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Białoskórska M, Rucińska A, Boczkowska M. Molecular Mechanisms Underlying Freezing Tolerance in Plants: Implications for Cryopreservation. Int J Mol Sci 2024; 25:10110. [PMID: 39337593 PMCID: PMC11432106 DOI: 10.3390/ijms251810110] [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: 08/13/2024] [Revised: 09/16/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Cryopreservation is a crucial technique for the long-term ex situ conservation of plant genetic resources, particularly in the context of global biodiversity decline. This process entails freezing biological material at ultra-low temperatures using liquid nitrogen, which effectively halts metabolic activities and preserves plant tissues over extended periods. Over the past seven decades, a plethora of techniques for cryopreserving plant materials have been developed. These include slow freezing, vitrification, encapsulation dehydration, encapsulation-vitrification, droplet vitrification, cryo-plates, and cryo-mesh techniques. A key challenge in the advancement of cryopreservation lies in our ability to understand the molecular processes underlying plant freezing tolerance. These mechanisms include cold acclimatization, the activation of cold-responsive genes through pathways such as the ICE-CBF-COR cascade, and the protective roles of transcription factors, non-coding RNAs, and epigenetic modifications. Furthermore, specialized proteins, such as antifreeze proteins (AFPs) and late embryogenesis abundant (LEA) proteins, play crucial roles in protecting plant cells during freezing and thawing. Despite its potential, cryopreservation faces significant challenges, particularly in standardizing protocols for a wide range of plant species, especially those from tropical and subtropical regions. This review highlights the importance of ongoing research and the integration of omics technologies to improve cryopreservation techniques, ensuring their effectiveness across diverse plant species and contributing to global efforts regarding biodiversity conservation.
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Affiliation(s)
- Magdalena Białoskórska
- Plant Breeding and Acclimatization Institute-National Research Institute in Radzików, 05-870 Błonie, Poland
| | - Anna Rucińska
- Plant Breeding and Acclimatization Institute-National Research Institute in Radzików, 05-870 Błonie, Poland
- Botanical Garden, Center for Biological Diversity Conservation in Powsin, Polish Academy of Science, Prawdziwka 2, 02-976 Warszawa, Poland
| | - Maja Boczkowska
- Plant Breeding and Acclimatization Institute-National Research Institute in Radzików, 05-870 Błonie, Poland
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Iqbal B, Ahmad N, Li G, Jalal A, Khan AR, Zheng X, Naeem M, Du D. Unlocking Plant Resilience: Advanced Epigenetic Strategies Against Heavy Metal and Metalloid Stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 349:112265. [PMID: 39277048 DOI: 10.1016/j.plantsci.2024.112265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/09/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
The escalating threat of heavy metal and metalloid stress on plant ecosystems requires innovative strategies to strengthen plant resilience and ensure agricultural sustainability. This review provides important insights into the advanced epigenetic pathways to improve plant tolerance to toxic heavy metals and metalloid stress. Epigenetic modifications, including deoxyribonucleic acid (DNA) methylation, histone modifications, and small ribonucleic acid (RNA) engineering, offer innovative avenues for tailoring plant responses to mitigate the impact of heavy metal and metalloid stress. Technological advancements in high-throughput genome sequencing and functional genomics have unraveled the complexities of epigenetic regulation in response to heavy metal and metalloid contamination. Recent strides in this field encompass identifying specific epigenetic markers associated with stress resilience, developing tools for editing the epigenome, and integrating epigenetic data into breeding programs for stress-resistant crops. Understanding the dynamic interaction between epigenetics and stress responses holds immense potential to engineer resilient crops that thrive in environments contaminated with heavy metals and metalloids. Eventually, harnessing epigenetic strategies presents a promising trajectory toward sustainable agriculture in the face of escalating environmental challenges. Plant epigenomics expands, the potential for sustainable agriculture by implementing advanced epigenetic approaches becomes increasingly evident. These developments lay the foundation for understanding the growing significance of epigenetics in plant stress biology and its potential to mitigate the detrimental effects of heavy metal and metalloid pollution on global agriculture.
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Affiliation(s)
- Babar Iqbal
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Guanlin Li
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, People's Republic of China
| | - Arshad Jalal
- School of Engineering, Department of Plant Health, Rural Engineering and Soils, São Paulo State University - UNESP-FEIS, Ilha Solteira, 15385-000, São Paulo, Brazil
| | - Ali Raza Khan
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Xiaojun Zheng
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Muhammad Naeem
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
| | - Daolin Du
- Jingjiang College, Institute of Environment and Ecology, School of Emergency Management, School of Environment and Safety Engineering, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China.
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Labella-Ortega M, Martín C, Valledor L, Castiglione S, Castillejo MÁ, Jorrín-Novo JV, Rey MD. Unravelling DNA methylation dynamics during developmental stages in Quercus ilex subsp. ballota [Desf.] Samp. BMC PLANT BIOLOGY 2024; 24:823. [PMID: 39223458 PMCID: PMC11370289 DOI: 10.1186/s12870-024-05553-z] [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: 05/23/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND DNA methylation is a critical factor influencing plant growth, adaptability, and phenotypic plasticity. While extensively studied in model and crop species, it remains relatively unexplored in holm oak and other non-domesticated forest trees. This study conducts a comprehensive in-silico mining of DNA methyltransferase and demethylase genes within the holm oak genome to enhance our understanding of this essential process in these understudied species. The expression levels of these genes in adult and seedling leaves, as well as embryos, were analysed using quantitative real-time PCR (qRT-PCR). Global DNA methylation patterns were assessed through methylation-sensitive amplified polymorphism (MSAP) techniques. Furthermore, specific methylated genomic sequences were identified via MSAP sequencing (MSAP-Seq). RESULT A total of 13 DNA methyltransferase and three demethylase genes were revealed in the holm oak genome. Expression levels of these genes varied significantly between organs and developmental stages. MSAP analyses revealed a predominance of epigenetic over genetic variation among organs and developmental stages, with significantly higher global DNA methylation levels observed in adult leaves. Embryos exhibited frequent demethylation events, while de novo methylation was prevalent in seedling leaves. Approximately 35% of the genomic sequences identified by MSAP-Seq were methylated, predominantly affecting nuclear genes and intergenic regions, as opposed to repetitive sequences and chloroplast genes. Methylation was found to be more pronounced in the exonic regions of nuclear genes compared to their promoter and intronic regions. The methylated genes were predominantly associated with crucial biological processes such as photosynthesis, ATP synthesis-coupled electron transport, and defence response. CONCLUSION This study opens a new research direction in analysing variability in holm oak by evaluating the epigenetic events and mechanisms based on DNA methylation. It sheds light on the enzymatic machinery governing DNA (de)methylation, and the changes in the expression levels of methylases and demethylases in different organs along the developmental stages. The expression level was correlated with the DNA methylation pattern observed, showing the prevalence of de novo methylation and demethylation events in seedlings and embryos, respectively. Several methylated genes involved in the regulation of transposable element silencing, lipid biosynthesis, growth and development, and response to biotic and abiotic stresses are highlighted. MSAP-seq integrated with whole genome bisulphite sequencing and advanced sequencing technologies, such as PacBio or Nanopore, will bring light on epigenetic mechanisms regulating the expression of specific genes and its correlation with the phenotypic variability and the differences in the response to environmental cues, especially those related to climate change.
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Affiliation(s)
- Mónica Labella-Ortega
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, 14014, Spain.
| | - Carmen Martín
- Department of Biotechnology-Plant Biology, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Ciudad Universitaria s/n, Madrid, 28040, Spain
| | - Luis Valledor
- Plant Physiology Lab, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Cat. Rodrigo Uría s/n, Oviedo, 33006, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, Fisciano, Salerno, 84084, Italy
| | - María-Ángeles Castillejo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, 14014, Spain
| | - Jesús V Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, 14014, Spain
| | - María-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, 14014, Spain.
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Talarico E, Zambelli A, Araniti F, Greco E, Chiappetta A, Bruno L. Unravelling the Epigenetic Code: DNA Methylation in Plants and Its Role in Stress Response. EPIGENOMES 2024; 8:30. [PMID: 39189256 PMCID: PMC11348131 DOI: 10.3390/epigenomes8030030] [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: 05/31/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024] Open
Abstract
Environmental stress significantly affects plant growth, development, and survival. Plants respond to stressors such as temperature fluctuations, water scarcity, nutrient deficiencies, and pathogen attacks through intricate molecular and physiological adaptations. Epigenetic mechanisms are crucial in regulating gene expression in response to environmental stress. This review explores the current understanding of epigenetic modifications, including DNA methylation, and their roles in modulating gene expression patterns under environmental stress conditions. The dynamic nature of epigenetic modifications, their crosstalk with stress-responsive pathways, and their potential implications for plant adaptation and crop improvement are highlighted in the face of changing environmental conditions.
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Affiliation(s)
- Emanuela Talarico
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
| | - Alice Zambelli
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy; (A.Z.); (F.A.)
| | - Fabrizio Araniti
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy; (A.Z.); (F.A.)
| | - Eleonora Greco
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
| | - Adriana Chiappetta
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
| | - Leonardo Bruno
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
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Poupin MJ, González B. Embracing complexity in plant-microbiome systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70000. [PMID: 39189551 PMCID: PMC11348195 DOI: 10.1111/1758-2229.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/27/2024] [Indexed: 08/28/2024]
Abstract
Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.
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Affiliation(s)
- María Josefina Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
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6
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da Costa GS, Cerqueira AF, de Brito CR, Mielke MS, Gaiotto FA. Epigenetics Regulation in Responses to Abiotic Factors in Plant Species: A Systematic Review. PLANTS (BASEL, SWITZERLAND) 2024; 13:2082. [PMID: 39124200 PMCID: PMC11314046 DOI: 10.3390/plants13152082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 08/12/2024]
Abstract
Plants have several mechanisms to adapt or acclimate to environmental stress. Morphological, physiological, or genetic changes are examples of complex plant responses. In recent years, our understanding of the role of epigenetic regulation, which encompasses changes that do not alter the DNA sequence, as an adaptive mechanism in response to stressful conditions has advanced significantly. Some studies elucidated and synthesized epigenetic mechanisms and their relationships with environmental change, while others explored the interplay between epigenetic modifications and environmental shifts, aiming to deepen our understanding of these complex processes. In this study, we performed a systematic review of the literature to analyze the progression of epigenetics studies on plant species' responses to abiotic factors. We also aimed to identify the most studied species, the type of abiotic factor studied, and the epigenetic technique most used in the scientific literature. For this, a search for articles in databases was carried out, and after analyzing them using pre-established inclusion criteria, a total of 401 studies were found. The most studied species were Arabidopsis thaliana and Oryza sativa, highlighting the gap in studies of non-economic and tropical plant species. Methylome DNA sequencing is the main technique used for the detection of epigenetic interactions in published studies. Furthermore, most studies sought to understand the plant responses to abiotic changes in temperature, water, and salinity. It is worth emphasizing further research is necessary to establish a correlation between epigenetic responses and abiotic factors, such as extreme temperatures and light, associated with climate change.
