2020] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications, such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation, and nearby gene expression in additional plant species. Here, we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for 11 natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated with a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon.
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Affiliation(s)
- Michele Wyler
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - Christoph Stritt
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | | | - Célia Baroux
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - Anne C Roulin
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
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Malinowska M, Nagy I, Wagemaker CAM, Ruud AK, Svane SF, Thorup-Kristensen K, Jensen CS, Eriksen B, Krusell L, Jahoor A, Jensen J, Eriksen LB, Asp T. The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth. THE PLANT GENOME 2020; 13:e20049. [PMID: 33217208 DOI: 10.1002/tpg2.20049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/14/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgare L.) genome across several commercial and historical cultivars. This study adapted a genotyping-by-sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context-specific DNA methylation at the single-base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10-fold higher levels than those in Arabidopsis thaliana (L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long-terminal repeats (LTR) retrotransposons Gypsy and Copia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome-level structural and functional aspects of methylation in barley.
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Affiliation(s)
- Marta Malinowska
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
- Center for Quantitative Genetics & Genomics, Aarhus University, Slagelse, Denmark
| | - Istvan Nagy
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
- Center for Quantitative Genetics & Genomics, Aarhus University, Slagelse, Denmark
| | | | - Anja K Ruud
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
- Center for Quantitative Genetics & Genomics, Aarhus University, Slagelse, Denmark
| | - Simon F Svane
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | | | | | | | | | | | | | - Lars Bonde Eriksen
- Landbrug & Fødevarer, SEGES, Aarhus, Denmark
- LIMAGRAIN A/S, Horsens, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
- Center for Quantitative Genetics & Genomics, Aarhus University, Slagelse, Denmark
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Saban JM, Watson-Lazowski A, Chapman MA, Taylor G. The methylome is altered for plants in a high CO 2 world: Insights into the response of a wild plant population to multigenerational exposure to elevated atmospheric [CO 2 ]. GLOBAL CHANGE BIOLOGY 2020; 26:6474-6492. [PMID: 32902071 DOI: 10.1111/gcb.15249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Unravelling plant responses to rising atmospheric CO2 concentration ([CO2 ]) has largely focussed on plastic functional attributes to single generation [CO2 ] exposure. Quantifying the consequences of long-term, decadal multigenerational exposure to elevated [CO2 ] and the genetic changes that may underpin evolutionary mechanisms with [CO2 ] as a driver remain largely unexplored. Here, we investigated both plastic and evolutionary plant responses to elevated [CO2 ] by applying multi-omic technologies using populations of Plantago lanceolata L., grown in naturally high [CO2 ] for many generations in a CO2 spring. Seed from populations at the CO2 spring and an adjacent control site (ambient [CO2 ]) were grown in a common environment for one generation, and then offspring were grown in ambient or elevated [CO2 ] growth chambers. Low overall genetic differentiation between the CO2 spring and control site populations was found, with evidence of weak selection in exons. We identified evolutionary divergence in the DNA methylation profiles of populations derived from the spring relative to the control population, providing the first evidence that plant methylomes may respond to elevated [CO2 ] over multiple generations. In contrast, growth at elevated [CO2 ] for a single generation induced limited methylome remodelling (an order of magnitude fewer differential methylation events than observed between populations), although some of this appeared to be stably transgenerationally inherited. In all, 59 regions of the genome were identified where transcripts exhibiting differential expression (associated with single generation or long-term natural exposure to elevated [CO2 ]) co-located with sites of differential methylation or with single nucleotide polymorphisms exhibiting significant inter-population divergence. This included genes in pathways known to respond to elevated [CO2 ], such as nitrogen use efficiency and stomatal patterning. This study provides the first indication that DNA methylation may contribute to plant adaptation to future atmospheric [CO2 ] and identifies several areas of the genome that are targets for future study.
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Affiliation(s)
- Jasmine M Saban
- School of Biological Sciences, University of Southampton, Southampton, UK
| | | | - Mark A Chapman
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, UK
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
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Genitoni J, Vassaux D, Delaunay A, Citerne S, Portillo Lemus L, Etienne MP, Renault D, Stoeckel S, Barloy D, Maury S. Hypomethylation of the aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala mimics the adaptive transition into the terrestrial morphotype. PHYSIOLOGIA PLANTARUM 2020; 170:280-298. [PMID: 32623739 DOI: 10.1111/ppl.13162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Ongoing global changes affect ecosystems and open up new opportunities for biological invasion. The ability of invasive species to rapidly adapt to new environments represents a relevant model for studying short-term adaptation mechanisms. The aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala, is classified as harmful in European rivers. In French wet meadows, this species has shown a rapid transition from aquatic to terrestrial environments with emergence of two distinct morphotypes in 5 years. To understand the heritable mechanisms involved in adjustment to such a new environment, we investigate both genetic and epigenetic as possible sources of flexibility involved in this fast terrestrial transition. We found a low overall genetic differentiation between the two morphotypes arguing against the possibility that terrestrial morphotype emerged from a new adaptive genetic capacity. Artificial hypomethylation was induced on both morphotypes to assess the epigenetic hypothesis. We analyzed global DNA methylation, morphological changes, phytohormones and metabolite profiles of both morphotype responses in both aquatic and terrestrial conditions in shoot and root tissues. Hypomethylation significantly affected morphological variables, phytohormone levels and the amount of some metabolites. The effects of hypomethylation depended on morphotypes, conditions and plant tissues, which highlighted differences among the morphotypes and their plasticity. Using a correlative integrative approach, we showed that hypomethylation of the aquatic morphotype mimicked the characteristics of the terrestrial morphotype. Our data suggest that DNA methylation rather than a new adaptive genetic capacity is playing a key role in L. grandiflora subsp. hexapetala plasticity during its rapid aquatic to terrestrial transition.
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Affiliation(s)
- Julien Genitoni
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Danièle Vassaux
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Alain Delaunay
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Luis Portillo Lemus
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Marie-Pierre Etienne
- Institut Agro, CNRS, Université Rennes, IRMAR (Institut de Recherche Mathématique de Rennes) - UMR 6625, Rennes, F-35000, France
| | - David Renault
- UMR CNRS 6553 EcoBio, University of Rennes 1, Rennes, France
- Institut Universitaire de France, 1 rue Descartes, Paris, France
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université Rennes, Le Rheu, 35653, France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
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67
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Geng Y, Chang N, Zhao Y, Qin X, Lu S, Crabbe MJC, Guan Y, Zhang T. Increased epigenetic diversity and transient epigenetic memory in response to salinity stress in Thlaspi arvense. Ecol Evol 2020; 10:11622-11630. [PMID: 33144988 PMCID: PMC7593180 DOI: 10.1002/ece3.6795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 01/20/2023] Open
Abstract
Epigenetic diversity could play an important role in adaptive evolution of organisms, especially for plant species occurring in new and stressful environments. Thlaspi arvense (field pennycress), a valuable oilseed crop, is widespread in temperate regions of the northern hemisphere. In this study, we investigated the effect of salinity stress on the epigenetic variation of DNA methylation and epigenetic stress memory in pennycress using methylation-sensitive amplification polymorphism (MSAP) markers. We examined how the status of DNA methylation changes across individuals in response to salinity stress and whether such an effect of maternal stress could be transferred to offspring for one or two generations in nonstressed environments. Our results based on 306 epiloci indicated no consistent change of DNA methylation status in specific epiloci across individuals within the same conditions. In contrast, we found that the epigenetic diversity at population level increased significantly in response to the stimulation of salinity stress; and this "stimulation effect" could be transferred partially in the form of stress memory to at least two generations of offspring in nonstressed environments. In addition, we observed a parallel change in functionally important traits, that is, phenotypic variation was significantly higher in plants grown under salinity stress compared with those of control groups. Taken together, our results provide novel clues for the increased spontaneous epimutation rate in response to stress in plants, of potential adaptive significance.
