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Plskova Z, Van Breusegem F, Kerchev P. Redox regulation of chromatin remodelling in plants. PLANT, CELL & ENVIRONMENT 2024; 47:2780-2792. [PMID: 38311877 DOI: 10.1111/pce.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/23/2023] [Accepted: 01/22/2024] [Indexed: 02/06/2024]
Abstract
Changes in the cellular redox balance that occur during plant responses to unfavourable environmental conditions significantly affect a myriad of redox-sensitive processes, including those that impact on the epigenetic state of the chromatin. Various epigenetic factors, like histone modifying enzymes, chromatin remodelers, and DNA methyltransferases can be targeted by oxidative posttranslational modifications. As their combined action affects the epigenetic regulation of gene expression, they form an integral part of plant responses to (a)biotic stress. Epigenetic changes triggered by unfavourable environmental conditions are intrinsically linked with primary metabolism that supplies intermediates and donors, such acetyl-CoA and S-adenosyl-methionine, that are critical for the epigenetic decoration of histones and DNA. Here, we review the recent advances in our understanding of redox regulation of chromatin remodelling, dynamics of epigenetic marks, and the interplay between epigenetic control of gene expression, redox signalling and primary metabolism within an (a)biotic stress context.
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Affiliation(s)
- Zuzana Plskova
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Frank Van Breusegem
- VIB Center of Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, UGent, Ghent, Belgium
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
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Mahmood T, He S, Abdullah M, Sajjad M, Jia Y, Ahmar S, Fu G, Chen B, Du X. Epigenetic insight into floral transition and seed development in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111926. [PMID: 37984609 DOI: 10.1016/j.plantsci.2023.111926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.
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Affiliation(s)
- Tahir Mahmood
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Muhammad Abdullah
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Guoyong Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China.
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Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
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Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
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Maniatis G, Tani E, Katsileros A, Avramidou EV, Pitsoli T, Sarri E, Gerakari M, Goufa M, Panagoulakou M, Xipolitaki K, Klouvatos K, Megariti S, Pappi P, Papadakis IE, Bebeli PJ, Kapazoglou A. Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the 'Epirus' Region of Greece upon Consecutive Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 13:27. [PMID: 38202337 PMCID: PMC10780352 DOI: 10.3390/plants13010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/06/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars 'Debina' and 'Dichali' displayed significant differences in their response to drought stress as judged by morpho-physiological analysis, indicating higher drought tolerance for Dichali. Hence, they were selected for further study aiming to identify genetic and epigenetic mechanisms possibly regulating drought adaptability. Specifically, self-rooted and heterografted on 'Richter 110' rootstock plants were subjected to two phases of drought with a recovery period in between. Gene expression analysis was performed for two stress-related miRNAs and their target genes: (a) miRNA159 and putative targets, VvMYB101, VvGATA-26-like, VvTOPLESS-4-like and (b) miRNA156 and putative target gene VvCONSTANS-5. Overall, grafted plants exhibited a higher drought tolerance than self-rooted plants, suggesting beneficial rootstock-scion interactions. Comparative analysis revealed differential gene expression under repetitive drought stresses between the two cultivars as well as between the self-rooted and grafted plants. 'Dichali' exhibited an up-regulation of most of the genes examined, which may be associated with increased tolerance. Nevertheless, the profound down-regulation of VvTOPLESS-4-like (a transcriptional co-repressor of transcription factors) upon drought and the concomitant up-regulation of miRNA159 highlights the importance of this 'miRNA-target' module in drought responsiveness. DNA methylation profiling using MSAP analysis revealed differential methylation patterns between the two genotypes in response to drought. Further investigations of gene expression and DNA methylation will contribute to our understanding of the epigenetic mechanisms underlying grapevine tolerance to drought stress.
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Affiliation(s)
- Grigorios Maniatis
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Anastasios Katsileros
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Ilisia, 11528 Athens, Greece;
| | - Theodora Pitsoli
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Lykovrysi, 14123 Athens, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Maria Goufa
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Maria Panagoulakou
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Konstantina Xipolitaki
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Kimon Klouvatos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Stamatia Megariti
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Polixeni Pappi
- Laboratory of Plant Virology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA (ELGO-DIMITRA), Kastorias 32A, Mesa Katsampas, 71307 Heraklion, Crete, Greece;
| | - Ioannis E. Papadakis
- Laboratory of Pomology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece;
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Lykovrysi, 14123 Athens, Greece;
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5
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Du J, Wang J, Shan S, Mi T, Song Y, Xia Y, Ma S, Zhang G, Ma L, Niu N. Low-Temperature-Mediated Promoter Methylation Relates to the Expression of TaPOR2D, Affecting the Level of Chlorophyll Accumulation in Albino Wheat ( Triticum aestivum L.). Int J Mol Sci 2023; 24:14697. [PMID: 37834145 PMCID: PMC10573025 DOI: 10.3390/ijms241914697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Chlorophyll is an indispensable photoreceptor in plant photosynthesis. Its anabolic imbalance is detrimental to individual growth and development. As an essential epigenetic modification, DNA methylation can induce phenotypic variations, such as leaf color transformation, by regulating gene expression. Albino line XN1376B is a natural mutation of winter wheat cultivar XN1376; however, the regulatory mechanism of its albinism is still unclear. In this study, we found that low temperatures induced albinism in XN1376B. The number of chloroplasts decreased as the phenomenon of bleaching intensified and the fence tissue and sponge tissue slowly dissolved. We identified six distinct TaPOR (protochlorophyllide oxidoreductase) genes in the wheat genome, and TaPOR2D was deemed to be related to the phenomenon of albinism based on the expression in different color leaves (green leaves, white leaves and returned green leaves) and the analysis of promoters' cis-acting elements. TaPOR2D was localized to chloroplasts. TaPOR2D overexpression (TaPOR2D-OE) enhanced the chlorophyll significantly in Arabidopsis, especially at two weeks; the amount of chlorophyll was 6.46 mg/L higher than in WT. The methylation rate of the TaPOR2D promoter in low-temperature albino leaves is as high as 93%, whereas there was no methylation in green leaves. Correspondingly, three DNA methyltransferase genes (TaMET1, TaDRM and TaCMT) were up-regulated in white leaves. Our study clarified that the expression of TaPOR2D is associated with its promoter methylation at a low temperature; it affects the level of chlorophyll accumulation, which probably causes the abnormal development of plant chloroplasts in albino wheat XN1376B. The results provide a theoretical basis for in-depth analysis of the regulation of development of plant chloroplasts and color variation in wheat XN1376B leaves.
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Affiliation(s)
- Jingjing Du
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Junwei Wang
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Sicong Shan
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Tian Mi
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Yulong Song
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Yu Xia
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Shoucai Ma
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Gaisheng Zhang
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Lingjian Ma
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
| | - Na Niu
- College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.D.); (J.W.); (S.S.); (T.M.); (Y.S.); (Y.X.); (S.M.); (G.Z.)
- Key Laboratory of Crop Heterosis of Shaanxi Province, Xianyang 712100, China
- Wheat Breeding Engineering Research Center of Ministry of Education, Xianyang 712100, China
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Eren B, Türkoğlu A, Haliloğlu K, Demirel F, Nowosad K, Özkan G, Niedbała G, Pour-Aboughadareh A, Bujak H, Bocianowski J. Investigation of the Influence of Polyamines on Mature Embryo Culture and DNA Methylation of Wheat ( Triticum aestivum L.) Using the Machine Learning Algorithm Method. PLANTS (BASEL, SWITZERLAND) 2023; 12:3261. [PMID: 37765424 PMCID: PMC10536335 DOI: 10.3390/plants12183261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/21/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Numerous factors can impact the efficiency of callus formation and in vitro regeneration in wheat cultures through the introduction of exogenous polyamines (PAs). The present study aimed to investigate in vitro plant regeneration and DNA methylation patterns utilizing the inter-primer binding site (iPBS) retrotransposon and coupled restriction enzyme digestion-iPBS (CRED-iPBS) methods in wheat. This investigation involved the application of distinct types of PAs (Put: putrescine, Spd: spermidine, and Spm: spermine) at varying concentrations (0, 0.5, 1, and 1.5 mM). The subsequent outcomes were subjected to predictive modeling using diverse machine learning (ML) algorithms. Based on the specific polyamine type and concentration utilized, the results indicated that 1 mM Put and Spd were the most favorable PAs for supporting endosperm-associated mature embryos. Employing an epigenetic approach, Put at concentrations of 0.5 and 1.5 mM exhibited the highest levels of genomic template stability (GTS) (73.9%). Elevated Spd levels correlated with DNA hypermethylation while reduced Spm levels were linked to DNA hypomethylation. The in vitro and epigenetic characteristics were predicted using ML techniques such as the support vector machine (SVM), extreme gradient boosting (XGBoost), and random forest (RF) models. These models were employed to establish relationships between input variables (PAs, concentration, GTS rates, Msp I polymorphism, and Hpa II polymorphism) and output parameters (in vitro measurements). This comparative analysis aimed to evaluate the performance of the models and interpret the generated data. The outcomes demonstrated that the XGBoost method exhibited the highest performance scores for callus induction (CI%), regeneration efficiency (RE), and the number of plantlets (NP), with R2 scores explaining 38.3%, 73.8%, and 85.3% of the variances, respectively. Additionally, the RF algorithm explained 41.5% of the total variance and showcased superior efficacy in terms of embryogenic callus induction (ECI%). Furthermore, the SVM model, which provided the most robust statistics for responding embryogenic calluses (RECs%), yielded an R2 value of 84.1%, signifying its ability to account for a substantial portion of the total variance present in the data. In summary, this study exemplifies the application of diverse ML models to the cultivation of mature wheat embryos in the presence of various exogenous PAs and concentrations. Additionally, it explores the impact of polymorphic variations in the CRED-iPBS profile and DNA methylation on epigenetic changes, thereby contributing to a comprehensive understanding of these regulatory mechanisms.