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Affiliation(s)
| | | | | | | | - Fernanda Amato Gaiotto
- Laboratório de Ecologia Aplicada à Conservação, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil; (G.S.d.C.)
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7
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Chen L, Ma J, Xu W, Shen F, Yang Z, Sonne C, Dietz R, Li L, Jie X, Li L, Yan G, Zhang X. Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet-driven adaptive evolution. Evol Appl 2024; 17:e13731. [PMID: 38894980 PMCID: PMC11183199 DOI: 10.1111/eva.13731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Epigenetic regulation plays an important role in the evolution of species adaptations, yet little information is available on the epigenetic mechanisms underlying the adaptive evolution of bamboo-eating in both giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens). To investigate the potential contribution of epigenetic to the adaptive evolution of bamboo-eating in giant and red pandas, we performed hepatic comparative transcriptome and methylome analyses between bamboo-eating pandas and carnivorous polar bears (Ursus maritimus). We found that genes involved in carbohydrate, lipid, amino acid, and protein metabolism showed significant differences in methylation and expression levels between the two panda species and polar bears. Clustering analysis of gene expression revealed that giant pandas did not form a sister group with the more closely related polar bears, suggesting that the expression pattern of genes in livers of giant pandas and red pandas have evolved convergently driven by their similar diets. Compared to polar bears, some key genes involved in carbohydrate metabolism and biological oxidation and cholesterol synthesis showed hypomethylation and higher expression in giant and red pandas, while genes involved in fat digestion and absorption, fatty acid metabolism, lysine degradation, resistance to lipid peroxidation and detoxification showed hypermethylation and low expression. Our study elucidates the special nutrient utilization mechanism of giant pandas and red pandas and provides some insights into the molecular mechanism of their adaptive evolution of bamboo feeding. This has important implications for the breeding and conservation of giant pandas and red pandas.
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Affiliation(s)
- Lei Chen
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Jinnan Ma
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
- College of Continuing EducationYunnan Normal UniversityKunmingChina
| | - Wencai Xu
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Fujun Shen
- Sichuan Key Laboratory for Conservation Biology of Endangered WildlifeChengdu Research Base of Giant Panda BreedingChengduChina
| | | | - Christian Sonne
- Arctic Research Centre, Faculty of Science and Technology, Department of EcoscienceAarhus UniversityRoskildeDenmark
| | - Rune Dietz
- Arctic Research Centre, Faculty of Science and Technology, Department of EcoscienceAarhus UniversityRoskildeDenmark
| | - Linzhu Li
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Xiaodie Jie
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Lu Li
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Guoqiang Yan
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Xiuyue Zhang
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life SciencesSichuan UniversityChengduChina
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Fan Y, Sun C, Yan K, Li P, Hein I, Gilroy EM, Kear P, Bi Z, Yao P, Liu Z, Liu Y, Bai J. Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1400. [PMID: 38794470 PMCID: PMC11125032 DOI: 10.3390/plants13101400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
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Affiliation(s)
- Youfang Fan
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Pengcheng Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Ingo Hein
- The James Hutton Institute, Dundee DD2 5DA, UK; (I.H.); (E.M.G.)
| | | | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing 102199, China;
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
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9
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Perron N, Kirst M, Chen S. Bringing CAM photosynthesis to the table: Paving the way for resilient and productive agricultural systems in a changing climate. PLANT COMMUNICATIONS 2024; 5:100772. [PMID: 37990498 PMCID: PMC10943566 DOI: 10.1016/j.xplc.2023.100772] [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: 06/20/2023] [Revised: 07/27/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Abstract
Modern agricultural systems are directly threatened by global climate change and the resulting freshwater crisis. A considerable challenge in the coming years will be to develop crops that can cope with the consequences of declining freshwater resources and changing temperatures. One approach to meeting this challenge may lie in our understanding of plant photosynthetic adaptations and water use efficiency. Plants from various taxa have evolved crassulacean acid metabolism (CAM), a water-conserving adaptation of photosynthetic carbon dioxide fixation that enables plants to thrive under semi-arid or seasonally drought-prone conditions. Although past research on CAM has led to a better understanding of the inner workings of plant resilience and adaptation to stress, successful introduction of this pathway into C3 or C4 plants has not been reported. The recent revolution in molecular, systems, and synthetic biology, as well as innovations in high-throughput data generation and mining, creates new opportunities to uncover the minimum genetic tool kit required to introduce CAM traits into drought-sensitive crops. Here, we propose four complementary research avenues to uncover this tool kit. First, genomes and computational methods should be used to improve understanding of the nature of variations that drive CAM evolution. Second, single-cell 'omics technologies offer the possibility for in-depth characterization of the mechanisms that trigger environmentally controlled CAM induction. Third, the rapid increase in new 'omics data enables a comprehensive, multimodal exploration of CAM. Finally, the expansion of functional genomics methods is paving the way for integration of CAM into farming systems.
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Affiliation(s)
- Noé Perron
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32608, USA
| | - Matias Kirst
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32608, USA; School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32603, USA.
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS 38677-1848, USA.
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10
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Rahman A, Yadav NS, Byeon B, Ilnytskyy Y, Kovalchuk I. Genomic and Epigenomic Changes in the Progeny of Cold-Stressed Arabidopsis thaliana Plants. Int J Mol Sci 2024; 25:2795. [PMID: 38474042 DOI: 10.3390/ijms25052795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Plants are continuously exposed to various environmental stresses. Because they can not escape stress, they have to develop mechanisms of remembering stress exposures somatically and passing it to the progeny. We studied the Arabidopsis thaliana ecotype Columbia plants exposed to cold stress for 25 continuous generations. Our study revealed that multigenerational exposure to cold stress resulted in the changes in the genome and epigenome (DNA methylation) across generations. Main changes in the progeny were due to the high frequency of genetic mutations rather than epigenetic changes; the difference was primarily in single nucleotide substitutions and deletions. The progeny of cold-stressed plants exhibited the higher rate of missense non-synonymous mutations as compared to the progeny of control plants. At the same time, epigenetic changes were more common in the CHG (C = cytosine, H = cytosine, adenine or thymine, G = guanine) and CHH contexts and favored hypomethylation. There was an increase in the frequency of C to T (thymine) transitions at the CHH positions in the progeny of cold stressed plants; because this type of mutations is often due to the deamination of the methylated cytosines, it can be hypothesized that environment-induced changes in methylation contribute to mutagenesis and may be to microevolution processes and that RNA-dependent DNA methylation plays a crucial role. Our work supports the existence of heritable stress response in plants and demonstrates that genetic changes prevail.
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Affiliation(s)
- Ashif Rahman
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Boseon Byeon
- Biomedical and Health Informatics, Computer Science Department, State University of New York, 2 S Clinton St, Syracuse, NY 13202, USA
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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11
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Valverde J, Medrano M, Herrera CM, Alonso C. Comparative epigenetic and genetic spatial structure in Mediterranean mountain plants: a multispecies study. Heredity (Edinb) 2024; 132:106-116. [PMID: 38233486 PMCID: PMC10844209 DOI: 10.1038/s41437-024-00668-3] [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: 06/06/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
Changes in epigenetic states can allow individuals to cope with environmental changes. If such changes are heritable, this may lead to epigenetic adaptation. Thus, it is likely that in sessile organisms such as plants, part of the spatial epigenetic variation found across individuals will reflect the environmental heterogeneity within populations. The departure of the spatial epigenetic structure from the baseline genetic variation can help in understanding the value of epigenetic regulation in species with different breadth of optimal environmental requirements. Here, we hypothesise that in plants with narrow environmental requirements, epigenetic variability should be less structured in space given the lower variability in suitable environmental conditions. We performed a multispecies study that considered seven pairs of congeneric plant species, each encompassing a narrow endemic with habitat specialisation and a widespread species. In three populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the spatial genetic and epigenetic structures. Narrow endemics showed a significantly lower epigenetic than genetic differentiation between populations. Within populations, epigenetic variation was less spatially structured than genetic variation, mainly in narrow endemics. In these species, structural equation models revealed that such pattern was associated to a lack of correlation between epigenetic and genetic information. Altogether, these results show a greater decoupling of the spatial epigenetic variation from the baseline spatial genetic pattern in endemic species. These findings highlight the value of studying genetic and epigenetic spatial variation to better understand habitat specialisation in plants.
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Affiliation(s)
- Javier Valverde
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain.
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain.
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain.
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12
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Dainelli M, Castellani MB, Pignattelli S, Falsini S, Ristori S, Papini A, Colzi I, Coppi A, Gonnelli C. Growth, physiological parameters and DNA methylation in Spirodela polyrhiza (L.) Schleid exposed to PET micro-nanoplastic contaminated waters. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108403. [PMID: 38290343 DOI: 10.1016/j.plaphy.2024.108403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
The effects of polyethylene terephthalate micro-nanoplastics (PET-MNPs) were tested on the model freshwater species Spirodela polyrhiza (L.) Schleid., with focus on possible particle-induced epigenetic effects (i.e. alteration of DNA methylation status). MNPs (size ∼ 200-300 nm) were produced as water dispersions from PET bottles through repeated cycles of homogenization and used to prepare N-medium at two environmentally relevant concentrations (∼0.05 g L-1 and ∼0.1 g L-1 of MNPs). After 10 days of exposure, a reduction in fresh and dry weight was observed in treated plants, even if the average specific growth rate for both frond number and area was not altered. Impaired growth was coupled with a MNP-induced decrease of chlorophyll fluorescence parameters (i.e. ΨETo and Piabs, indicators of photochemical efficiency) and starch concentration, as well as with alterations in plant ionomic profile and oxidative status. The methylation-sensitive amplification polymorphism (MSAP) technique was used to assess possible changes in DNA methylation levels induced by plastic particles. The analysis showed unusual hypermethylation in 5'-CCGG sites that could be implicated in DNA protection from dangerous agents (i.e. reactive oxygen species) or in the formation of new epialleles. This work represents the first evidence of MNP-induced epigenetic modifications in the plant world.