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Affiliation(s)
- Yupeng Geng
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Na Chang
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Yuewan Zhao
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Xiaoying Qin
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Shugang Lu
- School of Life SciencesYunnan UniversityKunmingChina
| | - M. James C. Crabbe
- Wolfson CollegeOxford UniversityUK
- Institute of Biomedical and Environmental Science & TechnologyUniversity of BedfordshireLutonUK
- School of Life ScienceShanxi UniversityTaiyuanChina
| | - Yabin Guan
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
- School of Life SciencesYunnan UniversityKunmingChina
| | - Ticao Zhang
- College of Chinese Material MedicaYunnan University of Chinese MedicineKunmingChina
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68
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do Amaral MN, Auler PA, Rossatto T, Barros PM, Oliveira MM, Braga EJB. Long-term somatic memory of salinity unveiled from physiological, biochemical and epigenetic responses in two contrasting rice genotypes. PHYSIOLOGIA PLANTARUM 2020; 170:248-268. [PMID: 32515828 DOI: 10.1111/ppl.13149] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Plants are constantly exposed to environmental fluctuations, that may occur in a single day or over longer periods. In many cases, abiotic stresses are transient and recurrent, impacting how plants respond in subsequent adverse conditions. Adaptation mechanisms may occur at the physiological, biochemical and molecular level, modifying transcriptional response, regulatory proteins, epigenetic marks or metabolites. Here, we aimed to uncover the different strategies that rice uses to respond to recurrent stress. We tested varieties with contrasting behavior towards salinity (tolerance or sensitivity) and imposed salt stress (150 mM NaCl) during 48 h at vegetative and/or reproductive stages. After 48 h of stress in reproductive stage, leaves and roots were harvested separately or otherwise the plants were submitted to a 24 h recovery, prior to sample harvesting. Plants submitted to a recurrent stress responded differently from those suffering a single stress event. In the case of the sensitive genotype, recurrent stress led to lower Na/K ratio in roots and lower hydrogen peroxide accumulation and lipid peroxidation in leaves, but maintenance of global DNA methylation levels. In the tolerant genotype, recurrent stress did neither affect the Na/K ratio nor the stomatal conductance, although the levels of superoxide anion and hydrogen peroxide accumulation were lower, as also observed for global levels of DNA methylation. Our work shows that a short pre-exposure to salt stress may improve rice tolerance to subsequent stress, trough biochemical, physiological and epigenetic processes, with more significant changes visible in the tolerant genotype.
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Affiliation(s)
| | - Priscila Ariane Auler
- Department of Botany, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Tatiana Rossatto
- Department of Botany, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Pedro M Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress - Plant Functional Genomics Lab, Av. da República, Oeiras, 2780-157, Portugal
| | - Maria Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress - Plant Functional Genomics Lab, Av. da República, Oeiras, 2780-157, Portugal
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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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70
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Gahlaut V, Samtani H, Khurana P. Genome-wide identification and expression profiling of cytosine-5 DNA methyltransferases during drought and heat stress in wheat (Triticum aestivum). Genomics 2020; 112:4796-4807. [PMID: 32890700 DOI: 10.1016/j.ygeno.2020.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 01/25/2023]
Abstract
DNA methylation is a potential epigenetic mechanism that regulates genome stability, development, and stress mitigation in plants. It is mediated by cytosine-5 DNA methyltransferases (C5-MTases). We identified 52 wheat C5-MTases; and based on domain structure and phylogenetics, these 52 C5-MTases were classified into four sub-families including MET, CMT, DRM and DNMT2; and were distributed on 18 chromosomes. Cis-acting regulatory elements analysis identified abiotic stress-responsive, phytohormone-responsive, development-related and light-related elements in the promoters of TaC5-MTases. We also examined the transcript abundance of TaC5-MTases in different tissues, developmental stages and under abiotic stresses. Notably, most of the TaC5-MTases (TaCMT2, TaCMT3b, TaCMT3c, TaMET1, TaDRM10, TaDNMT2) showed differential regulation of their transcript abundance during drought and heat stress. Overall, the above results provide significant insights into the expression and the probable functions of TaC5-MTases and will also expedite future research programs to explore the mechanisms of epigenetic regulation in wheat.
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Affiliation(s)
- Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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71
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Pecinka A, Chevalier C, Colas I, Kalantidis K, Varotto S, Krugman T, Michailidis C, Vallés MP, Muñoz A, Pradillo M. Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5205-5222. [PMID: 31626285 DOI: 10.1093/jxb/erz457] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.