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Affiliation(s)
- Barış Eren
- Department of Agricultural Biotechnology, Faculty of Agriculture, Igdır University, Igdir 76000, Türkiye; (B.E.); (F.D.)
| | - Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye;
| | - Fatih Demirel
- Department of Agricultural Biotechnology, Faculty of Agriculture, Igdır University, Igdir 76000, Türkiye; (B.E.); (F.D.)
| | - Kamila Nowosad
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Grunwaldzki 24A, 53-363 Wrocław, Poland;
| | - Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, Ankara 06100, Türkiye;
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznan University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland;
| | - Alireza Pour-Aboughadareh
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj P.O. Box 3158854119, Iran;
| | - Henryk Bujak
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Grunwaldzki 24A, 53-363 Wrocław, Poland;
- Research Centre for Cultivar Testing (COBORU), Słupia Wielka 34, 63-022 Słupia Wielka, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
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7
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Ahn MA, Lee J, Hyun TK. Histone Deacetylase Inhibitor, Sodium Butyrate-Induced Metabolic Modulation in Platycodon grandiflorus Roots Enhances Anti-Melanogenic Properties. Int J Mol Sci 2023; 24:11804. [PMID: 37511563 PMCID: PMC10380954 DOI: 10.3390/ijms241411804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
While the status of histone acetylation is a critical regulator of chromatin's structure with a significant impact on plant physiology, our understanding of epigenetic regulation in the biosynthesis of active compounds in plants is limited. In this study, Platycodon grandiflorus was treated with sodium butyrate (NaB), a histone deacetylase inhibitor, to investigate the influence of histone acetylation on secondary metabolism. Its treatment with NaB increased the acetylation of histone H3 at lysine 9, 14, and 27 and enhanced the anti-melanogenic properties of P. grandiflorus roots. Through transcriptome and differentially expressed gene analyses, we found that NaB influenced the expression of genes that were involved in both primary and secondary metabolic pathways. In addition, NaB treatment caused the accumulation of polyphenolic compounds, including dihydroquercetin, gallic acid, and 2,4-dihydroxybenzoic acid. The NaB-induced transcriptional activation of genes in the phenylpropanoid biosynthetic pathway influenced the anti-melanogenic properties of P. grandiflorus roots. Overall, these findings suggest the potential of an epigenomic approach to enhance the medicinal qualities of medicinal plants.
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Affiliation(s)
- Min-A Ahn
- Department of Industrial Plant Science and Technology, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Jinsu Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
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8
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Kumar M, Rani K. Epigenomics in stress tolerance of plants under the climate change. Mol Biol Rep 2023:10.1007/s11033-023-08539-6. [PMID: 37294468 DOI: 10.1007/s11033-023-08539-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO2, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence. EPIGENETIC MECHANISMS AND MARKS The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles. EPIGENOMICS IN CROP IMPROVEMENT To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding. CONCLUSIONS AND FUTURE PROSPECTUS A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.
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Affiliation(s)
- Mithlesh Kumar
- AICRN On Potential Crops, ARS Mandor, Agriculture University, Jodhpur, 342 304, Rajasthan, India.
| | - Kirti Rani
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Jodhpur, 342 003, Rajasthan, India
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9
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Laanen P, Cuypers A, Saenen E, Horemans N. Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:246-259. [PMID: 36731286 DOI: 10.1016/j.plaphy.2023.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.
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Affiliation(s)
- Pol Laanen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Ann Cuypers
- Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Eline Saenen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium.
| | - Nele Horemans
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
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10
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Guo X, Huang D, Jing G, Feng J, Zhu S. Nitric oxide-mediated DNA methylation enhances cold resistance in postharvest peach fruit. Food Chem 2023; 404:134660. [DOI: 10.1016/j.foodchem.2022.134660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/17/2022] [Accepted: 10/15/2022] [Indexed: 11/22/2022]
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11
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Mai Y, Sun P, Suo Y, Li H, Han W, Diao S, Wang L, Yuan J, Wang Y, Ye L, Zhang Y, Li F, Fu J. Regulatory mechanism of MeGI on sexuality in Diospyros oleifera. FRONTIERS IN PLANT SCIENCE 2023; 14:1046235. [PMID: 36909399 PMCID: PMC9994623 DOI: 10.3389/fpls.2023.1046235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Dioecy system is an important strategy for maintaining genetic diversity. The transcription factor MeGI, contributes to dioecy by promoting gynoecium development in Diospyros lotus and D. kaki. However, the function of MeGI in D. oleifera has not been identified. In this study, we confirmed that MeGI, cloned from D. oleifera, repressed the androecium development in Arabidopsis thaliana. Subsequently, chromatin immunoprecipitation-sequencing (ChIP-seq), DNA affinity purification-sequencing (DAP-seq), and RNA-seq were used to uncover the gene expression response to MeGI. The results showed that the genes upregulated and downregulated in response to MeGI were mainly enriched in the circadian rhythm-related and flavonoid biosynthetic pathways, respectively. Additionally, the WRKY DNA-binding protein 28 (WRKY28) gene, which was detected by ChIP-seq, DAP-seq, and RNA-seq, was emphasized. WRKY28 has been reported to inhibit salicylic acid (SA) biosynthesis and was upregulated in MeGI-overexpressing A. thaliana flowers, suggesting that MeGI represses the SA level by increasing the expression level of WRKY28. This was confirmed that SA level was lower in D. oleifera female floral buds than male. Overall, our findings indicate that the MeGI mediates its sex control function in D. oleifera mainly by regulating genes in the circadian rhythm, SA biosynthetic, and flavonoid biosynthetic pathways.
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Affiliation(s)
- Yini Mai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Peng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yujing Suo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Huawei Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Weijuan Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Liyuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Chinese Academy of Sciences (CAS) Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jiaying Yuan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yiru Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Lingshuai Ye
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Fangdong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Jianmin Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
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12
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Niu X, Chen L, Kato A, Ito H. Regulatory mechanism of a heat-activated retrotransposon by DDR complex in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:1048957. [PMID: 36618621 PMCID: PMC9811314 DOI: 10.3389/fpls.2022.1048957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The RNA-directed DNA methylation (RdDM) pathway plays an essential role in the transposon silencing mechanism; the DDR complex, consisting of DRD1, DMS3, and RDM1, is an essential component of the RdDM pathway. ONSEN, identified in Arabidopsis, is a retrotransposon activated by heat stress at 37°C; however, studies on the regulation of ONSEN are limited. In this study, we analyzed the regulation of ONSEN activity by the DDR complex in Arabidopsis. We elucidated that loss of any component of the DDR complex increased ONSEN transcript levels. Transgenerational transposition of ONSEN was observed in the DDR-complex mutants treated with heat stress for 48 h. Furthermore, the DDR complex components DRD1, DMS3, and RDM1 played independent roles in suppressing ONSEN transcription and transposition. Moreover, we found that the duration of heat stress affects ONSEN activity. Therefore, the results of this study provide new insights into the retrotransposon regulatory mechanisms of the DDR complex in the RdDM pathway.
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Affiliation(s)
- Xiaoying Niu
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Lu Chen
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Atsushi Kato
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hidetaka Ito
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
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13
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Yan Y, Li C, Liu Z, Zhuang JJ, Kong JR, Yang ZK, Yu J, Shah Alam M, Ruan CC, Zhang HM, Xu JH. A new demethylase gene, OsDML4, is involved in high temperature-increased grain chalkiness in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7273-7284. [PMID: 36073837 DOI: 10.1093/jxb/erac367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
High temperature (HT) can affect the accumulation of seed storage materials and cause adverse effects on the yield and quality of rice. DNA methylation plays an important role in plant growth and development. Here, we identified a new demethylase gene OsDML4 and discovered its function in cytosine demethylation to affect endosperm formation. Loss of function of OsDML4 induced chalky endosperm only under HT and dramatically reduced the transcription and accumulation of glutelins and 16 kDa prolamin. The expression of two transcription factor genes RISBZ1 and RPBF was significantly decreased in the osdml4 mutants, which caused adverse effects on the formation of protein bodies (PBs) with greatly decreased PB-II number, and incomplete and abnormally shaped PB-IIs. Whole-genome bisulfite sequencing analysis of seeds at 15 d after pollination revealed much higher global methylation levels of CG, CHG, and CHH contexts in the osdml4 mutants compared with the wild type. Moreover, the RISBZ1 promoter was hypermethylated but the RPBF promoter was almost unchanged under HT. No significant difference was detected between the wild type and osdml4 mutants under normal temperature. Our study demonstrated a novel OsDML4-mediated DNA methylation involved in the formation of chalky endosperm only under HT and provided a new perspective in regulating endosperm development and the accumulation of seed storage proteins in rice.