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Affiliation(s)
- Marco Dainelli
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Maria Beatrice Castellani
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Sara Pignattelli
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Sara Falsini
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Sandra Ristori
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Firenze, Italy
| | - Alessio Papini
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Ilaria Colzi
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy.
| | - Andrea Coppi
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Cristina Gonnelli
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
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13
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Sammarco I, Díez Rodríguez B, Galanti D, Nunn A, Becker C, Bossdorf O, Münzbergová Z, Latzel V. DNA methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (Fragaria vesca). THE NEW PHYTOLOGIST 2024; 241:1621-1635. [PMID: 38058250 DOI: 10.1111/nph.19464] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Due to the accelerating climate change, it is crucial to understand how plants adapt to rapid environmental changes. Such adaptation may be mediated by epigenetic mechanisms like DNA methylation, which could heritably alter phenotypes without changing the DNA sequence, especially across clonal generations. However, we are still missing robust evidence of the adaptive potential of DNA methylation in wild clonal populations. Here, we studied genetic, epigenetic and transcriptomic variation of Fragaria vesca, a predominantly clonally reproducing herb. We examined samples from 21 natural populations across three climatically distinct geographic regions, as well as clones of the same individuals grown in a common garden. We found that epigenetic variation was partly associated with climate of origin, particularly in non-CG contexts. Importantly, a large proportion of this variation was heritable across clonal generations. Additionally, a subset of these epigenetic changes affected the expression of genes mainly involved in plant growth and responses to pathogen and abiotic stress. These findings highlight the potential influence of epigenetic changes on phenotypic traits. Our findings indicate that variation in DNA methylation, which can be environmentally inducible and heritable, may enable clonal plant populations to adjust to their environmental conditions even in the absence of genetic adaptation.
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Affiliation(s)
- Iris Sammarco
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Bárbara Díez Rodríguez
- Natural Resources and Climate Area, CARTIF Technology Centre, Parque Tecnológico de Boecillo, parc. 205, 47151, Boecillo, Valladolid, Spain
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, D-35043, Marburg, Germany
- Department of Forest Genetics, Albert-Ludwigs-Universität Freiburg, Bertoldstraße 17, 79098, Freiburg i. Br., Germany
| | - Dario Galanti
- Royal Botanic Gardens, Kew, Richmond, UK
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Adam Nunn
- ecSeq Bioinformatics GmbH, Sternwartenstraße 29, 04103, Saxony, Germany
- Department of Computer Science, University of Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr Bohr-Gasse 3, 1030, Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, Grosshaderner Str. 2-4, 82152, Martinsried, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Zuzana Münzbergová
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czechia
| | - Vít Latzel
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
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14
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Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024; 59:69-98. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [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: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
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Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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15
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DeLorenzo L, Powder KE. Epigenetics and the evolution of form: Experimental manipulation of a chromatin modification causes species-specific changes to the craniofacial skeleton. Evol Dev 2024; 26:e12461. [PMID: 37850843 PMCID: PMC10842503 DOI: 10.1111/ede.12461] [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: 03/08/2023] [Revised: 08/18/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023]
Abstract
A central question in biology is the molecular origins of phenotypic diversity. While genetic changes are key to the genotype-phenotype relationship, alterations to chromatin structure and the physical packaging of histone proteins may also be important drivers of vertebrate divergence. We investigate the impact of such an epigenetic mechanism, histone acetylation, within a textbook example of an adaptive radiation. Cichlids of Lake Malawi have adapted diverse craniofacial structures, and here we investigate how histone acetylation influences morphological variation in these fishes. Specifically, we assessed the effect of inhibiting histone deacetylation using the drug trichostatin A (TSA) on developing facial structures. We examined this during three critical developmental windows in two cichlid species with alternate adult morphologies. Exposure to TSA during neural crest cell (NCC) migration and as postmigratory NCCs proliferate in the pharyngeal arches resulted in significant changes in lateral and ventral shape in Maylandia, but not in Tropheops. This included an overall shortening of the head, widening of the lower jaw, and steeper craniofacial profile, all of which are paedomorphic morphologies. In contrast, treatment with TSA during early chondrogenesis did not result in significant morphological changes in either species. Together, these data suggest a sensitivity to epigenetic alterations that are both time- and species-dependent. We find that morphologies are due to nonautonomous or potentially indirect effects on NCC development, including in part a global developmental delay. Our research bolsters the understanding that proper histone acetylation is essential for early craniofacial development and identifies a species-specific robustness to developmental change. Overall, this study demonstrates how epigenetic regulation may play an important role in both generating and buffering morphological variation.
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Affiliation(s)
- Leah DeLorenzo
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Kara E Powder
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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16
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Xie Y, Chan LY, Cheung MY, Li MW, Lam HM. Current technical advancements in plant epitranscriptomic studies. THE PLANT GENOME 2023; 16:e20316. [PMID: 36890704 DOI: 10.1002/tpg2.20316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of plants are the result of the interplay between the internal developmental programming and plant-environment interactions. Gene expression regulations in plants are made up of multi-level networks. In the past few years, many studies were carried out on co- and post-transcriptional RNA modifications, which, together with the RNA community, are collectively known as the "epitranscriptome." The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third-generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant-environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi-omics investigations using the recent technical advancements.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Long-Yiu Chan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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17
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Zhang K, Feng X, Liu Y, Yang Y, Hao X, Li D, Wang X, Wang L. Integrative transcriptome and whole-genome bisulfite sequencing analyses of a temperature-sensitive albino tea plant cultivar. PHYSIOLOGIA PLANTARUM 2023; 175:e14064. [PMID: 38148243 DOI: 10.1111/ppl.14064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/28/2023]
Abstract
Green tea made from albino buds and leaves has a strong umami taste and aroma. The cultivar 'Zhonghuang 2' (ZH2, Camellia sinensis) is a natural mutant with young shoots that are yellow in spring and green or yellow-green in summer. However, the mechanism of leaf color change remains unclear. Here, we found that young shoots of ZH2 were yellow at low temperature (LT) and green at high temperature (HT), indicating that ZH2 is a temperature-sensitive cultivar. Transmission electron microscopy analysis showed that the grana in the chloroplasts of young shoots grown at LT were poorly stacked, which caused a lack of photoreactions and chlorophyll. RNA-seq results showed 1279 genes differentially expressed in the young shoots grown at LT compared with those at HT, including genes related to cytochrome synthesis, chloroplast development, photosynthesis, and DNA methylation. A whole-genome bisulfite sequencing assay revealed that the dynamics of DNA methylation levels in the CG, CHG, and CHH contexts decreased under LT, and the change was most obvious in the CHH context. Furthermore, 72 genes showed significant changes in both expression and DNA methylation levels, and most of them were related to cytochrome synthesis, chloroplast development, photosynthesis, transcription factors, and signaling pathways. These results demonstrate that DNA methylation is involved in the LT-regulated albino processes of ZH2. Changes in DNA methylation levels were associated with changes in gene expression levels, affecting the structure and function of chloroplasts, which may have a phenotypic impact on shoot and leaf color.
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Affiliation(s)
- Kexin Zhang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xia Feng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Liu
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yajun Yang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyuan Hao
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Dongliang Li
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Xinchao Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Lu Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, Hainan, China
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18
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Hamid R, Jacob F, Ghorbanzadeh Z, Jafari L, Alishah O. Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2023; 23:488. [PMID: 37828433 PMCID: PMC10571366 DOI: 10.1186/s12870-023-04495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages. RESULTS Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid. CONCLUSIONS These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran.
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, India
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Leila Jafari
- Horticultural Science Department, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas, Iran
- Research Group of Agroecology in Dryland Areas, University of Hormozgan, Bandar Abbas, Iran
| | - Omran Alishah
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran
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Zhang H, Zhang X, Xiao J. Epigenetic Regulation of Nitrogen Signaling and Adaptation in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2725. [PMID: 37514337 PMCID: PMC10386408 DOI: 10.3390/plants12142725] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Nitrogen (N) is a crucial nutrient that plays a significant role in enhancing crop yield. Its availability, including both supply and deficiency, serves as a crucial signal for plant development. However, excessive N use in agriculture leads to environmental and economic issues. Enhancing nitrogen use efficiency (NUE) is, therefore, essential to minimize negative impacts. Prior studies have investigated the genetic factors involved in N responses and the process of low-nitrogen (LN) adaptation. In this review, we discuss recent advances in understanding how epigenetic modifications, including DNA methylation, histone modification, and small RNA, participate in the regulation of N response and LN adaptation. We highlight the importance of decoding the epigenome at various levels to accelerate the functional study of how plants respond to N availability. Understanding the epigenetic control of N signaling and adaptation can lead to new strategies to improve NUE and enhance crop productivity sustainably.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing 100101, China
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20
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Schott J, Jantzen F, Hilker M. Elm tree defences against a specialist herbivore are moderately primed by an infestation in the previous season. TREE PHYSIOLOGY 2023; 43:1218-1232. [PMID: 37010106 PMCID: PMC10335851 DOI: 10.1093/treephys/tpad038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/06/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
The studies of the long-term effects of insect infestations on plant anti-herbivore defences tend to focus on feeding-induced damage. Infestations by an entire insect generation, including egg depositions as well as the feeding insects, are often neglected. Whilst there is increasing evidence that the presence of insect eggs can intensify plants' anti-herbivore defences against hatching larvae in the short term, little is known about how insect infestations, including insect egg depositions, affect plant defences in the long term. We addressed this knowledge gap by investigating long-term effects of insect infestation on elm's (Ulmus minor Mill. cv. 'Dahlem') defences against subsequent infestation. In greenhouse experiments, elms were exposed to elm leaf beetle (ELB, Xanthogaleruca luteola) infestation (adults, eggs and larvae). Thereafter, the trees cast their leaves under simulated winter conditions and were re-infested with ELB after the regrowth of their leaves under simulated summer conditions. Elm leaf beetles performed moderately worse on previously infested elms with respect to several developmental parameters. The concentrations of the phenylpropanoids kaempferol and quercetin, which are involved in egg-mediated, short-term effects on elm defences, were slightly higher in the ELB-challenged leaves of previously infested trees than in the challenged leaves of naïve trees. The expression of several genes involved in the phenylpropanoid pathway, jasmonic acid signalling, and DNA and histone modifications appeared to be affected by ELB infestation; however, prior infestation did not alter the expression intensities of these genes. The concentrations of several phytohormones were similarly affected in the currently challenged leaves of previously infested trees and naïve trees. Our study shows that prior infestation of elms by a specialised insect leads to moderately improved defences against subsequent infestation in the following growing season. Prior infestation adds a long-term effect to the short-term enhancer effect that plants show in response to egg depositions when defending against hatching larvae.