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Affiliation(s)
- Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Agricultural and Biotechnological Research, Olomouc, Czech Republic
| | | | - Isabelle Colas
- James Hutton Institute, Cell and Molecular Science, Pr Waugh's Lab, Invergowrie, Dundee, UK
| | - Kriton Kalantidis
- Department of Biology, University of Crete, and Institute of Molecular Biology Biotechnology, FoRTH, Heraklion, Greece
| | - Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment (DAFNAE) University of Padova, Agripolis viale dell'Università, Legnaro (PD), Italy
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Christos Michailidis
- Institute of Experimental Botany, Czech Acad Sci, Praha 6 - Lysolaje, Czech Republic
| | - María-Pilar Vallés
- Department of Genetics and Plant Breeding, Estación Experimental Aula Dei (EEAD), Spanish National Research Council (CSIC), Zaragoza, Spain
| | - Aitor Muñoz
- Department of Plant Molecular Genetics, National Center of Biotechnology/Superior Council of Scientific Research, Autónoma University of Madrid, Madrid, Spain
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
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Varotto S, Tani E, Abraham E, Krugman T, Kapazoglou A, Melzer R, Radanović A, Miladinović D. Epigenetics: possible applications in climate-smart crop breeding. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5223-5236. [PMID: 32279074 PMCID: PMC7475248 DOI: 10.1093/jxb/eraa188] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/09/2020] [Indexed: 05/23/2023]
Abstract
To better adapt transiently or lastingly to stimuli from the surrounding environment, the chromatin states in plant cells vary to allow the cells to fine-tune their transcriptional profiles. Modifications of chromatin states involve a wide range of post-transcriptional histone modifications, histone variants, DNA methylation, and activity of non-coding RNAs, which can epigenetically determine specific transcriptional outputs. Recent advances in the area of '-omics' of major crops have facilitated identification of epigenetic marks and their effect on plant response to environmental stresses. As most epigenetic mechanisms are known from studies in model plants, we summarize in this review recent epigenetic studies that may be important for improvement of crop adaptation and resilience to environmental changes, ultimately leading to the generation of stable climate-smart crops. This has paved the way for exploitation of epigenetic variation in crop breeding.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals, and the Environment, University of Padova, Agripolis, Viale dell’Università, Padova, Italy
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Athens, Greece
| | - Eleni Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Demeter (HAO-Demeter), Lykovrysi, Greece
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
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Alterations of Rice ( Oryza sativa L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus. Int J Mol Sci 2020; 21:ijms21165753. [PMID: 32796598 PMCID: PMC7570085 DOI: 10.3390/ijms21165753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/31/2022] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) causes severe yield losses in rice (Oryza sativa L.) in China. Studies have shown that the mechanisms of DNA methylation-mediated plant defense against DNA viruses and RNA viruses are different. However, in rice its function in response to infection of RBSDV, a double-stranded RNA virus, remains unclear. In this study, high-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice. Widespread differences were identified in CG and non-CG contexts between the RBSDV-infected and RBSDV-free rice. We identified a large number of differentially methylated regions (DMRs) along the genome of RBSDV-infected rice. Additionally, the transcriptome sequencing analysis obtained 1119 differentially expressed genes (DEGs). Correlation analysis of DMRs-related genes (DMGs) and DEGs filtered 102 genes with positive correlation and 71 genes with negative correlation between methylation level at promoter regions and gene expression. Key genes associated with maintaining DNA methylation in rice were analyzed by RT-qPCR and indicated that OsDMT702 might be responsible for the global increase of DNA methylation level in rice under RBSDV stress. Our results suggest important roles of rice DNA methylation in response to RBSDV and provide potential target genes for rice antiviral immunity.
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74
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Ostrowska-Mazurek A, Kasprzak P, Kubala S, Zaborowska M, Sobieszczuk-Nowicka E. Epigenetic Landmarks of Leaf Senescence and Crop Improvement. Int J Mol Sci 2020; 21:ijms21145125. [PMID: 32698545 PMCID: PMC7404090 DOI: 10.3390/ijms21145125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 01/04/2023] Open
Abstract
This review synthesizes knowledge on epigenetic regulation of leaf senescence and discusses the possibility of using this knowledge to improve crop quality. This control level is implemented by different but interacting epigenetic mechanisms, including DNA methylation, covalent histone modifications, and non-covalent chromatin remodeling. The genetic and epigenetic changes may act alone or together and regulate the gene expression, which may result in heritable (stress memory) changes and may lead to crop survival. In the review, the question also arises whether the mitotically stable epigenetic information can be used for crop improvement. The barley crop model for early and late events of dark-induced leaf senescence (DILS), where the point of no return was defined, revealed differences in DNA and RNA modifications active in DILS compared to developmental leaf senescence. This suggests the possibility of a yet-to-be-discovered epigenetic-based switch between cell survival and cell death. Conclusions from the analyzed research contributed to the hypothesis that chromatin-remodeling mechanisms play a role in the control of induced leaf senescence. Understanding this mechanism in crops might provide a tool for further exploitation toward sustainable agriculture: so-called epibreeding.
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Affiliation(s)
- Agnieszka Ostrowska-Mazurek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
| | - Piotr Kasprzak
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
| | - Szymon Kubala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5A, 02-106 Warsaw, Poland; (S.K.); (M.Z.)
| | - Magdalena Zaborowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5A, 02-106 Warsaw, Poland; (S.K.); (M.Z.)
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
- Correspondence: ; Tel.: +48-61-829-5892
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DNA methylation reprogramming during seed development and its functional relevance in seed size/weight determination in chickpea. Commun Biol 2020; 3:340. [PMID: 32620865 PMCID: PMC7335156 DOI: 10.1038/s42003-020-1059-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/08/2020] [Indexed: 11/21/2022] Open
Abstract
Seed development is orchestrated via complex gene regulatory networks and pathways. Epigenetic factors may also govern seed development and seed size/weight. Here, we analyzed DNA methylation in a large-seeded chickpea cultivar (JGK 3) during seed development stages. Progressive gain of CHH context DNA methylation in transposable elements (TEs) and higher frequency of small RNAs in hypermethylated TEs during seed development suggested a role of the RNA-dependent DNA methylation pathway. Frequency of intragenic TEs was higher in CHH context differentially methylated region (DMR) associated differentially expressed genes (DEGs). CG context hyper/hypomethylation within the gene body was observed for most of DMR-associated DEGs in JGK 3 as compared to small-seeded chickpea cultivar (Himchana 1). We identified candidate genes involved in seed size/weight determination exhibiting CG context hypermethylation within the gene body and higher expression in JGK 3. This study provides insights into the role of DNA methylation in seed development and seed size/weight determination in chickpea. Rajkumar et al. report progressive gain of CHH context DNA methylation in transposable elements during seed development in chickpea, of which hypermethylation is associated with small RNAs. The candidate genes that determine seed size/weight in chickpea show CG context hypermethylation in the gene body and higher expression in large-seeded cultivar.
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N'Diaye A, Byrns B, Cory AT, Nilsen KT, Walkowiak S, Sharpe A, Robinson SJ, Pozniak CJ. Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat. THE PLANT GENOME 2020; 13:e20027. [PMID: 33016606 DOI: 10.1002/tpg2.20027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/24/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is a mechanism of epigenetic modification in eukaryotic organisms. Generally, methylation within genes promoter inhibits regulatory protein binding and represses transcription, whereas gene body methylation is associated with actively transcribed genes. However, it remains unclear whether there is interaction between methylation levels across genic regions and which site has the biggest impact on gene regulation. We investigated and used the methylation patterns of the bread wheat cultivar Chinese Spring to uncover differentially expressed genes (DEGs) between roots and leaves, using six machine learning algorithms and a deep neural network. As anticipated, genes with higher expression in leaves were mainly involved in photosynthesis and pigment biosynthesis processes whereas genes that were not differentially expressed between roots and leaves were involved in protein processes and membrane structures. Methylation occurred preponderantly (60%) in the CG context, whereas 35 and 5% of methylation occurred in CHG and CHH contexts, respectively. Methylation levels were highly correlated (r = 0.7 to 0.9) between all genic regions, except within the promoter (r = 0.4 to 0.5). Machine learning models gave a high (0.81) prediction accuracy of DEGs. There was a strong correlation (p-value = 9.20×10-10 ) between all features and gene expression, suggesting that methylation across all genic regions contribute to gene regulation. However, the methylation of the promoter, the CDS and the exon in CG context was the most impactful. Our study provides more insights into the interplay between DNA methylation and gene expression and paves the way for identifying tissue-specific genes using methylation profiles.