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Affiliation(s)
- Yan Yan
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chao Li
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong 276034, China
| | - Zhen Liu
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China
| | - Jun-Jie Zhuang
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Jia-Rui Kong
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Zhen-Kun Yang
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Jie Yu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China
| | - Mohammad Shah Alam
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Cheng-Cheng Ruan
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Heng-Mu Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian-Hong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong 276034, China
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China
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14
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Chen B, Guo Y, Zhang X, Wang L, Cao L, Zhang T, Zhang Z, Zhou W, Xie L, Wang J, Sun S, Yang C, Zhang Q. Climate-responsive DNA methylation is involved in the biosynthesis of lignin in birch. FRONTIERS IN PLANT SCIENCE 2022; 13:1090967. [PMID: 36531363 PMCID: PMC9757698 DOI: 10.3389/fpls.2022.1090967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Lignin is one of the most important secondary metabolites and essential to the formation of cell walls. Changes in lignin biosynthesis have been reported to be associated with environmental variations and can influence plant fitness and their adaptation to abiotic stresses. However, the molecular mechanisms underlying this association remain unclear. In this study, we evaluated the relations between the lignin biosynthesis and environmental factors and explored the role of epigenetic modification (DNA methylation) in contributing to these relations if any in natural birch. Significantly negative correlations were observed between the lignin content and temperature ranges. Analyzing the transcriptomes of birches in two habitats with different temperature ranges showed that the expressions of genes and transcription factors (TFs) involving lignin biosynthesis were significantly reduced at higher temperature ranges. Whole-genome bisulfite sequencing revealed that promoter DNA methylation of two NAC-domain TFs, BpNST1/2 and BpSND1, may be involved in the inhibition of these gene expressions, and thereby reduced the content of lignin. Based on these results we proposed a DNA methylation-mediated lignin biosynthesis model which responds to environmental factors. Overall, this study suggests the possibility of environmental signals to induce epigenetic variations that result in changes in lignin content, which can aid to develop resilient plants to combat ongoing climate changes or to manipulate secondary metabolite biosynthesis for agricultural, medicinal, or industrial values.
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Affiliation(s)
- Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yile Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Lishan Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zihui Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Wei Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Linan Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Jiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shanwen Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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15
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Liu Y, Wang J, Liu B, Xu ZY. Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2252-2274. [PMID: 36149776 DOI: 10.1111/jipb.13368] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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16
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Wang Y, Liu Y, Qu S, Liang W, Sun L, Ci D, Ren Z, Fan LM, Qian W. Nitrogen starvation induces genome-wide activation of transposable elements in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2374-2384. [PMID: 36178606 DOI: 10.1111/jipb.13376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen (N) availability is a major limiting factor for plant growth and agricultural productivity. Although the gene regulation network in response to N starvation has been extensively studied, it remains unknown whether N starvation has an impact on the activity of transposable elements (TEs). Here, we report that TEs can be transcriptionally activated in Arabidopsis under N starvation conditions. Through genetic screening of idm1-14 suppressors, we cloned GLU1, which encodes a glutamate synthase that catalyzes the synthesis of glutamate in the primary N assimilation pathway. We found that glutamate synthase 1 (GLU1) and its functional homologs GLU2 and glutamate transport 1 (GLT1) are redundantly required for TE silencing, suggesting that N metabolism can regulate TE activity. Transcriptome and methylome analyses revealed that N starvation results in genome-wide TE activation without inducing obvious alteration of DNA methylation. Genetic analysis indicated that N starvation-induced TE activation is also independent of other well-established epigenetic mechanisms, including histone methylation and heterochromatin decondensation. Our results provide new insights into the regulation of TE activity under stressful environments in planta.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yi Liu
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shaofeng Qu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Wenjie Liang
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Dong Ci
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, China
| | - Zhitong Ren
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Liu-Min Fan
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, China
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17
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Ge W, Luo M, Sun H, Wei B, Zhou X, Zhou Q, Ji S. The CaMYB340 transcription factor induces chilling injury in post-harvest bell pepper by inhibiting fatty acid desaturation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:800-818. [PMID: 35653257 DOI: 10.1111/tpj.15854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Bell pepper (Capsicum annuum L.) is a tradable and desirable crop; however, its perishable nature requires low-temperature handling. Paradoxically, cold causes chilling injury (CI) and post-harvest waste. Current knowledge about CI in pepper is limited. The mechanism of CI is multi-faceted; therefore, we focused on fatty acid (FA) desaturation. We identified an upstream nuclear transcription factor (TF), CaMYB340, belonging to the R2R3 MYB subfamily, that negatively regulates FA desaturation and CaCBF3 expression and whose gene and protein expression is induced by low temperature (4°C). Specifically, McrBC treatment and bisulfite sequencing PCR indicate that exposure to cold triggers DNA methylation on one of the CHH sites in the CaMYB340 promoter. This epigenetic event at least partly contributes to the upregulation of CaMYB340 transcript levels. Increased expression of CaMYB340 results in the formation of protein complexes with CabHLH93 and CaMYB1R1, which in turn downregulate the expression of downstream genes. For peppers held at low temperature, transient overexpression of CaMYB340 reduced unsaturated FA content and membrane fluidity, resulting in cold-induced poor peel texture. Transient CaMYB340 silencing increased FA desaturation and lowered electrolyte leakage, enhancing cold tolerance in CaMYB340 knockdown fruits. Overall, these results underscore the intricacy of transcriptional networks in plants and highlight the role of CaMYB340 in CI occurrence in pepper fruits.
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Affiliation(s)
- Wanying Ge
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Manli Luo
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Huajun Sun
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Baodong Wei
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xin Zhou
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qian Zhou
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shujuan Ji
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
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18
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Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution. Int J Mol Sci 2022; 23:ijms23158299. [PMID: 35955429 PMCID: PMC9368846 DOI: 10.3390/ijms23158299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 01/06/2023] Open
Abstract
DNA methylation is an epigenetic modification of the genome involved in the regulation of gene expression and modulation of chromatin structure. Plant genomes are widely methylated, and the methylation generally occurs on the cytosine bases through the activity of specific enzymes called DNA methyltransferases. On the other hand, methylated DNA can also undergo demethylation through the action of demethylases. The methylation landscape is finely tuned and assumes a pivotal role in plant development and evolution. This review illustrates different molecular aspects of DNA methylation and some plant physiological processes influenced by this epigenetic modification in model species, crops, and ornamental plants such as orchids. In addition, this review aims to describe the relationship between the changes in plant DNA methylation levels and the response to biotic and abiotic stress. Finally, we discuss the possible evolutionary implications and biotechnological applications of DNA methylation.
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19
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Kumari P, Khan S, Wani IA, Gupta R, Verma S, Alam P, Alaklabi A. Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal. Front Genet 2022; 13:819941. [PMID: 35664328 PMCID: PMC9157814 DOI: 10.3389/fgene.2022.819941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression patterns which occur without altering DNA sequence. These changes are reversible and do not change the sequence of the DNA but can alter the way in which the DNA sequences are read. Epigenetic modifications are induced by DNA methylation, histone modification, and RNA-mediated mechanisms which alter the gene expression, primarily at the transcriptional level. Such alterations do control genome activity through transcriptional silencing of transposable elements thereby contributing toward genome stability. Plants being sessile in nature are highly susceptible to the extremes of changing environmental conditions. This increases the likelihood of epigenetic modifications within the composite network of genes that affect the developmental changes of a plant species. Genetic and epigenetic reprogramming enhances the growth and development, imparts phenotypic plasticity, and also ensures flowering under stress conditions without changing the genotype for several generations. Epigenetic modifications hold an immense significance during the development of male and female gametophytes, fertilization, embryogenesis, fruit formation, and seed germination. In this review, we focus on the mechanism of epigenetic modifications and their dynamic role in maintaining the genomic integrity during plant development and reproduction.
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Affiliation(s)
- Priyanka Kumari
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajid Khan
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ishfaq Ahmad Wani
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Renu Gupta
- Division of Soil Sciences & Agricultural Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha, India
| | - Susheel Verma
- Department of Botany, University of Jammu, Jammu, India
- *Correspondence: Susheel Verma,
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University (PSAU), Alkharj, Saudi Arabia
| | - Abdullah Alaklabi
- Department of Biology, College of Science, University of Bisha, Bisha, Saudi Arabia
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20
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Stochastic Variation in DNA Methylation Modulates Nucleosome Occupancy and Alternative Splicing in Arabidopsis thaliana. PLANTS 2022; 11:plants11091105. [PMID: 35567106 PMCID: PMC9101026 DOI: 10.3390/plants11091105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022]
Abstract
Plants use complex gene regulatory mechanisms to overcome diverse environmental challenges. For instance, cold stress induces rapid and massive transcriptome changes via alternative splicing (AS) to confer cold tolerance in plants. In mammals, mounting evidence suggests chromatin structure can regulate co-transcriptional AS. Recent evidence also supports co-transcriptional regulation of AS in plants, but how dynamic changes in DNA methylation and the chromatin structure influence the AS process upon cold stress remains poorly understood. In this study, we used the DNA methylation inhibitor 5-Aza-2′-Deoxycytidine (5-aza-dC) to investigate the role of stochastic variations in DNA methylation and nucleosome occupancy in modulating cold-induced AS, in Arabidopsis thaliana (Arabidopsis). Our results demonstrate that 5-aza-dC derived stochastic hypomethylation modulates nucleosome occupancy and AS profiles of genes implicated in RNA metabolism, plant hormone signal transduction, and of cold-related genes in response to cold stress. We also demonstrate that cold-induced remodelling of DNA methylation regulates genes involved in amino acid metabolism. Collectively, we demonstrate that sudden changes in DNA methylation via drug treatment can influence nucleosome occupancy levels and modulate AS in a temperature-dependent manner to regulate plant metabolism and physiological stress adaptation.