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Affiliation(s)
- Johanna Schott
- Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Haderslebener Str. 9, 12163 Berlin, Germany
| | - Friederike Jantzen
- Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Haderslebener Str. 9, 12163 Berlin, Germany
| | - Monika Hilker
- Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Haderslebener Str. 9, 12163 Berlin, Germany
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21
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Popov M, Kubeš J, Vachová P, Hnilička F, Zemanová V, Česká J, Praus L, Lhotská M, Kudrna J, Tunklová B, Štengl K, Krucký J, Turnovec T. Effect of Arsenic Soil Contamination on Stress Response Metabolites, 5-Methylcytosine Level and CDC25 Expression in Spinach. TOXICS 2023; 11:568. [PMID: 37505533 PMCID: PMC10383220 DOI: 10.3390/toxics11070568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Experimental spinach plants grown in soil with (5, 10 and 20 ppm) arsenic (As) contamination were sampled in 21 days after As(V) contamination. Levels of As in spinach samples (from 0.31 ± 0.06 µg g-1 to 302.69 ± 11.83 µg g-1) were higher in roots and lower in leaves, which indicates a low ability of spinach to translocate As into leaves. Species of arsenic, As(III) and As(V), were represented in favor of the As (III) specie in contaminated variants, suggesting enzymatic arsenate reduction. In relation to predominant As accumulation in roots, changes in malondialdehyde levels were observed mainly in roots, where they decreased significantly with growing As contamination (from 11.97 ± 0.54 µg g-1 in control to 2.35 ± 0.43 µg g-1 in 20 ppm As). Higher values in roots than in leaves were observed in the case of 5-methylcytosine (5-mC). Despite that, a change in 5-mC by As contamination was further deepened in leaves (from 0.20 to 14.10%). In roots of spinach, expression of the CDC25 gene increased by the highest As contamination compared to the control. In the case of total phenolic content, total flavonoid content, total phenolic acids content and total antioxidant capacity were higher levels in leaves in all values, unlike the roots.
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Affiliation(s)
- Marek Popov
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Jan Kubeš
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Pavla Vachová
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - František Hnilička
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Veronika Zemanová
- Department of Agroenvironmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Jana Česká
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Lukáš Praus
- Laboratory of Environmental Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Marie Lhotská
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Jiří Kudrna
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Barbora Tunklová
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Karel Štengl
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Jiří Krucký
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
| | - Tomáš Turnovec
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic
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Tang M, Li R, Chen P. Exogenous glutathione can alleviate chromium toxicity in kenaf by activating antioxidant system and regulating DNA methylation. CHEMOSPHERE 2023:139305. [PMID: 37364644 DOI: 10.1016/j.chemosphere.2023.139305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
Glutathione (GSH) participates in plant response to heavy metals (HMs) stress, however, the epigenetic regulating mechanisms of GSH in HMs detoxification remains unclear. In this study, to reveal the potential epigenetic regulating mechanisms, kenaf seedlings were treated with/without GSH under chromium (Cr) stress. A comprehensive physiological, genome-wide DNA methylation and gene functional analysis were performed. Results showed that external GSH obviously recovered Cr-induced growth inhibition, significantly decreased H2O2, O2.- and MDA accumulation, increased the activities of antioxidant enzymes (SOD, CAT, GR and APX) in kenaf exposed to Cr. In addition, the expression level of the main DNA methyltransferase (MET1, CMT3 and DRM1) and demethylase (ROS1, DEM, DML2, DML3 and DDM1) genes were investigated by qRT-PCR. The result indicated that Cr stress decreased DNA methyltransferase genes expression while increased demethylase genes expression; however, apply exogenous GSH led to the recovery trend. These indicating exogenous GSH alleviation Cr stress on kenaf seedlings by increasing DNA methylation level. At the same time, the MethylRAD-seq genome-wide DNA methylation analysis showed the DNA methylation level was significantly increased after GSH treatment compared with Cr treatment alone. The differentially methylated genes (DMGs) were uniquely enriched in DNA repair, flavin adenine dinucleotide binding and oxidoreductase activity. Furthermore, a ROS homeostasis-associated DMG, HcTrx, was selected for further functional analysis. Results showed that the knock-down of HcTrx kenaf seedlings displayed yellow-green phenotype and impaired antioxidant enzyme activity; in contrast, the overexpression lines of HcTrx improved chlorophyll levels and enhanced Cr tolerance in Arabidopsis. Taken together, our results illustrate the novel role of GSH-mediated Cr detoxification in kenaf by modulating the DNA methylation, and thus further affect the activation of antioxidant defense systems. The present characterized Cr tolerant gene resource could be further used for kenaf Cr tolerant breeding via genetic improvement.
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Affiliation(s)
- Meiqiong Tang
- Guangxi Key Laboratory of Agro-environment and Agric-products Safety, Key Laboratory of Crop Genetics Breeding and Germplasm Innovation, College of Agriculture, Guangxi University, Nanning, 530004, China; Guangxi Botanical Garden of Medicinal Plants, Guangxi Key Laboratory Resources Protection and Genetic Improvement, Nanning, China.
| | - Ru Li
- College of Life Science & Technology, Guangxi University, Nanning, China.
| | - Peng Chen
- Guangxi Key Laboratory of Agro-environment and Agric-products Safety, Key Laboratory of Crop Genetics Breeding and Germplasm Innovation, College of Agriculture, Guangxi University, Nanning, 530004, China.
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Giannelli G, Potestio S, Visioli G. The Contribution of PGPR in Salt Stress Tolerance in Crops: Unravelling the Molecular Mechanisms of Cross-Talk between Plant and Bacteria. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112197. [PMID: 37299176 DOI: 10.3390/plants12112197] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Soil salinity is a major abiotic stress in global agricultural productivity with an estimated 50% of arable land predicted to become salinized by 2050. Since most domesticated crops are glycophytes, they cannot be cultivated on salt soils. The use of beneficial microorganisms inhabiting the rhizosphere (PGPR) is a promising tool to alleviate salt stress in various crops and represents a strategy to increase agricultural productivity in salt soils. Increasing evidence underlines that PGPR affect plant physiological, biochemical, and molecular responses to salt stress. The mechanisms behind these phenomena include osmotic adjustment, modulation of the plant antioxidant system, ion homeostasis, modulation of the phytohormonal balance, increase in nutrient uptake, and the formation of biofilms. This review focuses on the recent literature regarding the molecular mechanisms that PGPR use to improve plant growth under salinity. In addition, very recent -OMICs approaches were reported, dissecting the role of PGPR in modulating plant genomes and epigenomes, opening up the possibility of combining the high genetic variations of plants with the action of PGPR for the selection of useful plant traits to cope with salt stress conditions.
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Affiliation(s)
- Gianluigi Giannelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Silvia Potestio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Giovanna Visioli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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24
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Rawal HC, Ali S, Mondal TK. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. Int J Biol Macromol 2023; 242:125172. [PMID: 37268077 DOI: 10.1016/j.ijbiomac.2023.125172] [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: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India; School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India; Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.
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25
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Kumar S, Seem K, Mohapatra T. Biochemical and Epigenetic Modulations under Drought: Remembering the Stress Tolerance Mechanism in Rice. Life (Basel) 2023; 13:life13051156. [PMID: 37240801 DOI: 10.3390/life13051156] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
A plant, being a sessile organism, needs to modulate biochemical, physiological, and molecular responses to the environment in a quick and efficient manner to be protected. Drought stress is a frequently occurring abiotic stress that severely affects plant growth, development, and productivity. Short- and long-term memories are well-known phenomena in animals; however, the existence of such remembrance in plants is still being discovered. In this investigation, different rice genotypes were imposed with drought stress just before flowering and the plants were re-watered for recovery from the stress. Seeds collected from the stress-treated (stress-primed) plants were used to raise plants for the subsequent two generations under a similar experimental setup. Modulations in physio-biochemical (chlorophyll, total phenolics and proline contents, antioxidant potential, lipid peroxidation) and epigenetic [5-methylcytosine (5-mC)] parameters were analyzed in the leaves of the plants grown under stress as well as after recovery. There was an increase in proline (>25%) and total phenolic (>19%) contents, antioxidant activity (>7%), and genome-wide 5-mC level (>56%), while a decrease (>9%) in chlorophyll content was recorded to be significant under the stress. Interestingly, a part of the increased proline content, total phenolics content, antioxidant activity, and 5-mC level was retained even after the withdrawal of the stress. Moreover, the increased levels of biochemical and epigenetic parameters were observed to be transmitted/inherited to the subsequent generations. These might help in developing stress-tolerant crops and improving crop productivity under the changing global climate for sustainable food production and global food security.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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26
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Bondarenko V, Geras'kin S, Bondarenko E, Yoschenko V, Bondarenko S, Khanova A, Garbaruk D, Nanba K. Comparative analysis of epigenetic variability in two pine species exposed to chronic radiation in the chernobyl and fukushima affected zones. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 330:121799. [PMID: 37169241 DOI: 10.1016/j.envpol.2023.121799] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
Comparative analysis of epigenetic variability in two pine species affected as a result of the Chernobyl and Fukushima accidents is presented. The absorbed dose rate within the affected Chernobyl sites varies over a wider range (1.5-24.6 μGy/h) than within the Fukushima sites (3.5-6.5 μGy/h). It was shown that chronic irradiation can change the level of whole genome methylation in pine populations, but in different ways. The genomes of Japanese red pines are hypomethylated, and the degree of methylation and hydroxymethylation decreases with an increase in the level of radiation exposure. In contrast, the percentages of genome methylation and hydroxymethylation in Scots pine populations exceed the reference levels. The observed discrepancy in the patterns of genome-wide DNA methylation can be attributed partly to the design of the study (differences in the climate, radiation dose, age and species of the pines) which could affect the results. In the frame of IRAP analysis, a larger number of different bands was observed in the Chernobyl populations compared to the Japanese populations. Both the Japanese and Chernobyl populations are characterized by significant genetic variability. However, the main part of this variability is observed within populations. The dendrograms, based on presence/absence of IRAP fragments and Nei's genetic distances, revealed subdivisions of the Chernobyl and Japanese populations according to the level of radioactive contamination. Analysis of the results presented will improve our understanding of the mechanisms underlying the responses of pine trees to chronic radiation exposure.