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Affiliation(s)
- Amidou N'Diaye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Brook Byrns
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Aron T Cory
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Kirby T Nilsen
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Sean Walkowiak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Andrew Sharpe
- Global Institute for Food Security, Saskatoon, SK, Canada, S7N 0W9
| | - Stephen J Robinson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Curtis J Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
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Ahmed IM, Nadira UA, Qiu CW, Cao F, Chen ZH, Vincze E, Wu F. The Barley S-Adenosylmethionine Synthetase 3 Gene HvSAMS3 Positively Regulates the Tolerance to Combined Drought and Salinity Stress in Tibetan Wild Barley. Cells 2020; 9:cells9061530. [PMID: 32585935 PMCID: PMC7349212 DOI: 10.3390/cells9061530] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 11/16/2022] Open
Abstract
Drought and salinity are two of the most frequently co-occurring abiotic stresses. Despite recent advances in the elucidation of the effects of these stresses individually during the vegetative stage of plants, significant gaps exist in our understanding of the combined effects of these two frequently co-occurring stresses. Here, Tibetan wild barley XZ5 (drought tolerant), XZ16 (salt tolerant), and cultivated barley cv. CM72 (salt tolerant) were subjected to drought (D), salinity (S), or a combination of both treatments (D+S). Protein synthesis is one of the primary activities of the green part of the plant. Therefore, leaf tissue is an important parameter to evaluate drought and salinity stress conditions. Sixty differentially expressed proteins were identified by mass spectrometry (MALDI-TOF/TOF) and classified into 9 biological processes based on Gene Ontology annotation. Among them, 21 proteins were found to be expressed under drought or salinity alone; however, under D+S, 7 proteins, including S-adenosylmethionine synthetase 3 (SAMS3), were exclusively upregulated in drought-tolerant XZ5 but not in CM72. HvSAMS3 carries both N-terminal and central domains compared with Arabidopsis and activates the expression of several ethylene (ET)-responsive transcription factors. HvSAMS3 is mainly expressed in the roots and stems, and HvSAMS3 is a secretory protein located in the cell membrane and cytoplasm. Barley stripe mosaic virus-based virus-induced gene silencing (BSMV-VIGS) of HvSAMS3 in XZ5 severely compromised its tolerance to D+S and significantly reduced plant growth and K+ uptake. The reduced tolerance to the combined stress was associated with the inhibition of polyamines such as spermidine and spermine, polyamine oxidase, ethylene, biotin, and antioxidant enzyme activities. Furthermore, the exogenous application of ethylene and biotin improved the tolerance to D+S in BSMV-VIGS:HvSAMS3-inoculated plants. Our findings highlight the significance of HvSAMS3 in the tolerance to D+S in XZ5.
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Affiliation(s)
- Imrul Mosaddek Ahmed
- Department of Agronomy and Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (I.M.A.); (U.A.N.); (C.-W.Q.); (F.C.)
- Plant Physiology Division, Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh
| | - Umme Aktari Nadira
- Department of Agronomy and Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (I.M.A.); (U.A.N.); (C.-W.Q.); (F.C.)
| | - Cheng-Wei Qiu
- Department of Agronomy and Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (I.M.A.); (U.A.N.); (C.-W.Q.); (F.C.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Fangbin Cao
- Department of Agronomy and Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (I.M.A.); (U.A.N.); (C.-W.Q.); (F.C.)
| | - Zhong-Hua Chen
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia;
| | - Eva Vincze
- Department of Molecular Biology and Genetics, Aarhus University, Fosøgsvej 1, DK-4200 Slagelse, Denmark;
| | - Feibo Wu
- Department of Agronomy and Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (I.M.A.); (U.A.N.); (C.-W.Q.); (F.C.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-571-8898-2827
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78
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Recurrent Water Deficit and Epigenetic Memory in Medicago sativa L. Varieties. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10093110] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Global DNA methylation changes in response to recurrent drought stress were investigated in two common Greek Medicago sativa L. varieties (Lamia and Chaironia-Institute of Ιndustrial and Forage Crops). The water deficit was implemented in two phases. At the end of the first phase, which lasted for 60 days, the plants were cut at the height of 5 cm and were watered regularly for two months before being subjected to the second drought stress, which lasted for two weeks. Finally, the following groups of plants were formed: CC (controls both in phase I and phase II), CD2 (Controls in phase I, experiencing drought in phase II), and D1D2 (were subjected to drought in both phase I and phase II). At the end of phase II, samples were taken for global DNA methylation analysis with the Methylation Sensitive Amplification Polymorphism (MSAP) method, and all plants were harvested in order to measure the fresh and dry weight of roots and shoots. The variety Lamia responded better, especially the D1D2 group, compared to Chaironia in terms of root and shoot dry weight. Additionally, the shoots of Lamia had a constant water status for CD2 and D1D2 group of plants. According to DNA methylation analysis by the MSAP method, Lamia had lower total DNA methylation percentage after the second drought episode (D1D2) as compared to the plants CD2 that had experienced only one drought episode. On the other hand, the total DNA methylation percentage of Chaironia was almost the same in plants grown under recurrent drought stress conditions compared to control plants. In conclusion, the decrease of DNA methylation of Lamia stressed plants probably indicates the existence of an epigenetic mechanism that may render drought tolerance.
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Rajkumar MS, Shankar R, Garg R, Jain M. Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars. Genomics 2020; 112:3537-3548. [PMID: 32278023 DOI: 10.1016/j.ygeno.2020.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/13/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022]
Abstract
DNA methylation governs gene regulation in plants in response to environmental conditions. Here, we analyzed role of DNA methylation under desiccation and salinity stresses in three (IR64, stress-sensitive; Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) rice cultivars via bisulphite sequencing. Methylation in CG context within gene body and methylation in CHH context in distal promoter regions were positively correlated with gene expression. Hypomethylation in Nagina 22 and hypermethylation in Pokkali in response to desiccation and salinity stresses, respectively, were correlated with higher expression of few abiotic stress response related genes. Most of the differentially methylated and differentially expressed genes (DMR-DEGs) were cultivar-specific, suggesting an important role of DNA methylation in abiotic stress responses in rice in cultivar-specific manner. DMR-DEGs harboring differentially methylated cytosines due to DNA polymorphisms between the sensitive and tolerant cultivars in their promoter regions and/or coding regions were identified, suggesting the role of epialleles in abiotic stress responses.
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Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rama Shankar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India.
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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80
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Method for Bisulfite Sequencing Data Analysis for Whole-Genome Level DNA Methylation Detection in Legumes. Methods Mol Biol 2020; 2107:127-145. [PMID: 31893445 DOI: 10.1007/978-1-0716-0235-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Methylation of cytosines in DNA is the most stable type of epigenetic modification that is established and maintained by different enzymes. In plants, DNA methylation is inherited from one generation to another leaving an epigenetic mark as a memory of previous state, which may include encounter with stress or pathogen. Advancement in the next generation sequencing technologies has enabled the profiling of methylation marks. Whole-genome bisulfite sequencing (WGBS) has the potential to unravel the patterns of DNA methylation at single-base resolution. Though the sequencing technologies have evolved drastically, analysis of WGBS data still remains challenging. Here, we provide a methodology for performing WGBS data analysis along with critical steps for identification of methylation marks in plant genomes including legumes.