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21
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Tang X, Zhang Y, Yuan HM, Zhai J, Huang X. Reprogramming of the Hevea brasiliensis Epigenome and Transcriptome in Response to Cold Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:831839. [PMID: 35386670 PMCID: PMC8979024 DOI: 10.3389/fpls.2022.831839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Low temperature is a key factor limiting the rubber plantation extending to high latitude area. Previous work has shown that cold-induced DNA demethylation was coordinated with the expression of cold-responsive (COR) genes in Hevea brasiliensis. In this work, reduced representation bisulphite sequencing analysis of H. brasiliensis showed that cold treatment induced global genomic DNA demethylation and altered the sequence contexts of methylated cytosines, but the levels of mCG methylation in transposable elements were slightly enhanced by cold treatment. Integrated analysis of the DNA methylome and transcriptome revealed 400 genes whose expression correlated with altered DNA methylation. DNA demethylation in the upstream region of gene seems to correlate with higher gene expression, whereas demethylation in the gene body has less association. Our results suggest that cold treatment globally change the genomic DNA methylation status of the rubber tree, which might coordinate reprogramming of the transcriptome.
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Affiliation(s)
- Xiao Tang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yonglei Zhang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
| | - Hong-Mei Yuan
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
| | - Jinling Zhai
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
| | - Xi Huang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Institute of Hainan University, Sanya, China
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22
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Multi-omics data integration reveals link between epigenetic modifications and gene expression in sugar beet (Beta vulgaris subsp. vulgaris) in response to cold. BMC Genomics 2022; 23:144. [PMID: 35176993 PMCID: PMC8855596 DOI: 10.1186/s12864-022-08312-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/13/2022] [Indexed: 12/19/2022] Open
Abstract
Background DNA methylation is thought to influence the expression of genes, especially in response to changing environmental conditions and developmental changes. Sugar beet (Beta vulgaris ssp. vulgaris), and other biennial or perennial plants are inevitably exposed to fluctuating temperatures throughout their lifecycle and might even require such stimulus to acquire floral competence. Therefore, plants such as beets, need to fine-tune their epigenetic makeup to ensure phenotypic plasticity towards changing environmental conditions while at the same time steering essential developmental processes. Different crop species may show opposing reactions towards the same abiotic stress, or, vice versa, identical species may respond differently depending on the specific kind of stress. Results In this study, we investigated common effects of cold treatment on genome-wide DNA methylation and gene expression of two Beta vulgaris accessions via multi-omics data analysis. Cold exposure resulted in a pronounced reduction of DNA methylation levels, which particularly affected methylation in CHH context (and to a lesser extent CHG) and was accompanied by transcriptional downregulation of the chromomethyltransferase CMT2 and strong upregulation of several genes mediating active DNA demethylation. Conclusion Integration of methylomic and transcriptomic data revealed that, rather than methylation having directly influenced expression, epigenetic modifications correlated with changes in expression of known players involved in DNA (de)methylation. In particular, cold triggered upregulation of genes putatively contributing to DNA demethylation via the ROS1 pathway. Our observations suggest that these transcriptional responses precede the cold-induced global DNA-hypomethylation in non-CpG, preparing beets for additional transcriptional alterations necessary for adapting to upcoming environmental changes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08312-2.
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23
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Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses. Genes (Basel) 2022; 13:genes13020314. [PMID: 35205359 PMCID: PMC8872020 DOI: 10.3390/genes13020314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
Cytosine-5 DNA methyltransferases (C5-MTases) and methyl-CpG-binding-domain (MBD) genes can be co-expressed. They directly control target gene expression by enhancing their DNA methylation levels in humans; however, the presence of this kind of cooperative relationship in plants has not been determined. A popular garden plant worldwide, petunia (Petunia hybrida) is also a model plant in molecular biology. In this study, 9 PhC5-MTase and 11 PhMBD proteins were identified in petunia, and they were categorized into four and six subgroups, respectively, on the basis of phylogenetic analyses. An expression correlation analysis was performed to explore the co-expression relationships between PhC5-MTases and PhMBDs using RNA-seq data, and 11 PhC5-MTase/PhMBD pairs preferentially expressed in anthers were identified as having the most significant correlations (Pearson’s correlation coefficients > 0.9). Remarkably, the stability levels of the PhC5-MTase and PhMBD pairs significantly decreased in different tissues and organs compared with that in anthers, and most of the selected PhC5-MTases and PhMBDs responded to the abiotic and hormonal stresses. However, highly correlated expression relationships between most pairs were not observed under different stress conditions, indicating that anther developmental processes are preferentially influenced by the co-expression of PhC5-MTases and PhMBDs. Interestingly, the nuclear localization genes PhDRM2 and PhMBD2 still had higher correlations under GA treatment conditions, implying that they play important roles in the GA-mediated development of petunia. Collectively, our study suggests a regulatory role for DNA methylation by C5-MTase and MBD genes in petunia anther maturation processes and multi-stress responses, and it provides a framework for the functional characterization of C5-MTases and MBDs in the future.
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24
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Agwunobi DO, Zhang M, Shi X, Zhang S, Zhang M, Wang T, Masoudi A, Yu Z, Liu J. DNA Methyltransferases Contribute to Cold Tolerance in Ticks Dermacentor silvarum and Haemaphysalis longicornis (Acari: Ixodidae). Front Vet Sci 2021; 8:726731. [PMID: 34513977 PMCID: PMC8426640 DOI: 10.3389/fvets.2021.726731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/05/2021] [Indexed: 12/01/2022] Open
Abstract
DNA methylation, mediated by DNA methyltransferases (Dnmts), is a typical epigenetic process that plays an important role in affecting organism acclimatization and adaptation to environmental changes. However, information about Dnmts and their associations with the cold tolerance of ticks remains meager. Hence, in the present study, the Dnmts in important vector ticks Dermacentor silvarum and Haemaphysalis longicornis were cloned and identified, and their functions in cold response were further explored. Results showed that the length of DsDnmt and DsDnmt1 in D. silvarum, and HlDnmt1 and HlDnmt in H. longicornis were 1,284, 549, 1,500, and 1,613 bp, respectively. Bioinformatics in protein analysis revealed that they were all unstable hydrophilic proteins and were mainly characterized with Dcm (DNA cytosine methyltransferase domain), Dnmt1-RFD (DNA methyltransferase replication foci domain), zf-CXXC (zinc finger-CXXC domain), and BAH (Bromo adjacent homology domain). The relative expression of these Dnmts was reduced after cold treatment for 3 days (P < 0.05), and increased with the extension of treatment. Western blot revealed that Dnmt1 decreased first and then increased significantly (P < 0.05) in both tick species, whereas other Dnmts fluctuated at varying degrees. RNA interference significantly silenced the genes Dnmts (P < 0.01), and mortality increased significantly (P < 0.05), when exposed to sub-lethal temperature, underscoring the important roles of Dnmts during the cold response of D. silvarum and H. longicornis. The above results lay the foundation for further understanding of the epigenetic regulation of DNA methylation in cold acclimatization and adaptation of ticks.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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25
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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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26
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Hereme R, Galleguillos C, Morales-Navarro S, Molina-Montenegro MA. What if the cold days return? Epigenetic mechanisms in plants to cold tolerance. PLANTA 2021; 254:46. [PMID: 34370110 DOI: 10.1007/s00425-021-03694-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
The epigenetic could be an important, but seldom assessed, mechanisms in plants inhabiting cold ecosystems. Thus, this review could help to fill a gap in the current literature. Low temperatures are one of the most critical environmental conditions that negatively affect the growth, development, and geographic distribution of plants. Exposure to low temperatures results in a suit of physiological, biochemical and molecular modifications through the reprogramming of the expression of genes and transcription factors. Scientific evidence shows that the average annual temperature has increased in recent years worldwide, with cold ecosystems (polar and high mountain) being among the most sensitive to these changes. However, scientific evidence also indicates that there would be specific events of low temperatures, due it is highly relevant to know the capacity for adaptation, regulation and epigenetic memory in the face of these events, by plants. Epigenetic regulation has been described to play an important role in the face of environmental stimuli, especially in response to abiotic stress. Several studies on epigenetic mechanisms have focused on responses to stress as drought and/or salinity; however, there is a gap in the current literature considering those related to low temperatures. In this review, we focus on systematizing the information published to date, related to the regulation of epigenetic mechanisms such as DNA methylation, histone modification, and non-coding RNA-dependent silencing mechanisms, in the face of plant´s stress due to low temperatures. Finally, we present a schematic model about the potential responses by plants taking in count their epigenetic memory; considering a global warming scenario and with the presence or absence of extreme specific events of low temperatures.