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Affiliation(s)
- Vladimir Bondarenko
- Russian Institute of Radiology and Agroecology, Kievskoe Shosse, 109 Km, Obninsk, Kaluga Region, 249032, Russian Federation
| | - Stanislav Geras'kin
- Russian Institute of Radiology and Agroecology, Kievskoe Shosse, 109 Km, Obninsk, Kaluga Region, 249032, Russian Federation.
| | - Ekaterina Bondarenko
- Russian Institute of Radiology and Agroecology, Kievskoe Shosse, 109 Km, Obninsk, Kaluga Region, 249032, Russian Federation
| | - Vasyl Yoschenko
- Institute of Environmental Radioactivity of Fukushima University, 1 Kanayagawa, Fukushima, 960-1296, Japan
| | - Sergey Bondarenko
- Russian Institute of Radiology and Agroecology, Kievskoe Shosse, 109 Km, Obninsk, Kaluga Region, 249032, Russian Federation
| | - Anastasiya Khanova
- Russian Institute of Radiology and Agroecology, Kievskoe Shosse, 109 Km, Obninsk, Kaluga Region, 249032, Russian Federation
| | - Dmitriy Garbaruk
- Polesye State Radiation-Ecological Reserve, 247618, Tereshkovoy Str. 7, Khoyniki, Belarus
| | - Kenji Nanba
- Institute of Environmental Radioactivity of Fukushima University, 1 Kanayagawa, Fukushima, 960-1296, Japan
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27
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Pierron F, Daffe G, Daramy F, Heroin D, Barré A, Bouchez O, Clérendeau C, Romero-Ramirez A, Nikolski M. Transgenerational endocrine disruptor effects of cadmium in zebrafish and contribution of standing epigenetic variation to adaptation. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131579. [PMID: 37163897 DOI: 10.1016/j.jhazmat.2023.131579] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023]
Abstract
Evidence has emerged that environmentally-induced epigenetic changes can have long-lasting effects on gene transcription across generations. These recent findings highlight the need to investigate the transgenerational impacts of pollutants to assess their long term effects on populations. In this study, we investigated the transgenerational effect of cadmium on zebrafish across 4 generations. A first whole methylome approach carried out on fish of the first two generations led us to focus our investigations on the estradiol receptor alpha gene (esr1). We observed a sex-dependent transgenerational inheritance of Cd-induced DNA methylation changes up to the last generation. These changes were associated with single nucleotide polymorphisms (SNPs) that were themselves at the origin of the creation or deletion of methylation sites. Thus, Cd-induced genetic selection gave rise to DNA methylation changes. We also analyzed the transcription level of various sections of esr1 as well as estrogen responsive genes. While Cd triggered transgenerational disorders, Cd-induced epigenetic changes in esr1 contributed to the rapid transgenerational adaptation of fish to Cd. Our results provide insight into the processes underpinning rapid adaptation and highlight the need to maintain genetic diversity within natural populations to bolster the resilience of species faced with the global environmental changes.
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Affiliation(s)
- Fabien Pierron
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France.
| | - Guillemine Daffe
- Univ. Bordeaux, CNRS, INRAE, La Rochelle Univ., UMS 2567 POREA, F-33615 Pessac, France
| | - Flore Daramy
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Débora Heroin
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Aurélien Barré
- Univ. Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, 31326, France
| | | | | | - Macha Nikolski
- Univ. Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France; Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux 33077, France
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28
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Ahmar S, Zolkiewicz K, Gruszka D. Analyses of genes encoding the Glycogen Synthase Kinases in rice and Arabidopsis reveal mechanisms which regulate their expression during development and responses to abiotic stresses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 332:111724. [PMID: 37142096 DOI: 10.1016/j.plantsci.2023.111724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
Plant Glycogen Synthase Kinases (GSKs) enable a crosstalk among the brassinosteroid signaling and phytohormonal- and stress-response pathways to regulate various physiological processes. Initial information about regulation of the GSK proteins' activity was obtained, however, mechanisms that modulate expression of the GSK genes during plant development and stress responses remain largely unknown. Taking into account the importance of the GSK proteins, combined with the lack of in-depth knowledge about modulation of their expression, research in this area may provide a significant insight into mechanisms regulating these aspects of plant biology. In the current study, a detailed analysis of the GSK promoters in rice and Arabidopsis was performed, including identification of the CpG/CpNpG islands, tandem repeats, cis-acting regulatory elements, conserved motifs, and transcription factor-binding sites. Moreover, characterization of expression profiles of the GSK genes in different tissues, organs and under various abiotic stress conditions was perfomed. Additionally, protein-protein interactions between products of the GSK genes were predicted. Results of this study provided intriguing information about these aspects and insight into various regulatory mechanisms that influence non-redundant and diverse functions of the GSK genes during development and stress responses.Therefore, they may constitute a reference for future research in other plant species.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Karolina Zolkiewicz
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
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29
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Manna I, Sahoo S, Bandyopadhyay M. Dynamic changes in global methylation and plant cell death mechanism in response to NiO nanoparticles. PLANTA 2023; 257:93. [PMID: 37017788 DOI: 10.1007/s00425-023-04127-x] [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: 03/20/2022] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
This report is a first comprehensive work on the potential of engineered nickel oxide nanoparticles affecting the epigenome and modulating global methylation leading to retention of transgenerational footprints. Nickel oxide nanoparticles (NiO-NPs) are known to instigate extensive phenotypic and physiological damage to plants. In the present work, it was shown that exposure to increasing concentrations of NiO-NP-induced cell death cascades in model systems, Allium cepa and tobacco BY-2 cells. NiO-NP also generated variation in global CpG methylation; its transgenerational transmission was shown in affected cells. Plant tissues exposed to NiO-NP showed progressive replacement of essential cations, like Fe and Mg, as seen in XANES and ICP-OES data, providing earliest signs of disturbed ionic homeostasis. Fluorescent staining based confocal microscopy confirmed upsurge of H2O2 and nitric oxide after NiO-NP exposure. A NiO-NP concentration gradient-based switching-on of the cell death cascades was observed when autophagosomes were seen in samples exposed to lower and median concentrations of NiO-NP (10-125 mg L-1). The apoptotic cell death marker, caspase-3 like protein, was noted in the median to higher doses (50-500 mg L-1), and leakage of lactate dehydrogenase marking necrotic cell death was observed in samples exposed to the highest doses (125-500 mg L-1) of NiO-NP. Concomitant increase of DNA hypermethylation (quantified by ELISA-based assay) and genomic DNA damage (evaluated through Comet-based analyses) was recorded at higher doses of NiO-NP. MSAP profiles confirmed that global methylation changes incurring in the parental generation upon NiO-NP exposure were transmitted through the two subsequent generations of BY-2 cells which was supported by data from A. cepa, too. Thus, it was evident that NiO-NP exposure incited DNA hypermethylation, as an aftermath of oxidative burst, and led to induction of autophagy, apoptotic and necrotic cell death pathways. Global methylation changes induced by NiO-NP exposure can be transmitted through subsequent cell generations.
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Affiliation(s)
- Indrani Manna
- Plant Molecular Cytogenetics Laboratory, Department of Botany, Center of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, India
| | - Saikat Sahoo
- Plant Molecular Cytogenetics Laboratory, Department of Botany, Center of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, India
- Department of Botany, Krishna Chandra College, Birbhum, India
| | - Maumita Bandyopadhyay
- Plant Molecular Cytogenetics Laboratory, Department of Botany, Center of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, India.
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30
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Liu J, Wu Y, Dong G, Zhu G, Zhou G. Progress of Research on the Physiology and Molecular Regulation of Sorghum Growth under Salt Stress by Gibberellin. Int J Mol Sci 2023; 24:ijms24076777. [PMID: 37047750 PMCID: PMC10094886 DOI: 10.3390/ijms24076777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023] Open
Abstract
Plant growth often encounters diverse abiotic stresses. As a global resource-based ecological problem, salinity is widely distributed and one of the major abiotic stresses affecting crop yields worldwide. Sorghum, a cereal crop with medium salt tolerance and great value for the development and utilization of salted soils, is an important source of food, brewing, energy, and forage production. However, in soils with high salt concentrations, sorghum experiences low emergence and suppressed metabolism. It has been demonstrated that the effects of salt stress on germination and seedling growth can be effectively mitigated to a certain extent by the exogenous amendment of hormonal gibberellin (GA). At present, most of the studies on sorghum salt tolerance at home and abroad focus on morphological and physiological levels, including the transcriptome analysis of the exogenous hormone on sorghum salt stress tolerance, the salt tolerance metabolism pathway, and the mining of key salt tolerance regulation genes. The high-throughput sequencing technology is increasingly widely used in the study of crop resistance, which is of great significance to the study of plant resistance gene excavation and mechanism. In this study, we aimed to review the effects of the exogenous hormone GA on leaf morphological traits of sorghum seedlings and further analyze the physiological response of sorghum seedling leaves and the regulation of sorghum growth and development. This review not only focuses on the role of GA but also explores the signal transduction pathways of GA and the performance of their responsive genes under salt stress, thus helping to further clarify the mechanism of regulating growth and production under salt stress. This will serve as a reference for the molecular discovery of key genes related to salt stress and the development of new sorghum varieties.