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81
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Gallo-Franco JJ, Sosa CC, Ghneim-Herrera T, Quimbaya M. Epigenetic Control of Plant Response to Heavy Metal Stress: A New View on Aluminum Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:602625. [PMID: 33391313 PMCID: PMC7772216 DOI: 10.3389/fpls.2020.602625] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/23/2020] [Indexed: 05/05/2023]
Abstract
High concentrations of heavy metal (HM) ions impact agronomic staple crop production in acid soils (pH ≤ 5) due to their cytotoxic, genotoxic, and mutagenic effects. Among cytotoxic ions, the trivalent aluminum cation (Al3+) formed by solubilization of aluminum (Al) into acid soils, is one of the most abundant and toxic elements under acidic conditions. In recent years, several studies have elucidated the different signal transduction pathways involved in HM responses, identifying complementary genetic mechanisms conferring tolerance to plants. Although epigenetics has become more relevant in abiotic stress studies, epigenetic mechanisms underlying plant responses to HM stress remain poorly understood. This review describes the main epigenetic mechanisms related to crop responses during stress conditions, specifically, the molecular evidence showing how epigenetics is at the core of plant adaptation responses to HM ions. We highlight the epigenetic mechanisms that induce Al tolerance. Likewise, we analyze the pivotal relationship between epigenetic and genetic factors associated with HM tolerance. Finally, using rice as a study case, we performed a general analysis over previously whole-genome bisulfite-seq published data. Specific genes related to Al tolerance, measured in contrasting tolerant and susceptible rice varieties, exhibited differences in DNA methylation frequency. The differential methylation patterns could be associated with epigenetic regulation of rice responses to Al stress, highlighting the major role of epigenetics over specific abiotic stress responses.
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Affiliation(s)
- Jenny Johana Gallo-Franco
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana, Cali, Cali, Colombia
| | - Chrystian Camilo Sosa
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana, Cali, Cali, Colombia
- Grupo de Investigación en Evolución, Ecología y Conservación EECO, Programa de Biología, Facultad de Ciencias Básicas y Tecnologías, Universidad del Quindío, Armenia, Colombia
| | | | - Mauricio Quimbaya
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana, Cali, Cali, Colombia
- *Correspondence: Mauricio Quimbaya,
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82
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Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem. Mol Biol Rep 2019; 47:1339-1360. [DOI: 10.1007/s11033-019-05236-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/08/2019] [Accepted: 12/07/2019] [Indexed: 11/26/2022]
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83
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Docimo T, De Stefano R, De Palma M, Cappetta E, Villano C, Aversano R, Tucci M. Transcriptional, metabolic and DNA methylation changes underpinning the response of Arundo donax ecotypes to NaCl excess. PLANTA 2019; 251:34. [PMID: 31848729 DOI: 10.1007/s00425-019-03325-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Arundo donax ecotypes react differently to salinity, partly due to differences in constitutive defences and methylome plasticity. Arundo donax L. is a C3 fast-growing grass that yields high biomass under stress. To elucidate its ability to produce biomass under high salinity, we investigated short/long-term NaCl responses of three ecotypes through transcriptional, metabolic and DNA methylation profiling of leaves and roots. Prolonged salt treatment discriminated the sensitive ecotype 'Cercola' from the tolerant 'Domitiana' and 'Canneto' in terms of biomass. Transcriptional and metabolic responses to NaCl differed between the ecotypes. In roots, constitutive expression of ion transporter and stress-related transcription factors' genes was higher in 'Canneto' and 'Domitiana' than 'Cercola' and 21-day NaCl drove strong up-regulation in all ecotypes. In leaves, unstressed 'Domitiana' confirmed higher expression of the above genes, whose transcription was repressed in 'Domitiana' but induced in 'Cercola' following NaCl treatment. In all ecotypes, salinity increased proline, ABA and leaf antioxidants, paralleled by up-regulation of antioxidant genes in 'Canneto' and 'Cercola' but not in 'Domitiana', which tolerated a higher level of oxidative damage. Changes in DNA methylation patterns highlighted a marked capacity of the tolerant 'Domitiana' ecotype to adjust DNA methylation to salt stress. The reduced salt sensitivity of 'Domitiana' and, to a lesser extent, 'Canneto' appears to rely on a complex set of constitutively activated defences, possibly due to the environmental conditions of the site of origin, and on higher plasticity of the methylome. Our findings provide insights into the mechanisms of adaptability of A. donax ecotypes to salinity, offering new perspectives for the improvement of this species for cultivation in limiting environments.
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Affiliation(s)
- Teresa Docimo
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Rosalba De Stefano
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Monica De Palma
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Elisa Cappetta
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Marina Tucci
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy.
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84
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Chen R, Li M, Zhang H, Duan L, Sun X, Jiang Q, Zhang H, Hu Z. Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots. BMC Genomics 2019; 20:730. [PMID: 31606033 PMCID: PMC6790039 DOI: 10.1186/s12864-019-6101-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/12/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Environmental stimuli can activate a series of physiological and biochemical responses in plants accompanied by extensive transcriptional reprogramming. Long non-coding RNAs (lncRNAs), as versatile regulators, control gene expression in multiple ways and participate in the adaptation to biotic and abiotic stresses. RESULTS In this study, soybean seedlings were continuously cultured for 15 days with high salinity solutions started from seed germination. Strand-specific whole transcriptome sequencing and stringent bioinformatic analysis led to the identification of 3030 long intergenic non-coding RNAs (lincRNAs) and 275 natural antisense transcripts (lncNATs) in soybean roots. In contrast to mRNAs, newly identified lncRNAs exhibited less exons, similar AU content to UTRs, even distribution across the genome and low evolutionary conservation. Remarkably, more than 75% of discovered lncRNAs that were activated or up-regulated by continuous salt stress mainly targeted proteins with binding and catalytic activities. Furthermore, two DNA methylation maps with single-base resolution were generated by using reduced representation bisulfite sequencing, offering a genome-wide perspective and important clues for epigenetic regulation of stress-associated lncRNAs and protein-coding genes. CONCLUSIONS Taken together, our findings systematically demonstrated the characteristics of continuous salt stress-induced lncRNAs and extended the knowledge of corresponding methylation profiling, providing valuable evidence for a better understanding of how plants cope with long-term salt stress circumstances.