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Affiliation(s)
- Rasme Hereme
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Talca, Chile
| | | | | | - Marco A Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Talca, Chile.
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Universidad Católica del Norte, Coquimbo, Chile.
- Centro de Investigaciones y Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Talca, Chile.
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27
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Wang S, Yan W, Yang X, Zhang J, Shi Q. Comparative methylome reveals regulatory roles of DNA methylation in melon resistance to Podosphaera xanthii. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 309:110954. [PMID: 34134849 DOI: 10.1016/j.plantsci.2021.110954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Powdery mildew caused by Podosphaera xanthii (P. xanthii) severely endangers melon (Cucumis melo L.) production, while the mechanistic understanding about its resistance to powdery mildew remains largely limited. In this study, we integrated transcriptomic and methylomic analyses to explore whether DNA methylation was involved in modulating transcriptional acclimation of melon to P. xanthii infection. Net photosynthetic rate (Pn), stomatal conductance (Gs), actual photochemical efficiency (ФPSII) and maximum PSII quantum yield (Fv/Fm) were significantly decreased in P. xanthii-infected plants relative to uninfected ones (Control), revealing apparent physiological disorders. Totally 4808 differentially expressed genes (DEGs) were identified by global analysis of gene expression in Control and P. xanthii-infected plants. Comparative methylome uncovered that 932 DEGs were associated with hypermethylation, while 603 DEGs were associated with hypomethylation in melon upon P. xanthii infection. Among these differential methylation-involved DEGs, a set of resistance-related genes including R genes and candidate genes in metabolic and defense pathways were further identified, demonstrating that DNA methylation might function as a new regulatory layer for melon resistance to P. xanthii infection. Altogether our study sheds new insights into the molecular mechanisms of melon against powdery mildew and provides some potential targets for improving melon disease resistance in future.
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Affiliation(s)
- Shuoshuo Wang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Weihao Yan
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Xiaoyu Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Jiayu Zhang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Qinghua Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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28
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Dalakouras A, Vlachostergios D. Epigenetic approaches to crop breeding: current status and perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5356-5371. [PMID: 34017985 DOI: 10.1093/jxb/erab227] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 05/10/2023]
Abstract
In order to tackle the cumulative adverse effects of global climate change, reduced farmland, and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued agronomical traits, but its potential is gradually being compromised by the menacing decline of genetic variation. Resorting to the epigenome as a source of variation could serve as a promising alternative. Here, we discuss current status of epigenetics-mediated crop breeding (epibreeding), highlight its advances and limitations, outline currently available methodologies, and propose novel RNA-based strategies to modify the epigenome in a gene-specific and transgene-free manner.
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Affiliation(s)
- Athanasios Dalakouras
- Institute of Industrial and Forage Crops, HAO-DEMETER, 41335 Larissa, Greece
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, 57001 Thessaloniki, Greece
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29
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Lephatsi MM, Meyer V, Piater LA, Dubery IA, Tugizimana F. Plant Responses to Abiotic Stresses and Rhizobacterial Biostimulants: Metabolomics and Epigenetics Perspectives. Metabolites 2021; 11:457. [PMID: 34357351 PMCID: PMC8305699 DOI: 10.3390/metabo11070457] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 01/14/2023] Open
Abstract
In response to abiotic stresses, plants mount comprehensive stress-specific responses which mediate signal transduction cascades, transcription of relevant responsive genes and the accumulation of numerous different stress-specific transcripts and metabolites, as well as coordinated stress-specific biochemical and physiological readjustments. These natural mechanisms employed by plants are however not always sufficient to ensure plant survival under abiotic stress conditions. Biostimulants such as plant growth-promoting rhizobacteria (PGPR) formulation are emerging as novel strategies for improving crop quality, yield and resilience against adverse environmental conditions. However, to successfully formulate these microbial-based biostimulants and design efficient application programs, the understanding of molecular and physiological mechanisms that govern biostimulant-plant interactions is imperatively required. Systems biology approaches, such as metabolomics, can unravel insights on the complex network of plant-PGPR interactions allowing for the identification of molecular targets responsible for improved growth and crop quality. Thus, this review highlights the current models on plant defence responses to abiotic stresses, from perception to the activation of cellular and molecular events. It further highlights the current knowledge on the application of microbial biostimulants and the use of epigenetics and metabolomics approaches to elucidate mechanisms of action of microbial biostimulants.
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Affiliation(s)
- Motseoa M. Lephatsi
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
| | - Vanessa Meyer
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, WITS, Johannesburg 2050, South Africa;
| | - Lizelle A. Piater
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa
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Zhang X, Li C, Tie D, Quan J, Yue M, Liu X. Epigenetic memory and growth responses of the clonal plant Glechoma longituba to parental recurrent UV-B stress. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:827-838. [PMID: 33820599 DOI: 10.1071/fp20303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
The responses of plants to recurrent stress may differ from their responses to a single stress event. In this study, we investigated whether clonal plants can remember past environments. Parental ramets of Glechoma longituba (Nakai) Kuprian were exposed to UV-B stress treatments either once or repeatedly (20 and 40 repetitions). Differences in DNA methylation levels and growth parameters among parents, offspring ramets and genets were analysed. Our results showed that UV-B stress reduced the DNA methylation level of parental ramets, and the reduction was enhanced by increasing the number of UV-B treatments. The epigenetic variation exhibited by recurrently stressed parents was maintained for a long time, but that of singly stressed parents was only short-term. Moreover, clonal plants responded to different UV-B stress treatments with different growth strategies. The one-time stress was a eustress that increased genet biomass by increasing offspring leaf allocation and defensive allocation in comparison to the older offspring. In contrast, recurring stress was a distress that reduced genet biomass, increased the biomass of storage stolons, and allocated more defensive substances to the younger ramets. This study demonstrated that the growth of offspring and genets was clearly affected by parental experience, and parental epigenetic memory and the transgenerational effect may play important roles in this effect.
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Affiliation(s)
- Xiaoyin Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Cunxia Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Dan Tie
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Jiaxin Quan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Xiao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China; and Corresponding author.
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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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Liu Z, Guo C, Tai P, Sun L, Chen Z. The exposure of gadolinium at environmental relevant levels induced genotoxic effects in Arabidopsis thaliana (L.). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 215:112138. [PMID: 33740487 DOI: 10.1016/j.ecoenv.2021.112138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/03/2021] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
Rare Earth Elements (REEs) are increasingly being used in agriculture and are also used to produce high end technological devices, thereby increasing their anthropogenic presence in the environment. However, the ecotoxicological mechanism of REEs on organisms is not fully understood. In this study, the effects of gadolinium (Gd) addition on Arabidopsis thaliana (L.) were investigated at both physiological and molecular levels. Four treatments (0, 10, 50 and 200 μmol·L-1 Gd) were used in the exposure tests. Biomass, root length and chlorophyll content in shoots/roots were measured to investigate the plant's physiological response to Gd stress. Random amplified polymorphic (RAPD)-Polymerase Chain Reaction (PCR) and methylation sensitive arbitrarily primed (MSAP)-PCR were used to investigate changes in genetic variation and DNA methylation of A. thaliana when exposed to Gd. At the physiological level, it was found that low concentration of Gd (10 μmol·L-1) could significantly increase the plant biomass and root length, while the growth of A. thaliana was significantly inhibited when exposed to 200 μmol·L-1 of Gd, yet the total soluble protein content in aerial plant parts increased significantly by 24.2% when compared to the control group. Among the 12 primers considered in the RAPD assessment, at the molecular level, only four primers revealed different patterns in their genomic DNA. Compared to the control group, the treatment with 50 μmol·L-1 of Gd was associated with lower polymorphism, while the treatment with 200 μmol·L-1 of Gd was associated with higher polymorphism. The polymorphism frequencies for the 50 μmol·L-1 of Gd and the 200 μmol·L-1 of Gd were 4.67% and 20.33%, respectively. The MSAP analysis revealed that the demethylation (D) type of Arabidopsis genomic DNA increased significantly under 10 and 50 μmol·L-1 of Gd, while the methylation (M) type was also significantly increased under 200 μmol·L-1 of Gd. Generally, the total methylation polymorphism (D+M) increased with an increase of Gd concentration. It was found that high concentrations of Gd appeared to cause DNA damage, but low concentrations of Gd (as low as 10 μmol·L-1) were associated with DNA methylation change. Further, it was verified by Real time Reverse Transcription PCR (RT-PCR) on the bands detected by the MSAP analysis, that the genes relative to processes including cell cycle, oxidative stress and apoptosis, appeared to be regulated by methylation under Gd stress. These findings reveal new insight regarding ecotoxicity mechanisms of REEs on plants.