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Affiliation(s)
- Jiao Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yanqing Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guichun Dong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guanglong Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guisheng Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
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Ban S, Jung JH. Somatic Mutations in Fruit Trees: Causes, Detection Methods, and Molecular Mechanisms. PLANTS (BASEL, SWITZERLAND) 2023; 12:1316. [PMID: 36987007 PMCID: PMC10056856 DOI: 10.3390/plants12061316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 06/19/2023]
Abstract
Somatic mutations are genetic changes that occur in non-reproductive cells. In fruit trees, such as apple, grape, orange, and peach, somatic mutations are typically observed as "bud sports" that remain stable during vegetative propagation. Bud sports exhibit various horticulturally important traits that differ from those of their parent plants. Somatic mutations are caused by internal factors, such as DNA replication error, DNA repair error, transposable elements, and deletion, and external factors, such as strong ultraviolet radiation, high temperature, and water availability. There are several methods for detecting somatic mutations, including cytogenetic analysis, and molecular techniques, such as PCR-based methods, DNA sequencing, and epigenomic profiling. Each method has its advantages and limitations, and the choice of method depends on the research question and the available resources. The purpose of this review is to provide a comprehensive understanding of the factors that cause somatic mutations, techniques used to identify them, and underlying molecular mechanisms. Furthermore, we present several case studies that demonstrate how somatic mutation research can be leveraged to discover novel genetic variations. Overall, considering the diverse academic and practical value of somatic mutations in fruit crops, especially those that require lengthy breeding efforts, related research is expected to become more active.
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Torres E, García-Fernández A, Iñigo D, Lara-Romero C, Morente-López J, Prieto-Benítez S, Rubio Teso ML, Iriondo JM. Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide. PLANTS (BASEL, SWITZERLAND) 2023; 12:1258. [PMID: 36986946 PMCID: PMC10053585 DOI: 10.3390/plants12061258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.
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Affiliation(s)
- Elena Torres
- Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfredo García-Fernández
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Diana Iñigo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Carlos Lara-Romero
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Javier Morente-López
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Grupo de Investigación de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 Tenerife, Spain
| | - Samuel Prieto-Benítez
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Ecotoxicology of Air Pollution, Environmental Department, CIEMAT, 28040 Madrid, Spain
| | - María Luisa Rubio Teso
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - José M. Iriondo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
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Fu QY, Yu CL, Dong R, Shi J, Luo FL, Gao JQ, Li HL, Dong BC, Yu FH. Transgenerational Herbivory Effects on Performance of Clonal Offspring of the Invasive Plant Alternanthera philoxeroides. PLANTS (BASEL, SWITZERLAND) 2023; 12:1180. [PMID: 36904040 PMCID: PMC10005396 DOI: 10.3390/plants12051180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Interactions between alien plants and local enemies in introduced ranges may determine plant invasion success. However, little is known about whether herbivory-induced responses are transmitted across vegetative generations of plants and whether epigenetic changes are involved during this process. In a greenhouse experiment, we examined the effects of herbivory by the generalist herbivore Spodoptera litura on the growth, physiology, biomass allocation and DNA methylation level of the invasive plant Alternanthera philoxeroides in the first- (G1), second- (G2) and third-generation (G3). We also tested the effects of root fragments with different branching orders (i.e., the primary- or secondary-root fragments of taproots) of G1 on offspring performance. Our results showed that G1 herbivory promoted the growth of the plants in G2 that sprouted from the secondary-root fragments of G1 but had a neutral or negative effect on the growth of the plants in G2 from the primary-root fragments. The growth of plants in G3 was significantly reduced by G3 herbivory but not affected by G1 herbivory. Plants in G1 exhibited a higher level of DNA methylation when they were damaged by herbivores than when they were not, while neither plants in G2 nor G3 showed herbivory-induced changes in DNA methylation. Overall, the herbivory-induced growth response within one vegetative generation may represent the rapid acclimatization of A. philoxeroides to the unpredictable generalist herbivores in the introduced ranges. Herbivory-induced trans-generational effects may be transient for clonal offspring of A. philoxeroides, which can be influenced by the branching order of taproots, but be less characterized by DNA methylation.
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Affiliation(s)
- Qiu-Yue Fu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, China
| | - Cheng-Ling Yu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Ran Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Juan Shi
- School of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Fang-Li Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
- The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Jun-Qin Gao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
- The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Hong-Li Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
- The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Bi-Cheng Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
- The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Fei-Hai Yu
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, China
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Popov M, Kudrna J, Lhotská M, Hnilička F, Tunklová B, Zemanová V, Kubeš J, Vachová P, Česká J, Praus L, Štengl K, Krucký J. Arsenic Soil Contamination and Its Effects on 5-Methylcytosine Levels in Onions and Arsenic Distribution and Speciation. TOXICS 2023; 11:237. [PMID: 36977002 PMCID: PMC10056666 DOI: 10.3390/toxics11030237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Arsenic represents a serious health threat in localities with a high arsenic-polluted environment and can easily get into the human food chain through agronomy production in areas affected by arsenic contamination. Onion plants that were grown in controlled conditions in arsenic-contaminated soil (5, 10, and 20 ppm) were harvested 21 days after contamination. Arsenic levels (from 0.43 ± 0.03 µg g-1 to 1761.11 ± 101.84 µg g-1) in the onion samples were high in the roots and low in the bulbs and leaves, which is probably caused by a reduced ability of the onions to transport arsenic from roots to bulbs and leaves. Arsenic species As(V) and As(III) in As(V)-contaminated soil samples were represented strongly in favor of the As(III) species. This indicates the presence of arsenate reductase. Levels of 5-methylcytosine (5-mC) (from 5.41 ± 0.28% to 21.17 ± 1.33%) in the onion samples were also higher in the roots than in the bulbs and leaves. Microscopic sections of the roots were examined, and the most damage was found in the 10 ppm As variant. Photosynthetic parameters pointed to a significant decrease in photosynthetic apparatus activity and the deterioration of the physiological state of plants as arsenic content increased in the soil.
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Affiliation(s)
- Marek Popov
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Jiří Kudrna
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Marie Lhotská
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - František Hnilička
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Barbora Tunklová
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Veronika Zemanová
- Department of Agroenvironmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Jan Kubeš
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Pavla Vachová
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Jana Česká
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Lukáš Praus
- Laboratory of Environmental Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Karel Štengl
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Jiří Krucký
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
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Wierzbicka M, Abratowska A, Bemowska-Kałabun O, Panufnik-Mędrzycka D, Wąsowicz P, Wróbel M, Trzybiński D, Woźniak K. Micro-Evolutionary Processes in Armeria maritima at Metalliferous Sites. Int J Mol Sci 2023; 24:ijms24054650. [PMID: 36902080 PMCID: PMC10003435 DOI: 10.3390/ijms24054650] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Tolerance to heavy metals in plants is a model process used to study adaptations to extremely unfavorable environments. One species capable of colonizing areas with high contents of heavy metals is Armeria maritima (Mill.) Wild. A. maritima plants growing in metalliferous areas differ in their morphological features and tolerance levels to heavy metals compared to individuals of the same species growing in non-metalliferous areas. The A. maritima adaptations to heavy metals occur at the organismal, tissue, and cellular levels (e.g., the retention of metals in roots, enrichment of the oldest leaves with metals, accumulation of metals in trichomes, and excretion of metals by salt glands of leaf epidermis). This species also undergoes physiological and biochemical adaptations (e.g., the accumulation of metals in vacuoles of the root's tannic cells and secretion of such compounds as glutathione, organic acids, or HSP17). This work reviews the current knowledge on A. maritima adaptations to heavy metals occurring in zinc-lead waste heaps and the species' genetic variation from exposure to such habitats. A. maritima is an excellent example of microevolution processes in plants inhabiting anthropogenically changed areas.
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Affiliation(s)
- Małgorzata Wierzbicka
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
- Correspondence:
| | | | | | | | - Paweł Wąsowicz
- Icelandic Institute of Natural History, Borgir vid Nordurslod, 600 Akureyri, Iceland
| | - Monika Wróbel
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Damian Trzybiński
- Biological and Chemical Research Centre, University of Warsaw, Żwirki I Wigury 101, 02-089 Warsaw, Poland
| | - Krzysztof Woźniak
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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Kambona CM, Koua PA, Léon J, Ballvora A. Stress memory and its regulation in plants experiencing recurrent drought conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:26. [PMID: 36788199 PMCID: PMC9928933 DOI: 10.1007/s00122-023-04313-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Developing stress-tolerant plants continues to be the goal of breeders due to their realized yields and stability. Plant responses to drought have been studied in many different plant species, but the occurrence of stress memory as well as the potential mechanisms for memory regulation is not yet well described. It has been observed that plants hold on to past events in a way that adjusts their response to new challenges without altering their genetic constitution. This ability could enable training of plants to face future challenges that increase in frequency and intensity. A better understanding of stress memory-associated mechanisms leading to alteration in gene expression and how they link to physiological, biochemical, metabolomic and morphological changes would initiate diverse opportunities to breed stress-tolerant genotypes through molecular breeding or biotechnological approaches. In this perspective, this review discusses different stress memory types and gives an overall view using general examples. Further, focusing on drought stress, we demonstrate coordinated changes in epigenetic and molecular gene expression control mechanisms, the associated transcription memory responses at the genome level and integrated biochemical and physiological responses at cellular level following recurrent drought stress exposures. Indeed, coordinated epigenetic and molecular alterations of expression of specific gene networks link to biochemical and physiological responses that facilitate acclimation and survival of an individual plant during repeated stress.
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Affiliation(s)
- Carolyn Mukiri Kambona
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany
| | - Patrice Ahossi Koua
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany
- Deutsche Saatveredelung AG, Thüler Str. 30, 33154, Salzkotten-Thüle, Germany
| | - Jens Léon
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany
- Field Lab Campus Klein-Altendorf, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Agim Ballvora
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany.