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Affiliation(s)
- Rui Chen
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.
| | - Ming Li
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Huiyuan Zhang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lijin Duan
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Xianjun Sun
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiyan Jiang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zheng Hu
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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85
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Latutrie M, Gourcilleau D, Pujol B. Epigenetic variation for agronomic improvement: an opportunity for vegetatively propagated crops. AMERICAN JOURNAL OF BOTANY 2019; 106:1281-1284. [PMID: 31505022 PMCID: PMC6856848 DOI: 10.1002/ajb2.1357] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/23/2019] [Indexed: 05/10/2023]
Affiliation(s)
- Mathieu Latutrie
- PSL Université Paris: EPHE‐UPVD‐CNRSUSR 3278 CRIOBEUniversité de Perpignan52 Avenue Paul Alduy66860Perpignan CedexFrance
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174)Université Fédérale de Toulouse Midi‐Pyrénées, CNRS, IRD, UPS.118 route de Narbonne, Bat 4R131062Toulouse cedex 9France
| | - Delphine Gourcilleau
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174)Université Fédérale de Toulouse Midi‐Pyrénées, CNRS, IRD, UPS.118 route de Narbonne, Bat 4R131062Toulouse cedex 9France
| | - Benoit Pujol
- PSL Université Paris: EPHE‐UPVD‐CNRSUSR 3278 CRIOBEUniversité de Perpignan52 Avenue Paul Alduy66860Perpignan CedexFrance
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174)Université Fédérale de Toulouse Midi‐Pyrénées, CNRS, IRD, UPS.118 route de Narbonne, Bat 4R131062Toulouse cedex 9France
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Razzaque S, Elias SM, Haque T, Biswas S, Jewel GMNA, Rahman S, Weng X, Ismail AM, Walia H, Juenger TE, Seraj ZI. Gene Expression analysis associated with salt stress in a reciprocally crossed rice population. Sci Rep 2019; 9:8249. [PMID: 31160691 PMCID: PMC6546764 DOI: 10.1038/s41598-019-44757-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/21/2019] [Indexed: 11/27/2022] Open
Abstract
The rice landrace Horkuch, endemic to the southern saline coast of Bangladesh, is known to have salt tolerance traits and can therefore contribute to a high yielding recipient for breeding purposes. In this study, we reciprocally crossed Horkuch with high yielding but salt sensitive IR29 to detect the complement of genes that were responsible for conferring salt tolerance versus sensitivity at the seedling developmental stage. We looked at tolerant and sensitive F3 families from individual F2 segregating plants and analyzed them for differential gene expressions using RNAseq. In general, we observed higher numbers of genes differentially expressed in leaves compared to root tissues. This included both upregulation and downregulation of gene expression across our experimental factors. Gene expression decreased in sensitive leaf after stress exposure where tolerant plants showed the opposite trend. In root, tolerant plants expression decreased at higher time points of stress exposure. We also observed a strong maternal cytoplasmic effect on gene expression and this was most evident in roots where there was upregulation in functional enrichments related to phosphorylation, electron carriers, transporter and cation transmembrane activities. Stress groups (tolerant and sensitive) response in F3 families were distinctive in both cytoplasmic backgrounds and involved uniquely upregulated genes in tolerant progenies including membrane sensor proteins, enzymes involved with signaling pathways, such as those producing trehalose and G-protein coupled receptor proteins, photosynthesis-related enzymes and golgi body recycling as well as prolamin precursor proteins involved in refolding of proteins. On the other hand, sensitivity was found to be associated with differential upregulation of only a few redox proteins and higher number of apoptosis related genes compared to the tolerant response. Overall, our highly replicated experimental design was powerful and allowed the detection of relatively subtle differential expression. Our future goal is to correlate these expression differences with QTLs in this population, which would help identify the relative importance of specific genetic loci and provide a direct avenue for combining higher levels of salt tolerance with better agronomic traits in rice.
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Affiliation(s)
- Samsad Razzaque
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Sabrina M Elias
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, 68583, USA
| | - Taslima Haque
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Sudip Biswas
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - G M Nurnabi Azad Jewel
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sazzadur Rahman
- Plant Physiology Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Xiaoyu Weng
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | | | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, 68583, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Zeba I Seraj
- Plant Biotechnology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh.
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87
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Li J, Chen C, Wei J, Pan Y, Su C, Zhang X. SpPKE1, a Multiple Stress-Responsive Gene Confers Salt Tolerance in Tomato and Tobacco. Int J Mol Sci 2019; 20:E2478. [PMID: 31137458 PMCID: PMC6566969 DOI: 10.3390/ijms20102478] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 01/25/2023] Open
Abstract
Understanding the mechanism of abiotic-tolerance and producing germplasm of abiotic tolerance are important in plant research. Wild species often show more tolerance of environmental stress factors than their cultivated counterparts. Genes from wild species show potential abilities to improve abiotic resistance in cultivated species. Here, a tomato proline-, lysine-, and glutamic-rich type gene SpPKE1 was isolated from abiotic-resistant species (Solanum pennellii LA0716) for over-expression in tomato and tobacco for salt tolerance. The protein encoded by SpPKE1 was predominantly localized in the cytoplasm in tobacco. SpPKE1 and SlPKE1 (from cultivated species S. lycopersicum cv. M82) shared 89.7% similarity in amino acid sequences and their transcripts abundance in flowers and fruits was reduced by the imposition of drought or oxidative stress and the exogenous supply of abscisic acid. The DNA of the PKE1 promoter was highly methylated in fruit and leaf, and the methylation of the coding sequence in leaf was significantly higher than that in fruit at different development stages. The over-expression of SpPKE1 under the control of a CaMV (Cauliflower Mosaic Virus) 35S promoter in transgenic tomato and tobacco plants enhanced their tolerance to salt stress. PKE1 was downregulated by abiotic stresses but enhanced the plant's salt stress tolerance. Therefore, this gene may be involved in post-transcriptional regulation and may be an important candidate for molecular breeding of salt-tolerant plants.
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Affiliation(s)
- Jinhua Li
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Chunrui Chen
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Juanjuan Wei
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Yu Pan
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Chenggang Su
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Xingguo Zhang
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
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88
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Cadmium-induced genome-wide DNA methylation changes in growth and oxidative metabolism in Drosophila melanogaster. BMC Genomics 2019; 20:356. [PMID: 31072326 PMCID: PMC6507226 DOI: 10.1186/s12864-019-5688-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Background Cadmium (Cd)-containing chemicals can cause serious damage to biological systems. In animals and plants, Cd exposure can lead to metabolic disorders or death. However, for the most part the effects of Cd on specific biological processes are not known. DNA methylation is an important mechanism for the regulation of gene expression. In this study we examined the effects of Cd exposure on global DNA methylation in a living organism by whole-genome bisulfite sequencing (WGBS) using Drosophila melanogaster as model. Results A total of 71 differentially methylated regions and 63 differentially methylated genes (DMGs) were identified by WGBS. A total of 39 genes were demethylated in the Cd treatment group but not in the control group, whereas 24 showed increased methylation in the former relative to the latter. In most cases, demethylation activated gene expression: genes such as Cdc42 and Mekk1 were upregulated as a result of demethylation. There were 37 DMGs that overlapped with differentially expressed genes from the digital expression library including baz, Act5C, and ss, which are associated with development, reproduction, and energy metabolism. Conclusions DNA methylation actively regulates the physiological response to heavy metal stress in Drosophila in part via activation of apoptosis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5688-z) contains supplementary material, which is available to authorized users.