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Affiliation(s)
- Zhihong Liu
- Faculty of Infrastructure Engineering, Dalian University of Technology, Dalian 116023, China
| | - Cheng Guo
- Liaoning Shihua University, Fushun 113001, China
| | - Peidong Tai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Lizong Sun
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Zhenbo Chen
- Faculty of Infrastructure Engineering, Dalian University of Technology, Dalian 116023, China
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Waseem M, Huang F, Wang Q, Aslam MM, Abbas F, Ahmad F, Ashraf U, Hassan W, Fiaz S, Ye X, Yu L, Ke Y. Identification, methylation profiling, and expression analysis of stress-responsive cytochrome P450 genes in rice under abiotic and phytohormones stresses. GM CROPS & FOOD 2021; 12:551-563. [PMID: 33877001 PMCID: PMC8820252 DOI: 10.1080/21645698.2021.1908813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cytochrome P450 (CYP) is a large and complex eukaryotic gene superfamily with enzymatic activities involved in several physiological and regulatory processes. As an objective, an in-silico genome-wide DNA methylation (5mC) analysis was performed in rice (Oryza sativa cv. Zhonghua11), and the epigenetic role of CYPs in two abiotic stresses was observed. Being a stable representative mark, DNA-methylation alters the gene expression under stressful environmental conditions. Rice plants under salinity and drought stresses were analyzed through MeDIP-chip hybridization, and 14 unique genes of the CYP family were identified in the rice genome with varying degrees of methylation. The gene structure, promoter sequences, and phylogenetic analysis were performed. Furthermore, the responses of CYPs to various abiotic stresses, including salinity, drought, and cold were revealed. Similarly, the expression profile of potential CYPs was also investigated under various phytohormone stresses, which revealed the potential involvement of CYPs to hormone regulations. Overall, the current study provides evidence for CYP's stress regulation and fundamental for further characterization and understanding their epigenetic roles in gene expression regulation and environmental stress regulation in higher plants.
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Affiliation(s)
- Muhammad Waseem
- College of Horticulture, South China Agricultural University, P.R. China
| | - Feiyan Huang
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Centre, Kunming University, Kunming China
| | - Qiyu Wang
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Centre, Kunming University, Kunming China
| | - Mehtab Muhammad Aslam
- College of Life Sciences, Joint International Research Laboratory of Water and 5 Nutrient in Cops, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Farhat Abbas
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou P.R. China
| | - Fiaz Ahmad
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing PR China
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education Lahore, Punjab, Pakistan
| | - Waseem Hassan
- Institute of Environment and Sustainable Development in Agricultural, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Xianwen Ye
- Kunming Tobacco Corporation of Yunnan Province, Kunming China
| | - Lei Yu
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Centre, Kunming University, Kunming China
| | - Yanguo Ke
- College of Economics and Management, Kunming University, Kunming China
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Quan J, Latzel V, Tie D, Zhang Y, Münzbergová Z, Chai Y, Liu X, Yue M. Ultraviolet B Radiation Triggers DNA Methylation Change and Affects Foraging Behavior of the Clonal Plant Glechoma longituba. FRONTIERS IN PLANT SCIENCE 2021; 12:633982. [PMID: 33719308 PMCID: PMC7952652 DOI: 10.3389/fpls.2021.633982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 06/01/2023]
Abstract
Clonal plants in heterogeneous environments can benefit from their habitat selection behavior, which enables them to utilize patchily distributed resources efficiently. It has been shown that such behavior can be strongly influenced by their memories on past environmental interactions. Epigenetic variation such as DNA methylation was proposed to be one of the mechanisms involved in the memory. Here, we explored whether the experience with Ultraviolet B (UV-B) radiation triggers epigenetic memory and affects clonal plants' foraging behavior in an UV-B heterogeneous environment. Parental ramets of Glechoma longituba were exposed to UV-B radiation for 15 days or not (controls), and their offspring ramets were allowed to choose light environment enriched with UV-B or not (the species is monopodial and can only choose one environment). Sizes and epigenetic profiles (based on methylation-sensitive amplification polymorphism analysis) of parental and offspring plants from different environments were also analyzed. Parental ramets that have been exposed to UV-B radiation were smaller than ramets from control environment and produced less and smaller offspring ramets. Offspring ramets were placed more often into the control light environment (88.46% ramets) than to the UV-B light environment (11.54% ramets) when parental ramets were exposed to UV-B radiation, which is a manifestation of "escape strategy." Offspring of control parental ramets show similar preference to the two light environments. Parental ramets exposed to UV-B had lower levels of overall DNA methylation and had different epigenetic profiles than control parental ramets. The methylation of UV-B-stressed parental ramets was maintained among their offspring ramets, although the epigenetic differentiation was reduced after several asexual generations. The parental experience with the UV-B radiation strongly influenced foraging behavior. The memory on the previous environmental interaction enables clonal plants to better interact with a heterogeneous environment and the memory is at least partly based on heritable epigenetic variation.
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Affiliation(s)
- Jiaxin Quan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Vít Latzel
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Dan Tie
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Yuhan Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Zuzana Münzbergová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Yongfu Chai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Xiao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- Xi’an Botanical Garden of Shaanxi Province/Institute of Botany of Shaanxi Province, Xi’an, China
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Syngelaki E, Daubert M, Klatt S, Hörandl E. Phenotypic Responses, Reproduction Mode and Epigenetic Patterns under Temperature Treatments in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae). BIOLOGY 2020; 9:E315. [PMID: 33003474 PMCID: PMC7600421 DOI: 10.3390/biology9100315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/04/2022]
Abstract
Plant life in alpine habitats is shaped by harsh abiotic conditions and cold climates. Phenotypic variation of morphological characters and reproduction can be influenced by temperature stress. Nevertheless, little is known about the performance of different cytotypes under cold stress and how epigenetic patterns could relate to phenotypic variation. Ranunculus kuepferi, a perennial alpine plant, served as a model system for testing the effect of cold stress on phenotypic plasticity, reproduction mode, and epigenetic variation. Diploid and autotetraploid individuals were placed in climate growth cabinets under warm and cold conditions. Morphological traits (height, leaves and flowers) and the proportion of well-developed seeds were measured as fitness indicators, while flow cytometric seed screening (FCSS) was utilized to determine the reproduction mode. Subsequently, comparisons with patterns of methylation-sensitive amplified fragment-length polymorphisms (AFLPs) were conducted. Diploids grew better under warm conditions, while tetraploids performed better in cold treatments. Epigenetic patterns were correlated with the expressed morphological traits. Cold stress reduced the reproduction fitness but did not induce apomixis in diploids. Overall, our study underlines the potential of phenotypic plasticity for acclimation under environmental conditions and confirms the different niche preferences of cytotypes in natural populations. Results help to understand the pattern of geographical parthenogenesis in the species.
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Affiliation(s)
- Eleni Syngelaki
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-Universität Göttingen, 37073 Göttingen, Germany;
| | - Mareike Daubert
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129 Oldenburg, Germany;
| | - Simone Klatt
- Section Safety and Environmental Protection, Georg-August-Universität Göttingen, 37073 Göttingen, Germany;
| | - Elvira Hörandl
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-Universität Göttingen, 37073 Göttingen, Germany;
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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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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: 53] [Impact Index Per Article: 13.3] [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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Kuriyama K, Tabara M, Moriyama H, Kanazawa A, Koiwa H, Takahashi H, Fukuhara T. Disturbance of floral colour pattern by activation of an endogenous pararetrovirus, petunia vein clearing virus, in aged petunia plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:497-511. [PMID: 32100385 PMCID: PMC7496347 DOI: 10.1111/tpj.14728] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 05/22/2023]
Abstract
White areas of star-type bicolour petals of petunia (Petunia hybrida) are caused by post-transcriptional gene silencing (PTGS) of the key enzyme of anthocyanin biosynthesis. We observed blotched flowers and a vein-clearing symptom in aged petunia plants. To determine the cause of blotched flowers, we focused on an endogenous pararetrovirus, petunia vein clearing virus (PVCV), because this virus may have a suppressor of PTGS (VSR). Transcripts and episomal DNAs derived from proviral PVCVs accumulated in aged plants, indicating that PVCV was activated as the host plant aged. Furthermore, DNA methylation of CG and CHG sites in the promoter region of proviral PVCV decreased in aged plants, suggesting that poor maintenance of DNA methylation activates PVCV. In parallel, de novo DNA methylation of CHH sites in its promoter region was also detected. Therefore, both activation and inactivation of PVCV occurred in aged plants. The accumulation of PVCV transcripts and episomal DNAs in blotched regions and the detection of VSR activity support a mechanism in which suppression of PTGS by PVCV causes blotched flowers.