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Mogilicherla K, Roy A. Epigenetic regulations as drivers of insecticide resistance and resilience to climate change in arthropod pests. Front Genet 2023; 13:1044980. [PMID: 36685945 PMCID: PMC9853188 DOI: 10.3389/fgene.2022.1044980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Arthropod pests are remarkably capable of rapidly adapting to novel forms of environmental stress, including insecticides and climate change. The dynamic interplay between epigenetics and genetics explains the largely unexplored reality underlying rapid climatic adaptation and the development of insecticide resistance in insects. Epigenetic regulation modulates gene expression by methylating DNA and acetylating histones that play an essential role in governing insecticide resistance and adaptation to climate change. This review summarises and discusses the significance of recent advances in epigenetic regulation that facilitate phenotypic plasticity in insects and their symbiotic microbes to cope with selection pressure implied by extensive insecticide applications and climate change. We also discuss how epigenetic changes are passed on to multiple generations through sexual recombination, which remains enigmatic. Finally, we explain how these epigenetic signatures can be utilized to manage insecticide resistance and pest resilience to climate change in Anthropocene.
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Ferrari M, Muto A, Bruno L, Cozza R. DNA Methylation in Algae and Its Impact on Abiotic Stress Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:241. [PMID: 36678953 PMCID: PMC9861306 DOI: 10.3390/plants12020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites.
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Hudzenko VM, Buniak NM, Tsentylo LV, Demydov OA, Fedorenko IV, Fedorenko MV, Ishchenko VA, Kozelets HM, Khudolii LV, Lashuk SO, Syplyva NO. Evaluation of grain yield performance and its stability in various spring barley accessions under condition of different agroclimatic zones of Ukraine. BIOSYSTEMS DIVERSITY 2022. [DOI: 10.15421/012240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
Two extremely urgent problems of biological and agronomic research nowadays are ensuring an optimal balance between usage of natural resources to meet rapidly growing needs for food production and preservation of biodiversity. It is also important to extend the genetic diversity of the main crop varieties in agroecosystems. At the same time, modern varieties should be characterized by a combination of high yield and preserving yield stability under variable conditions. Solving the outlined tasks requires comprehensive research and involvement in breeding process of the genetical diversity concentrated in genebanks of the world. Barley (Hordeum vulgare L.) is one of the most important crops that satisfy the various needs of humanity. In respect to this, in 2020–2022, a multi-environment trial was conducted in three agroclimatic zones of Ukraine (Forest-Steppe, Polissia, and Northern Steppe). We studied 44 spring barley collection accessions of different ecological and geographical origin, different subspecies and groups of botanical varieties which were obtained from the National Center for Plant Genetic Resources of Ukraine. Statistical indices (Hom, Sc) and graphical models (GGE biplot, AMMI) were used to interpret the yield performance and its stability. Both individual ecological sites in different years and combinations of different sites and years of trials were characterized for productivity, discriminating power and representativeness. The environments differed quite strongly among themselves in terms of these indicators. It was established that most of the genotypes were characterized by higher adaptability to individual environmental conditions (stability in different years), compared to adaptability for all agroclimatic zones (wide adaptation). A strong cross-over genotype by environment interaction was found for most studied accessions. Nevertheless, both genotypes with very high stability in only one agroclimatic zone (Amil (UKR), Gateway (CAN)) and genotypes with a combination of high adaptability to one or two ecological niches and relatively higher wide adaptability (Stymul (UKR), Ly-1064 (UKR), Rannij (KAZ), Shedevr (UKR), and Arthur (CZE)) were identified. There were also the accessions which did not show maximum performance in the individual sites, but had relatively higher wide adaptability (Ly-1059 (UKR), Ly-1120 (UKR), Diantus (UKR), and Danielle (CZE)). In general, the naked barley genotypes were inferior to the covered ones in terms of yield potential and wide adaptability, but at the same time, some of them (CDC ExPlus (CAN), CDC Gainer (CAN), and Roseland (CAN)), accordingly to the statistical indicators, had increased stability in certain ecological sites. Among naked barley accessions relatively better wide adaptability according to the graphical analysis was found in the accession CDC McGwire (CAN), and by the statistical parameters CDC ExPlus (CAN) was better than standard. The peculiarities of yield manifestation and its variability in different spring barley genotypes in the multi-environment trial revealed in this study will contribute to the complementation and deepening of existing data in terms of the genotype by environment interaction. Our results can be used in further studies for developing spring barley variety models both with specific and wide adaptation under conditions of different agroclimatic zones of Ukraine. The disitnguished accessions of different origin and botanical affiliation are recommended for creating a new breeding material with the aim of simultaneously increasing yield potential and stability, as well as widening the genetic basis of spring barley varieties.
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Singh G, Sharma S, Rawat S, Sharma RK. Plant Specialised Glycosides (PSGs): their biosynthetic enzymatic machinery, physiological functions and commercial potential. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1009-1028. [PMID: 36038144 DOI: 10.1071/fp21294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Plants, the primary producers of our planet, have evolved from simple aquatic life to very complex terrestrial habitat. This habitat transition coincides with evolution of enormous chemical diversity, collectively termed as 'Plant Specialised Metabolisms (PSMs)', to cope the environmental challenges. Plant glycosylation is an important process of metabolic diversification of PSMs to govern their in planta stability, solubility and inter/intra-cellular transport. Although, individual category of PSMs (terpenoids, phenylpropanoids, flavonoids, saponins, alkaloids, phytohormones, glucosinolates and cyanogenic glycosides) have been well studied; nevertheless, deeper insights of physiological functioning and genomic aspects of plant glycosylation/deglycosylation processes including enzymatic machinery (CYPs, GTs, and GHs) and regulatory elements are still elusive. Therefore, this review discussed the paradigm shift on genomic background of enzymatic machinery, transporters and regulatory mechanism of 'Plant Specialised Glycosides (PSGs)'. Current efforts also update the fundamental understanding about physiological, evolutionary and adaptive role of glycosylation/deglycosylation processes during the metabolic diversification of PSGs. Additionally, futuristic considerations and recommendations for employing integrated next-generation multi-omics (genomics, transcriptomics, proteomics and metabolomics), including gene/genome editing (CRISPR-Cas) approaches are also proposed to explore commercial potential of PSGs.
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Affiliation(s)
- Gopal Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India; and Present address: Department of Plant Functional Metabolomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Shikha Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
| | - Sandeep Rawat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Present address: G. B. Pant National Institute of Himalayan Environment and Sustainable Development, Sikkim Regional Centre, Pangthang, Gangtok 737101, Sikkim, India
| | - Ram Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
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Hämälä T, Ning W, Kuittinen H, Aryamanesh N, Savolainen O. Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata. eLife 2022; 11:e83115. [PMID: 36306157 PMCID: PMC9616567 DOI: 10.7554/elife.83115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint - the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of OuluOuluFinland
| | - Weixuan Ning
- Department of Ecology and Genetics, University of OuluOuluFinland
| | - Helmi Kuittinen
- Department of Ecology and Genetics, University of OuluOuluFinland
| | - Nader Aryamanesh
- Department of Ecology and Genetics, University of OuluOuluFinland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of OuluOuluFinland
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Rajpal VR, Rathore P, Mehta S, Wadhwa N, Yadav P, Berry E, Goel S, Bhat V, Raina SN. Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions. Front Cell Dev Biol 2022; 10:1020958. [PMID: 36340045 PMCID: PMC9628676 DOI: 10.3389/fcell.2022.1020958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity in natural populations. Studies show that environmental changes induce epigenetic switches either independently or in complementation with the genetic variation. Although most of the induced epigenetic variability gets reset between generations and is short-lived, some variation becomes transgenerational and results in heritable phenotypic traits. The short-term epigenetic responses provide the first tier of transient plasticity required for local adaptations while transgenerational epigenetic changes contribute to stress memory and help the plants respond better to recurring or long-term stresses. These transgenerational epigenetic variations translate into an additional tier of diversity which results in stable epialleles. In recent years, studies have been conducted on epigenetic variation in natural populations related to various biological processes, ecological factors, communities, and habitats. With the advent of advanced NGS-based technologies, epigenetic studies targeting plants in diverse environments have increased manifold to enhance our understanding of epigenetic responses to environmental stimuli in facilitating plant fitness. Taking all points together in a frame, the present review is a compilation of present-day knowledge and understanding of the role of epigenetics and its fitness benefits in diverse ecological systems in natural populations.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | | | - Sahil Mehta
- School of Agricultural Sciences, K.R. Mangalam University, Gurugram, Haryana, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Eapsa Berry
- Maharishi Kanad Bhawan, Delhi School of Climate Change and Sustainability, University of Delhi, Delhi, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Vishnu Bhat
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
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Jie X, Wu H, Yang M, He M, Zhao G, Ling S, Huang Y, Yue B, Yang N, Zhang X. Whole genome bisulfite sequencing reveals DNA methylation roles in the adaptive response of wildness training giant pandas to wild environment. Front Genet 2022; 13:995700. [PMID: 36303550 PMCID: PMC9592921 DOI: 10.3389/fgene.2022.995700] [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: 07/16/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation modification can regulate gene expression without changing the genome sequence, which helps organisms to rapidly adapt to new environments. However, few studies have been reported in non-model mammals. Giant panda (Ailuropoda melanoleuca) is a flagship species for global biodiversity conservation. Wildness and reintroduction of giant pandas are the important content of giant pandas’ protection. However, it is unclear how wildness training affects the epigenetics of giant pandas, and we lack the means to assess the adaptive capacity of wildness training giant pandas. We comparatively analyzed genome-level methylation differences in captive giant pandas with and without wildness training to determine whether methylation modification played a role in the adaptive response of wildness training pandas. The whole genome DNA methylation sequencing results showed that genomic cytosine methylation ratio of all samples was 5.35%–5.49%, and the methylation ratio of the CpG site was the highest. Differential methylation analysis identified 544 differentially methylated genes (DMGs). The results of KEGG pathway enrichment of DMGs showed that VAV3, PLCG2, TEC and PTPRC participated in multiple immune-related pathways, and may participate in the immune response of wildness training giant pandas by regulating adaptive immune cells. A large number of DMGs enriched in GO terms may also be related to the regulation of immune activation during wildness training of giant pandas. Promoter differentially methylation analysis identified 1,199 genes with differential methylation at promoter regions. Genes with low methylation level at promoter regions and high expression such as, CCL5, P2Y13, GZMA, ANP32A, VWF, MYOZ1, NME7, MRPS31 and TPM1 were important in environmental adaptation for wildness training giant pandas. The methylation and expression patterns of these genes indicated that wildness training giant pandas have strong immunity, blood coagulation, athletic abilities and disease resistance. The adaptive response of giant pandas undergoing wildness training may be regulated by their negatively related promoter methylation. We are the first to describe the DNA methylation profile of giant panda blood tissue and our results indicated methylation modification is involved in the adaptation of captive giant pandas when undergoing wildness training. Our study also provided potential monitoring indicators for the successful reintroduction of valuable and threatened animals to the wild.