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89
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Cohen SP, Leach JE. Abiotic and biotic stresses induce a core transcriptome response in rice. Sci Rep 2019; 9:6273. [PMID: 31000746 PMCID: PMC6472405 DOI: 10.1038/s41598-019-42731-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/04/2019] [Indexed: 11/26/2022] Open
Abstract
Environmental stresses greatly limit crop yield. With the increase in extreme weather events due to climate change and the constant pressure of diseases and pests, there is an urgent need to develop crop varieties that can tolerate multiple stresses. However, our knowledge of how plants broadly respond to stress is limited. Here, we explore the rice core stress response via meta-analysis of publicly available rice transcriptome data. Our results confirm that rice universally down-regulates photosynthesis in response to both abiotic and biotic stress. Rice also generally up-regulates hormone-responsive genes during stress response, most notably genes in the abscisic acid, jasmonic acid and salicylic acid pathways. We identified several promoter motifs that are likely involved in stress-responsive regulatory mechanisms in rice. With this work, we provide a list of candidate genes to study for improving rice stress tolerance in light of environmental stresses. This work also serves as a proof of concept to show that meta-analysis of diverse transcriptome data is a valid approach to develop robust hypotheses for how plants respond to stress.
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Affiliation(s)
- Stephen P Cohen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, CO, 80523-1177, Fort Collins, USA.,Cell and Molecular Biology Graduate Program, Colorado State University, CO, 80523-1005, Fort Collins, USA
| | - Jan E Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, CO, 80523-1177, Fort Collins, USA.
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90
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Jha UC, Bohra A, Jha R, Parida SK. Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes. PLANT CELL REPORTS 2019; 38:255-277. [PMID: 30637478 DOI: 10.1007/s00299-019-02374-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/04/2019] [Indexed: 05/21/2023]
Abstract
Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Rintu Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067, India
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91
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Li P, Yang H, Wang L, Liu H, Huo H, Zhang C, Liu A, Zhu A, Hu J, Lin Y, Liu L. Physiological and Transcriptome Analyses Reveal Short-Term Responses and Formation of Memory Under Drought Stress in Rice. Front Genet 2019; 10:55. [PMID: 30800142 PMCID: PMC6375884 DOI: 10.3389/fgene.2019.00055] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/23/2019] [Indexed: 12/30/2022] Open
Abstract
In some plants, exposure to stress can induce a memory response, which appears to play an important role in adaptation to recurrent stress environments. However, whether rice exhibits drought stress memory and the molecular mechanisms that might underlie this process have remained unclear. Here, we ensured that rice drought memory was established after cycles of mild drought and re-watering treatment, and studied gene expression by whole-transcriptome strand-specific RNA sequencing (ssRNA-seq). We detected 6,885 transcripts and 238 lncRNAs involved in the drought memory response, grouped into 16 distinct patterns. Notably, the identified genes of dosage memory generally did not respond to the initial drought treatment. Our results demonstrate that stress memory can be developed in rice under appropriate water deficient stress, and lncRNA, DNA methylation and endogenous phytohormones (especially abscisic acid) participate in rice short-term drought memory, possibly acting as memory factors to activate drought-related memory transcripts in pathways such as photosynthesis and proline biosynthesis, to respond to the subsequent stresses.
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Affiliation(s)
- Ping Li
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Yang
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Wang
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
| | - Haoju Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Department of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Heqiang Huo
- Mid-Florida Research and Education Center, Department of Environmental Horticulture, University of Florida, Gainesville, FL, United States
| | - Chengjun Zhang
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
| | - Aizhong Liu
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
| | - Andan Zhu
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
| | - Jinyong Hu
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Li Liu
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
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92
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Feng Y, Liu J, Zhai L, Gan Z, Zhang G, Yang S, Wang Y, Wu T, Zhang X, Xu X, Han Z. Natural variation in cytokinin maintenance improves salt tolerance in apple rootstocks. PLANT, CELL & ENVIRONMENT 2019; 42:424-436. [PMID: 29989184 DOI: 10.1111/pce.13403] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 05/20/2023]
Abstract
Plants experiencing salt-induced stress often reduce cytokinin levels during the early phases of stress-response. Interestingly, we found that the cytokinin content in the apple rootstock "robusta" was maintained at a high level under salt stress. Through screening genes involved in cytokinin biosynthesis and catabolism, we found that the high expression levels of IPT5b in robusta roots were involved in maintaining the high cytokinin content. We identified a 42 bp deletion in the promoter region of IPT5b, which elevated IPT5b expression levels, and this deletion was linked to salt tolerance in robusta×M.9 segregating population. The 42 bp deletion resulted in the deletion of a Proline Response Element (ProRE), and our results suggest that ProRE negatively regulates IPT5b expression in response to proline. Under salt stress, the robusta cultivar maintains high cytokinin levels as IPT5b expression cannot be inhibited by proline due to the deletion of ProRE, leading to improve salt tolerance.
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Affiliation(s)
- Yi Feng
- College of Horticulture, China Agricultural University, Beijing, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jing Liu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Longmei Zhai
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zengyu Gan
- College of Horticulture, China Agricultural University, Beijing, China
| | - Guifen Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
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Ferreira LJ, Donoghue MTA, Barros P, Saibo NJ, Santos AP, Oliveira MM. Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance. EPIGENOMES 2019; 3:epigenomes3010004. [PMID: 34991273 PMCID: PMC8594724 DOI: 10.3390/epigenomes3010004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/07/2018] [Accepted: 01/15/2019] [Indexed: 11/18/2022] Open
Abstract
Chromatin structure, DNA methylation, and histone modifications act in a concerted manner to influence gene expression and therefore plant phenotypes. Environmental stresses are often associated with extensive chromatin rearrangements and modifications of epigenetic levels and patterns. Stress-tolerant plants can be a good tool to unveil potential connections between specific epigenetic modifications and stress tolerance capacity. We analyzed genome wide DNA methylation of a salt-tolerant rice variety under salinity and identified a set of differentially methylated regions (DMRs) between control and stress samples using high-throughput sequencing of DNA immunoprecipitated with the 5-methylcytosine antibody (MeDIP-Seq). The examination of DNA methylation pattern at DMRs regions revealed a general tendency for demethylation events in stress samples as compared to control. In addition, DMRs appear to influence the expression of genes located in their vicinity. We hypothesize that short regions as DMRs can shape the chromatin landscape of specific genomic regions and, therefore, may modulate the function of several genes. In this sense, the identification of DMRs represents one step towards to uncover new players in the regulation of stress-responsive genes and new target genes with potential application in enhancement of plant salinity-tolerance.