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Affiliation(s)
- Kazunori Kuriyama
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Midori Tabara
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Akira Kanazawa
- Research Faculty of AgricultureHokkaido UniversityKita 9, Nishi 9, Kita‐kuSapporo060‐8589Japan
| | - Hisashi Koiwa
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Department of Horticultural SciencesTexas A&M UniversityCollege StationTX77843USA
| | - Hideki Takahashi
- Graduate School of Agricultural ScienceTohoku University468‐1, Aramaki‐Aza‐AobaSendai980‐0845Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
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Lu H, Xue L, Cheng J, Yang X, Xie H, Song X, Qiang S. Polyploidization-driven differentiation of freezing tolerance in Solidago canadensis. PLANT, CELL & ENVIRONMENT 2020; 43:1394-1403. [PMID: 32092164 DOI: 10.1111/pce.13745] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
Solidago canadensis, originating from the temperate region of North America, has expanded southward to subtropical regions through polyploidization. Here we investigated whether freezing tolerance of S. canadensis was weakened during expansion. Measurement of the temperature causing 50% ruptured cells (LT50 ) in 35 S. canadensis populations revealed ploidy-related differentiation in freezing tolerance. Freezing tolerance was found to decrease with increasing ploidy. The polyploid populations of S. canadensis had lower ScICE1 gene expression levels but more ScICE1 gene copies than the diploids. Furthermore, more DNA methylation sites in the ScICE1 gene promoter were detected in the polyploids than in the diploids. The results suggest that promoter methylation represses the expression of multi-copy ScICE1 genes, leading to weaker freezing tolerance in polyploid S. canadensis compared to the diploids. The study provides empirical evidence that DNA methylation regulates expression of the gene copies and supports polyploidization-driven adaptation to new environments.
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Affiliation(s)
- Huan Lu
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Lifang Xue
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Jiliang Cheng
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Xianghong Yang
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Hongjie Xie
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Xiaoling Song
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Sheng Qiang
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
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Zhu YC, Zhang B, Allan AC, Lin-Wang K, Zhao Y, Wang K, Chen KS, Xu CJ. DNA demethylation is involved in the regulation of temperature-dependent anthocyanin accumulation in peach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:965-976. [PMID: 31923329 DOI: 10.1111/tpj.14680] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/03/2020] [Indexed: 05/10/2023]
Abstract
Anthocyanin biosynthesis is induced by low temperatures in a number of plants. However, in peach (cv Zhonghuashoutao), anthocyanin accumulation was observed in fruit stored at 16°C but not at or below 12°C. Fruit stored at 16°C showed elevated transcript levels of genes encoding anthocyanin biosynthetic enzymes, the transport protein glutathione S-transferase and key transcription factors. Higher transcript levels of PpPAL1/2, PpC4H, Pp4CL4/5/8, PpF3H, PpF3'H, PpDFR1/2/3 and PpANS, as well as transcription factor gene PpbHLH3, were associated with lower methylation levels in the promoter of these genes. The DNA methylation level was further highly correlated with the expression of the DNA methyltransferase genes and DNA demethylase genes. The application of DNA methylation inhibitor 5-azacytidine induced anthocyanin accumulation in peach flesh, further implicating a critical role for DNA demethylation in regulating anthocyanin accumulation in peach flesh. Our data reveal that temperature-dependent DNA demethylation is a key factor to the post-harvest temperature-dependent anthocyanin accumulation in peach flesh.
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Affiliation(s)
- Yong-Chao Zhu
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Bo Zhang
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Andrew C Allan
- Plant and Food Research, Auckland, New Zealand
- School of Biology Science, University of Auckland, Auckland, New Zealand
| | | | - Yun Zhao
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Ke Wang
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Kun-Song Chen
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Chang-Jie Xu
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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Lancíková V, Žiarovská J. Inter-retrotransposon amplified polymorphism markers revealed long terminal repeat retrotransposon insertion polymorphism in flax cultivated on the experimental fields around Chernobyl. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 55:957-963. [PMID: 32378983 DOI: 10.1080/10934529.2020.1760016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Ionizing radiation in environment comes from various natural and anthropogenic sources. The effect of radioactivity released after the CNPP (Chernobyl Nuclear Power Plant) on plant systems remains of great interest. Even now, more than three decades after the nuclear accident, the long-lived radionuclides represent a strong stress factor. Herein, the emphasis has been placed on analysis of genetic variability represented by activation of LTR (Long Terminal Repeat)-retrotransposons. Polymorphism in LTR-retrotransposon insertions has been investigated throughout the genome of two flax varieties, Kyivskyi and Bethune. For this purpose, two retrotransposon-based marker techniques, IRAP (Inter-Retrotransposon Amplified Polymorphism) and iPBS (inter-Primer Binding Site), have been employed. The hypothesis that chronic radioactive stress may induce mechanism of retransposition has been supported by the activation of FL9, FL11 and FL12 LTR-retrotransposons in flax seeds harvested from radioactive environment. Out of two retrotransposon-based approaches, IRAP appears to be more suitable for identification of LTR-retrotransposon polymorphism. Even though the LTR-retrotransposon polymorphism was identified, the results suggest the high level of plant adaptation in the radioactive Chernobyl area. However, it is not really surprising that plants developed an effective strategy to survive in radio-contaminated environment over the past 30 years.
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Affiliation(s)
- Veronika Lancíková
- Plant Science and Biodiversity Center, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Jana Žiarovská
- Department of Genetics and Plant Breeding, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Nitra, Slovakia
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Syngelaki E, Schinkel CCF, Klatt S, Hörandl E. Effects of Temperature Treatments on Cytosine-Methylation Profiles of Diploid and Autotetraploid Plants of the Alpine Species Ranunculus kuepferi (Ranunculaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:435. [PMID: 32322263 PMCID: PMC7158262 DOI: 10.3389/fpls.2020.00435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/25/2020] [Indexed: 05/23/2023]
Abstract
The exposure to environmental stress can trigger epigenetic variation, which may have several evolutionary consequences. Polyploidy seems to affect the DNA methylation profiles. Nevertheless, it abides unclear whether temperature stress can induce methylations changes in different cytotypes and to what extent a treatment shift is translated to an epigenetic response. A suitable model system for studying these questions is Ranunculus kuepferi, an alpine perennial herb. Diploid and autotetraploid individuals of R. kuepferi were exposed to cold (+7°C day/+2°C night; frost treatment -1°C cold shocks for 3 nights per week) and warm (+15° day/+10°C night) conditions in climate growth chambers for two consecutive flowering periods and shifted from one condition to the other after the first flowering period. Methylation-sensitive amplified fragment-length polymorphism markers were applied for both years, to track down possible alterations induced by the stress treatments. Patterns of methylation suggested that cytotypes differed significantly in their profiles, independent from year of treatment. Likewise, the treatment shift had an impact on both cytotypes, resulting in significantly less epiloci, regardless the shift's direction. The AMOVAs revealed higher variation within than among treatments in diploids. In tetraploids, internally-methylated loci had a higher variation among than within treatments, as a response to temperature's change in both directions, and support the hypothesis of temperature stress affecting the epigenetic variation. Results suggest that the temperature-sensitivity of DNA methylation patterns shows a highly dynamic phenotypic plasticity in R. kuepferi, as both cytotypes responded to temperature shifts. Furthermore, ploidy level, even without effects of hybridization, has an important effect on epigenetic background variation, which may be correlated with the DNA methylation dynamics during cold acclimation.
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Affiliation(s)
- Eleni Syngelaki
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Christoph C. F. Schinkel
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Simone Klatt
- Section Safety and Environmental Protection, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-Universität Göttingen, Göttingen, Germany
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Xiang N, Hu J, Wen T, Brennan MA, Brennan CS, Guo X. Effects of temperature stress on the accumulation of ascorbic acid and folates in sweet corn (Zea mays L.) seedlings. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:1694-1701. [PMID: 31803938 DOI: 10.1002/jsfa.10184] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/05/2019] [Accepted: 11/28/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Extreme temperatures are among the primary abiotic stresses that affect plant growth and development. Ascorbic acid (AsA) is an efficient antioxidant for scavenging relative oxygen species accumulated under stress. Folates play a significant role in DNA synthesis and protect plants against oxidative stress. Sweet corn (Zea mays L.), a crop grown worldwide, is sensitive to extreme temperatures at seedling stage, which may cause yield loss. This study was conducted to explore the biosynthetic regulative mechanism of AsA and folates in sweet corn seedlings under temperature stress. RESULTS The AsA and folate composition and relative gene expression in sweet corn seedlings grown under different temperature stresses (10, 25, and 40 °C) were evaluated. The imposition of temperature stress altered the AsA content mainly by modulating the expression of Zm DHAR, whose encoded enzyme dehydroascorbic reductase (DHAR) is essential in the AsA recycle pathway. Low temperature stress raised the expressions of relative genes, leading to folate accumulation. High temperature stress modulated the folate content by influencing the expression of the correspondence gene for aminodeoxychorismate synthase, Zm ADCS, as well as downstream genes that connected with DNA methylation. CONCLUSION These results provided a theoretical basis, at a genetic level, for understanding the stress responses mechanism in sweet corn seedlings, offering guidance for sweet corn cultivation. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Nan Xiang
- School of Food Science and Engineering, South China University of Technology, Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
| | - Jianguang Hu
- Key Laboratory of Crops Genetics Improvement of Guangdong Province, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tianxiang Wen
- Key Laboratory of Crops Genetics Improvement of Guangdong Province, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Margaret Anne Brennan
- Department of Wine, Food Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Charles Stephen Brennan
- School of Food Science and Engineering, South China University of Technology, Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
- Department of Wine, Food Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Xinbo Guo
- School of Food Science and Engineering, South China University of Technology, Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
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Xu P, Su H, Jin R, Mao Y, Xu A, Cheng H, Wang Y, Meng Q. Shading Effects on Leaf Color Conversion and Biosynthesis of the Major Secondary Metabolites in the Albino Tea Cultivar "Yujinxiang". JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2528-2538. [PMID: 32011878 DOI: 10.1021/acs.jafc.9b08212] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Albino became a novel kind of tea cultivar in China recently. In this study, transcriptome and whole-genome bisulfite sequencing (WGBS) were employed to investigate the shading effects on leaf color conversion and biosynthesis of three major secondary metabolites in the albino tea cultivar "Yujinxiang". The increased leaf chlorophyll level was likely the major cause for shaded leaf greening from young pale or yellow leaf. In comparison with the control, the total catechin level of the shading group was significantly decreased and the abundance of caffeine was markedly increased, while the theanine level was nearly not influenced. Meanwhile, differentially expressed genes (DEGs) enriched in some biological processes and pathways were identified by transcriptome analysis. Furthermore, whole-genome DNA methylation analysis revealed that the global genomic DNA methylation patterns of the shading period were remarkably altered in comparison with the control. In addition, differentially methylated regions (DMRs) and the DMR-related DEG analysis indicated that the DMR-related DEGs were the critical participants in biosynthesis of the major secondary metabolites. These findings suggest that DNA methylation is probably responsible for changes in the contents of the major secondary metabolites in Yujinxiang.