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Affiliation(s)
- Xiaodie Jie
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Honglin Wu
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | - Miao Yang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Ming He
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | - Guangqing Zhao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Shanshan Ling
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
- *Correspondence: Nan Yang, ; Xiuyue Zhang,
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Nan Yang, ; Xiuyue Zhang,
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Chapelle V, Silvestre F. Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations. EPIGENOMES 2022; 6:31. [PMID: 36278677 PMCID: PMC9589984 DOI: 10.3390/epigenomes6040031] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Population epigenetics explores the extent of epigenetic variation and its dynamics in natural populations encountering changing environmental conditions. In contrast to population genetics, the basic concepts of this field are still in their early stages, especially in animal populations. Epigenetic variation may play a crucial role in phenotypic plasticity and local adaptation as it can be affected by the environment, it is likely to have higher spontaneous mutation rate than nucleotide sequences do, and it may be inherited via non-mendelian processes. In this review, we aim to bring together natural animal population epigenetic studies to generate new insights into ecological epigenetics and its evolutionary implications. We first provide an overview of the extent of DNA methylation variation and its autonomy from genetic variation in wild animal population. Second, we discuss DNA methylation dynamics which create observed epigenetic population structures by including basic population genetics processes. Then, we highlight the relevance of DNA methylation variation as an evolutionary mechanism in the extended evolutionary synthesis. Finally, we suggest new research directions by highlighting gaps in the knowledge of the population epigenetics field. As for our results, DNA methylation diversity was found to reveal parameters that can be used to characterize natural animal populations. Some concepts of population genetics dynamics can be applied to explain the observed epigenetic structure in natural animal populations. The set of recent advancements in ecological epigenetics, especially in transgenerational epigenetic inheritance in wild animal population, might reshape the way ecologists generate predictive models of the capacity of organisms to adapt to changing environments.
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Affiliation(s)
- Valentine Chapelle
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth, and Environment, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
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Karalija E, Carbó M, Coppi A, Colzi I, Dainelli M, Gašparović M, Grebenc T, Gonnelli C, Papadakis V, Pilić S, Šibanc N, Valledor L, Poma A, Martinelli F. Interplay of plastic pollution with algae and plants: hidden danger or a blessing? JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129450. [PMID: 35999715 DOI: 10.1016/j.jhazmat.2022.129450] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/12/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
In the era of plastic pollution, plants have been discarded as a system that is not affected by micro and nanoplastics, but contrary to beliefs that plants cannot absorb plastic particles, recent research proved otherwise. The presented review gives insight into known aspects of plants' interplay with plastics and how plants' ability to absorb plastic particles can be utilized to remove plastics from water and soil systems. Microplastics usually cannot be absorbed by plant root systems due to their size, but some reports indicate they might enter plant tissues through stomata. On the other hand, nanoparticles can enter plant root systems, and reports of their transport via xylem to upper plant parts have been recorded. Bioaccumulation of nanoplastics in upper plant parts is still not confirmed. The prospects of using biosystems for the remediation of soils contaminated with plastics are still unknown. However, algae could be used to degrade plastic particles in water systems through enzyme facilitated degradation processes. Considering the amount of plastic pollution, especially in the oceans, further research is necessary on the utilization of algae in plastic degradation. Special attention should be given to the research concerning utilization of algae with restricted algal growth, ensuring that a different problem is not induced, "sea blooming", during the degradation of plastics.
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Affiliation(s)
- Erna Karalija
- Laboratory for Plant Physiology, Department for Biology, Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina.
| | - María Carbó
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain.
| | - Andrea Coppi
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121 Florence, Italy.
| | - Ilaria Colzi
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121 Florence, Italy.
| | - Marco Dainelli
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121 Florence, Italy.
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Kačićeva 26, 10000 Zagreb, Croatia.
| | - Tine Grebenc
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia.
| | - Cristina Gonnelli
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121 Florence, Italy.
| | - Vassilis Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, N. Plastira 100, GR-70013 Heraklion, Crete, Greece.
| | - Selma Pilić
- Laboratory for Plant Physiology, Department for Biology, Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Nataša Šibanc
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia.
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain.
| | - Anna Poma
- Department of Life, Health and Environmental Sciences, Università degli Studi dell'Aquila, Laboratory of Genetics and Mutagenesis, via Vetoio 1, 67100 L'Aquila, Italy.
| | - Federico Martinelli
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121 Florence, Italy.
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46
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Molecular and epigenetic basis of heat stress responses and acclimatization in plants. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00400-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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47
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Byregowda R, Prasad SR, Oelmüller R, Nataraja KN, Prasanna Kumar MK. Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes. Int J Mol Sci 2022; 23:ijms23169194. [PMID: 36012460 PMCID: PMC9408852 DOI: 10.3390/ijms23169194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.
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Affiliation(s)
- Roopashree Byregowda
- Department of Seed Science and Technology, University of Agricultural Sciences, Bangalore 560065, India
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University, 07743 Jena, Germany
| | | | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University, 07743 Jena, Germany
- Correspondence:
| | - Karaba N. Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore 560065, India
| | - M. K. Prasanna Kumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore 560065, India
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Ramakrishnan M, Rajan KS, Mullasseri S, Palakkal S, Kalpana K, Sharma A, Zhou M, Vinod KK, Ramasamy S, Wei Q. The plant epitranscriptome: revisiting pseudouridine and 2'-O-methyl RNA modifications. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1241-1256. [PMID: 35445501 PMCID: PMC9241379 DOI: 10.1111/pbi.13829] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 06/01/2023]
Abstract
There is growing evidence that post-transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to optimize RNA modifications in crops to improve productivity. The contributions of internal mRNA modifications such as N6-methyladenosine (m6 A) and 5-methylcytosine (m5 C) methylations to embryonic development, root development, leaf morphogenesis, flowering, fruit ripening and stress response are sufficiently known, but the roles of the two most abundant RNA modifications, pseudouridine (Ψ) and 2'-O-methylation (Nm), in the cell remain unclear due to insufficient advances in high-throughput technologies in plant development. Therefore, in this review, we discuss the latest methods and insights gained in mapping internal Ψ and Nm and their unique properties in plants and other organisms. In addition, we discuss the limitations that remain in high-throughput technologies for qualitative and quantitative mapping of these RNA modifications and highlight future challenges in regulating the plant epitranscriptome.
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Affiliation(s)
- Muthusamy Ramakrishnan
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
- Bamboo Research InstituteNanjing Forestry UniversityNanjingJiangsuChina
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology InstituteBar‐Ilan University52900Ramat‐GanIsrael
- Department of Chemical and Structural BiologyWeizmann Institute7610001RehovotIsrael
| | - Sileesh Mullasseri
- School of Ocean Science and TechnologyKerala University of Fisheries and Ocean StudiesCochinIndia
| | - Sarin Palakkal
- The Institute for Drug ResearchSchool of PharmacyThe Hebrew University of JerusalemJerusalemIsrael
| | - Krishnan Kalpana
- Department of Plant PathologyAgricultural College and Research InstituteTamilnadu Agricultural University625 104MaduraiTamil NaduIndia
| | - Anket Sharma
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouZhejiangChina
| | - Mingbing Zhou
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouZhejiangChina
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High‐Efficiency UtilizationZhejiang A&F UniversityHangzhouZhejiangChina
| | | | - Subbiah Ramasamy
- Cardiac Metabolic Disease LaboratoryDepartment of BiochemistrySchool of Biological SciencesMadurai Kamaraj UniversityMaduraiTamil NaduIndia
| | - Qiang Wei
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
- Bamboo Research InstituteNanjing Forestry UniversityNanjingJiangsuChina
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49
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Sun M, Yang Z, Liu L, Duan L. DNA Methylation in Plant Responses and Adaption to Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23136910. [PMID: 35805917 PMCID: PMC9266845 DOI: 10.3390/ijms23136910] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
Due to their sessile state, plants are inevitably affected by and respond to the external environment. So far, plants have developed multiple adaptation and regulation strategies to abiotic stresses. One such system is epigenetic regulation, among which DNA methylation is one of the earliest and most studied regulatory mechanisms, which can regulate genome functioning and induce plant resistance and adaption to abiotic stresses. In this review, we outline the most recent findings on plant DNA methylation responses to drought, high temperature, cold, salt, and heavy metal stresses. In addition, we discuss stress memory regulated by DNA methylation, both in a transient way and the long-term memory that could pass to next generations. To sum up, the present review furnishes an updated account of DNA methylation in plant responses and adaptations to abiotic stresses.
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Affiliation(s)
| | | | - Li Liu
- Correspondence: (L.L.); (L.D.)
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50
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Unraveling the DNA Methylation in the rDNA Foci in Mutagen-Induced Brachypodium distachyon Micronuclei. Int J Mol Sci 2022; 23:ijms23126797. [PMID: 35743241 PMCID: PMC9224279 DOI: 10.3390/ijms23126797] [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: 05/17/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 02/01/2023] Open
Abstract
Many years have passed since micronuclei were first observed then accepted as an indicator of the effect of mutagens. However, the possible mechanisms of their formation and elimination from the cell are still not fully understood. Various stresses, including mutagens, can alter gene expression through changes in DNA methylation in plants. In this study we demonstrate for the first time DNA methylation in the foci of 5S and 35S rDNA sequences in individual Brachypodium distachyon micronuclei that are induced by mutagenic treatment with maleic acid hydrazide (MH). The impact of MH on global epigenetic modifications in nuclei and micronuclei has been studied in plants before; however, no in situ analyses of DNA methylation in specific DNA sequence sites are known. To address this problem, we used sequential immunodetection of 5-methylcytosine and fluorescence in situ hybridization (FISH) with 5S and 25S rDNA probes on the non-dividing cells of B. distachyon. Such investigations into the presence or absence of DNA methylation within specific DNA sequences are extremely important in plant mutagenesis in the light of altering gene expression.
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