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Affiliation(s)
- Liliana J. Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, Portugal
| | | | - Pedro Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, Portugal
| | - Nelson J. Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, Portugal
| | - Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, Portugal
- Correspondence: ; Tel.: +351-214469660
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, Portugal
- IBET, Apartado 12, 2781-901 Oeiras, Portugal
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95
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Komivi D, Marie AM, Rong Z, Qi Z, Mei Y, Ndiaga C, Diaga D, Linhai W, Xiurong Z. The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with transcript accumulation in sesame. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:207-217. [PMID: 30466587 DOI: 10.1016/j.plantsci.2018.09.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 05/07/2023]
Abstract
DNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, probably because of its origin in Africa or India. Understanding DNA methylation patterns under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying sesame contrasting responses to these abiotic stresses. We combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, transcript accumulation, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes. Drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging stress decreased the level of methylation but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the levels of the differentially accumulated transcripts (DATs) highly correlated with the methylation patterns. We observed that DM was associated with an increase of DAT levels while DNM was correlated with a decrease of DAT levels. Altogether, sesame has divergent epigenetic programs that respond to drought and waterlogging stresses and an interplay among DNA methylation and transcript accumulation may partly modulate the contrasting responses to these stresses.
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Affiliation(s)
- Dossa Komivi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China; Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal; Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal.
| | - Ali Mmadi Marie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China; Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal; Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal
| | - Zhou Rong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Zhou Qi
- College of Life Science, Hubei University, Wuhan, China
| | - Yang Mei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Cisse Ndiaga
- Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal
| | - Diouf Diaga
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal
| | - Wang Linhai
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Zhang Xiurong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China.
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96
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Yang C, Zhang Y, Song Y, Lu X, Gao H. Genome-wide DNA methylation analysis of the regenerative and non-regenerative tissues in sika deer (Cervus nippon). Gene 2018; 676:249-255. [PMID: 30016669 DOI: 10.1016/j.gene.2018.07.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/06/2018] [Accepted: 07/10/2018] [Indexed: 01/20/2023]
Abstract
Deer antlers, the secondary organs of deer, are a unique model to study regeneration of organ/tissue in mammals. Pedicle periosteum (PP) is the key tissue type for antler regeneration. Based on our previous study, the DNA methylation was found to be the basic molecular mechanism underlying the antler regeneration. In this study, we compare the genome-wide DNA methylation level in regenerative tissues (the potentiated PP of antler, muscle, heart and liver) and non-regenerative tissue (the dormant PP) of deer by the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) method. Our results showed that DNA methylation level was significantly lower in the regenerative tissues compared to the non-regenerative tissue (P < 0.05). Furthermore, 26 T-DMRs which displayed different methylated status in regenerative and non-regenerative tissues were identified by the MSAP method, and were further confirmed by Southern blot analysis. Taken together, our data suggest that DNA methylation, an important epigenetic regulation mechanism, may play an important role in the mammalian tissue/organ regeneration.
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Affiliation(s)
- Chun Yang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, PR China; State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun, PR China.
| | - Yan Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, PR China
| | - Yanyan Song
- No. 2 Hospital of Jilin University, Changchun, PR China
| | - Xiao Lu
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, PR China; State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun, PR China
| | - Hang Gao
- No. 1 Hospital of Jilin University, Changchun, PR China.
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97
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Prudencio ÁS, Werner O, Martínez-García PJ, Dicenta F, Ros RM, Martínez-Gómez P. DNA Methylation Analysis of Dormancy Release in Almond ( Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing. Int J Mol Sci 2018; 19:ijms19113542. [PMID: 30423798 PMCID: PMC6274898 DOI: 10.3390/ijms19113542] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 01/26/2023] Open
Abstract
DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.
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Affiliation(s)
- Ángela S Prudencio
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Olaf Werner
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | | | - Federico Dicenta
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Rosa M Ros
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
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98
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Prudencio ÁS, Werner O, Martínez-García PJ, Dicenta F, Ros RM, Martínez-Gómez P. DNA Methylation Analysis of Dormancy Release in Almond ( Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing. Int J Mol Sci 2018. [PMID: 30423798 DOI: 10.3542/ijms19113542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.
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Affiliation(s)
- Ángela S Prudencio
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Olaf Werner
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | | | - Federico Dicenta
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Rosa M Ros
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
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99
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Parida AP, Raghuvanshi U, Pareek A, Singh V, Kumar R, Sharma AK. Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses. Mol Biol Rep 2018; 45:2653-2669. [PMID: 30350236 DOI: 10.1007/s11033-018-4435-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/10/2018] [Indexed: 01/25/2023]
Abstract
In tomato, DNA methylation has an inhibitory effect on fruit ripening. The inhibition of DNA methyltransferase by 5-azacytidine results in premature fruit ripening. Methyl CpG binding domain (MBD) proteins are the readers of DNA methylation marks and help in the recruitment of chromatin-modifying enzymes which affect gene expression. Therefore, we investigate their contribution during fruit development. In this study, we identified and analyzed 18 putative genes of Solanum lycopersicum and Solanum pimpinellifolium encoding MBD proteins. We also identified tomato MBD syntelogs in Capsicum annum and Solanum tuberosum. Sixty-three MBD genes identified from four different species of solanaceae were classified into three groups. An analysis of the conserved domains in these proteins identified additional domains along with MBD motif. The transcript profiling of tomato MBDs in wild-type and two non-ripening mutants, rin and Nr, indicated constructive information regarding their involvement during fruit development. When we performed a stage-specific expression analysis during fruit ripening, a gradual decrease in transcript accumulation in the wild-type fruit was detected. However, a very low expression was observed in the ripening mutants. Furthermore, many ethylene-responsive cis-elements were found in SlMBD gene promoters, and some of them were induced in the presence of exogenous ethylene. Further, we detected the possible role of these MBDs in abiotic stresses. We found that few genes were differentially expressed under various abiotic stress conditions. Our results provide an evidence of the involvement of the tomato MBDs in fruit ripening and abiotic stress responses, which would be helpful in further studies on these genes in tomato fruit ripening.
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Affiliation(s)
- Adwaita Prasad Parida
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Amit Pareek
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Vijendra Singh
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Rahul Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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100
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Viana VE, Busanello C, da Maia LC, Pegoraro C, Costa de Oliveira A. Activation of rice WRKY transcription factors: an army of stress fighting soldiers? CURRENT OPINION IN PLANT BIOLOGY 2018; 45:268-275. [PMID: 30060992 DOI: 10.1016/j.pbi.2018.07.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 05/04/2023]
Abstract
Rice WRKYs comprise a large family of transcription factors and present remarkable structure features and a unique DNA binding site. Their importance in plants goes beyond the response to stressful stimuli, since they participate in hormonal pathways and developmental processes. Indeed, the majority of WRKYs present an independent activation since they are able to perform self-transcriptional regulation. However, some WRKY activation depends on epigenetic and transcript regulation by micro RNAs. Their protein function depends, almost always, on the posttranslational changes. Taking to account its properties of auto-activation, all these regulators process are extremely important for complete WRKY regulation. In this sense, here we provide an overview of transcriptional activation and posttranscriptional and posttranslational regulation of rice WRKY genes under stresses.
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Affiliation(s)
- Vívian Ebeling Viana
- Graduate Program in Biotechnology, Center for Technological Development, Federal University of Pelotas, Pelotas-RS, Brazil; Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Carlos Busanello
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Luciano Carlos da Maia
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Camila Pegoraro
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Antonio Costa de Oliveira
- Graduate Program in Biotechnology, Center for Technological Development, Federal University of Pelotas, Pelotas-RS, Brazil; Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil.
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