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Affiliation(s)
- Ping Xu
- Department of Tea Science , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Hui Su
- Department of Tea Science , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Rong Jin
- Agricultural Experiment Station , Zhejiang University , Zijingang Campus, Hangzhou , People's Republic of China
| | - Yuxiao Mao
- Hangzhou Academy of Agricultural Sciences , Hangzhou 310000 , People's Republic of China
| | - Anan Xu
- Department of Tea Science , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Haiyan Cheng
- Department of Tea Science , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Yuefei Wang
- Department of Tea Science , Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Qing Meng
- College of Food Science , Southwest University , Chongqing 400715 , People's Republic of China
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Systematic Analysis of the DNA Methylase and Demethylase Gene Families in Rapeseed ( Brassica napus L.) and Their Expression Variations After Salt and Heat stresses. Int J Mol Sci 2020; 21:ijms21030953. [PMID: 32023925 PMCID: PMC7036824 DOI: 10.3390/ijms21030953] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 01/31/2023] Open
Abstract
DNA methylation is a process through which methyl groups are added to the DNA molecule, thereby modifying the activity of a DNA segment without changing the sequence. Increasing evidence has shown that DNA methylation is involved in various aspects of plant growth and development via a number of key processes including genomic imprinting and repression of transposable elements. DNA methylase and demethylase are two crucial enzymes that play significant roles in dynamically maintaining genome DNA methylation status in plants. In this work, 22 DNA methylase genes and six DNA demethylase genes were identified in rapeseed (Brassica napus L.) genome. These DNA methylase and DNA demethylase genes can be classified into four (BnaCMTs, BnaMET1s, BnaDRMs and BnaDNMT2s) and three (BnaDMEs, BnaDML3s and BnaROS1s) subfamilies, respectively. Further analysis of gene structure and conserved domains showed that each sub-class is highly conserved between rapeseed and Arabidopsis. Expression analysis conducted by RNA-seq as well as qRT-PCR suggested that these DNA methylation/demethylation-related genes may be involved in the heat/salt stress responses in rapeseed. Taken together, our findings may provide valuable information for future functional characterization of these two types of epigenetic regulatory enzymes in polyploid species such as rapeseed, as well as for analyzing their evolutionary relationships within the plant kingdom.
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Zhu C, Zhang S, Zhou C, Chen L, Fu H, Li X, Lin Y, Lai Z, Guo Y. Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant ( Camellia sinensis) under abiotic stress and withering processing. PeerJ 2020; 8:e8432. [PMID: 31976183 PMCID: PMC6968495 DOI: 10.7717/peerj.8432] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. In the plant kingdom, cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes have been identified in some plant species. However, to the best of our knowledge, no investigator has focused on the identification and analysis of C5-MTase and dMTase genes in tea plants (Camellia sinensis) based on genome-wide levels. In this study, eight CsC5-MTases and four dMTases were identified in tea plants. These CsC5-MTase genes were divided into four subfamilies, including CsMET, CsCMT, CsDRM and CsDNMT2. The CsdMTase genes can be classified into CsROS, CsDME and CsDML. Based on conserved domain analysis of these genes, the gene loss and duplication events occurred during the evolution of CsC5-MTase and CsdMTase. Furthermore, multiple cis-acting elements were observed in the CsC5-MTase and CsdMTase, including light responsiveness, phytohormone responsiveness, stress responsiveness, and plant growth and development-related elements. Then, we investigated the transcript abundance of CsC5-MTase and CsdMTase under abiotic stress (cold and drought) and withering processing (white tea and oolong tea). Notably, most CsC5-MTases, except for CsCMT1 and CsCMT2, were significantly downregulated under abiotic stress, while the transcript abundance of all four CsdMTase genes was significantly induced. Similarly, the same transcript abundance of CsC5-MTase and CsdMTase was found during withering processing of white tea and oolong tea, respectively. In total, our findings will provide a basis for the roles of CsC5-MTase and CsdMTase in response to abiotic stress and the potential functions of these two gene families in affecting tea flavor during tea withering processing.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Konate M, Wilkinson MJ, Taylor J, Scott ES, Berger B, Rodriguez Lopez CM. Greenhouse Spatial Effects Detected in the Barley ( Hordeum vulgare L.) Epigenome Underlie Stochasticity of DNA Methylation. FRONTIERS IN PLANT SCIENCE 2020; 11:553907. [PMID: 33013971 PMCID: PMC7511590 DOI: 10.3389/fpls.2020.553907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/24/2020] [Indexed: 05/10/2023]
Abstract
Environmental cues are known to alter the methylation profile of genomic DNA, and thereby change the expression of some genes. A proportion of such modifications may become adaptive by adjusting expression of stress response genes but others have been shown to be highly stochastic, even under controlled conditions. The influence of environmental flux on plants adds an additional layer of complexity that has potential to confound attempts to interpret interactions between environment, methylome, and plant form. We therefore adopt a positional and longitudinal approach to study progressive changes to barley DNA methylation patterns in response to salt exposure during development under greenhouse conditions. Methylation-sensitive amplified polymorphism (MSAP) and phenotypic analyses of nine diverse barley varieties were grown in a randomized plot design, under two salt treatments (0 and 75 mM NaCl). Combining environmental, phenotypic and epigenetic data analyses, we show that at least part of the epigenetic variability, previously described as stochastic, is linked to environmental micro-variations during plant growth. Additionally, we show that differences in methylation increase with time of exposure to micro-variations in environment. We propose that subsequent epigenetic studies take into account microclimate-induced epigenetic variability.
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Affiliation(s)
- Moumouni Konate
- Institut de l'Environnement et de Recherche Agricole (INERA), DRREA-Ouest, Bobo Dioulasso, Burkina Faso
| | - Michael J. Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth, United Kingdom
- *Correspondence: Carlos Marcelino Rodriguez Lopez, ; Michael J. Wilkinson,
| | - Julian Taylor
- Biometry Hub, School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Eileen S. Scott
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Bettina Berger
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Carlos Marcelino Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
- *Correspondence: Carlos Marcelino Rodriguez Lopez, ; Michael J. Wilkinson,
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Agarwal S, Khan S. Heavy Metal Phytotoxicity: DNA Damage. CELLULAR AND MOLECULAR PHYTOTOXICITY OF HEAVY METALS 2020. [DOI: 10.1007/978-3-030-45975-8_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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50
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Susceptibility of Winter Wheat and Triticale to Yellow Rust Influenced by Complex Interactions between Vernalisation, Temperature, Plant Growth Stage and Pathogen Race. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy10010013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Environmental factors influence the disease susceptibility of crop plants. In this study, we established an experimental system to investigate the effects of vernalisation, temperature and plant growth stage on the susceptibility of winter wheat and winter triticale to Puccinia striiformis, the causal agent of yellow (stripe) rust. Two temperature regimes: standard (18 °C day/12 °C night) and low (12 °C day/6 °C night), vernalised and non-vernalised seedlings, vernalised adult plants and two pathogen races were investigated. At low temperatures, vernalisation reduced the susceptibility of seedlings exposed to the ‘Warrior’ race, while this was only the case for five out of eight varieties exposed to the ‘Kranich’ race. Changing from standard to low temperature resulted in increased susceptibility of non-vernalised seedlings of seven varieties inoculated with the ‘Warrior’ race and five varieties inoculated with the ‘Kranich’ race. Increased susceptibility at low temperature was also detected for several varieties at the adult plant growth stage. Comparisons between vernalised seedlings and adult plants revealed an effect of plant growth stage on disease susceptibility (e.g., Adult Plant Resistance) in five varieties at standard temperature for the ‘Warrior’ race and in five and four varieties at standard and low temperature respectively, for the ‘Kranich’ race. The complex and unpredictable interactions between environment and pathogen influencing yellow rust susceptibility of individual varieties stress the importance of phenotyping for disease resistance under different environmental conditions and pathogen populations. The environmental impact on rust susceptibility should also be taken into account in early-warning systems targeting wheat and triticale breeding programmes and growers.
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