1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
Collapse
Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Epigenetic Changes Occurring in Plant Inbreeding. Int J Mol Sci 2023; 24:ijms24065407. [PMID: 36982483 PMCID: PMC10048984 DOI: 10.3390/ijms24065407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.
Collapse
|
5
|
Morgan BL, Donohue K. Parental methylation mediates how progeny respond to environments of parents and of progeny themselves. ANNALS OF BOTANY 2022; 130:883-899. [PMID: 36201313 PMCID: PMC9758305 DOI: 10.1093/aob/mcac125] [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: 06/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Environments experienced by both parents and offspring influence progeny traits, but the epigenetic mechanisms that regulate the balance of parental vs. progeny control of progeny phenotypes are not known. We tested whether DNA methylation in parents and/or progeny mediates responses to environmental cues experienced in both generations. METHODS Using Arabidopsis thaliana, we manipulated parental and progeny DNA methylation both chemically, via 5-azacytidine, and genetically, via mutants of methyltransferase genes, then measured progeny germination responses to simulated canopy shade in parental and progeny generations. KEY RESULTS We first found that germination of offspring responded to parental but not seed demethylation. We further found that parental demethylation reversed the parental effect of canopy in seeds with low (Cvi-1) to intermediate (Col) dormancy, but it obliterated the parental effect in seeds with high dormancy (Cvi-0). Demethylation did so by either suppressing germination of seeds matured under white-light (Cvi-1) or under canopy (Cvi-0), or by increasing the germination of seeds matured under canopy (Col). Disruption of parental methylation also prevented seeds from responding to their own light environment in one genotype (Cvi-0, most dormant), but it enabled seeds to respond to their own environment in another genotype (Cvi-1, least dormant). Using mutant genotypes, we found that both CG and non-CG DNA methylation were involved in parental effects on seed germination. CONCLUSIONS Parental methylation state influences seed germination more strongly than does the progeny's own methylation state, and it influences how seeds respond to environments of parents and progeny in a genotype-specific manner.
Collapse
Affiliation(s)
- Britany L Morgan
- University Program in Ecology Duke University, Durham, NC 27705, USA
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Kathleen Donohue
- University Program in Ecology Duke University, Durham, NC 27705, USA
- Biology Department, Duke University, Durham, NC 27705, USA
| |
Collapse
|
6
|
Lieberman-Lazarovich M, Kaiserli E, Bucher E, Mladenov V. Natural and induced epigenetic variation for crop improvement. CURRENT OPINION IN PLANT BIOLOGY 2022; 70:102297. [PMID: 36108411 DOI: 10.1016/j.pbi.2022.102297] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/27/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Maintaining global food security is a major challenge that requires novel strategies for crop improvement. Epigenetic regulation of plant responses to adverse environmental conditions provides a tunable mechanism to optimize plant growth, adaptation and ultimately yield. Epibreeding employs agricultural practices that rely on key epigenetic features as a means of engineering favorable phenotypic traits in target crops. This review summarizes recent findings on the role of epigenetic marks such as DNA methylation and histone modifications, in controlling phenotypic variation in crop species in response to environmental factors. The potential use of natural and induced epigenetic features as platforms for crop improvement via epibreeding, is discussed.
Collapse
Affiliation(s)
- Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel.
| | - Eirini Kaiserli
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Etienne Bucher
- Crop Genome Dynamics Group, Agroscope Changins, 1260, Nyon, Switzerland
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia
| |
Collapse
|
7
|
Kosová V, Latzel V, Hadincová V, Münzbergová Z. Effect of DNA methylation, modified by 5-azaC, on ecophysiological responses of a clonal plant to changing climate. Sci Rep 2022; 12:17262. [PMID: 36241768 PMCID: PMC9568541 DOI: 10.1038/s41598-022-22125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/10/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic regulation of gene expression is expected to be an important mechanism behind phenotypic plasticity. Whether epigenetic regulation affects species ecophysiological adaptations to changing climate remains largely unexplored. We compared ecophysiological traits between individuals treated with 5-azaC, assumed to lead to DNA demethylation, with control individuals of a clonal grass originating from and grown under different climates, simulating different directions and magnitudes of climate change. We linked the ecophysiological data to proxies of fitness. Main effects of plant origin and cultivating conditions predicted variation in plant traits, but 5-azaC did not. Effects of 5-azaC interacted with conditions of cultivation and plant origin. The direction of the 5-azaC effects suggests that DNA methylation does not reflect species long-term adaptations to climate of origin and species likely epigenetically adjusted to the conditions experienced during experiment set-up. Ecophysiology translated to proxies of fitness, but the intensity and direction of the relationships were context dependent and affected by 5-azaC. The study suggests that effects of DNA methylation depend on conditions of plant origin and current climate. Direction of 5-azaC effects suggests limited role of epigenetic modifications in long-term adaptation of plants. It rather facilitates fast adaptations to temporal fluctuations of the environment.
Collapse
Affiliation(s)
- Veronika Kosová
- grid.4491.80000 0004 1937 116XDepartment of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vít Latzel
- grid.418095.10000 0001 1015 3316Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Věroslava Hadincová
- grid.418095.10000 0001 1015 3316Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Zuzana Münzbergová
- grid.4491.80000 0004 1937 116XDepartment of Botany, Faculty of Science, Charles University, Prague, Czech Republic ,grid.418095.10000 0001 1015 3316Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| |
Collapse
|
8
|
Singh D, Chaudhary P, Taunk J, Kumar Singh C, Sharma S, Singh VJ, Singh D, Chinnusamy V, Yadav R, Pal M. Plant epigenomics for extenuation of abiotic stresses: challenges and future perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6836-6855. [PMID: 34302734 DOI: 10.1093/jxb/erab337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Climate change has escalated abiotic stresses, leading to adverse effects on plant growth and development, eventually having deleterious consequences on crop productivity. Environmental stresses induce epigenetic changes, namely cytosine DNA methylation and histone post-translational modifications, thus altering chromatin structure and gene expression. Stable epigenetic changes are inheritable across generations and this enables plants to adapt to environmental changes (epipriming). Hence, epigenomes serve as a good source of additional tier of variability for development of climate-smart crops. Epigenetic resources such as epialleles, epigenetic recombinant inbred lines (epiRILs), epigenetic quantitative trait loci (epiQTLs), and epigenetic hybrids (epihybrids) can be utilized in epibreeding for improving stress tolerance of crops. Epigenome engineering is also gaining momentum for developing sustainable epimarks associated with important agronomic traits. Different epigenome editing tools are available for creating, erasing, and reading such epigenetic codes in plant genomes. However, epigenome editing is still understudied in plants due to its complex nature. Epigenetic interventions such as epi-fingerprinting can be exploited in the near future for health and quality assessment of crops under stress conditions. Keeping in view the challenges and opportunities associated with this important technology, the present review intends to enhance understanding of stress-induced epigenetic changes in plants and its prospects for development of climate-ready crops.
Collapse
Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Shristi Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Vikram Jeet Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajbir Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
9
|
Dalakouras A, Vlachostergios D. Epigenetic approaches to crop breeding: current status and perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5356-5371. [PMID: 34017985 DOI: 10.1093/jxb/erab227] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 05/10/2023]
Abstract
In order to tackle the cumulative adverse effects of global climate change, reduced farmland, and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued agronomical traits, but its potential is gradually being compromised by the menacing decline of genetic variation. Resorting to the epigenome as a source of variation could serve as a promising alternative. Here, we discuss current status of epigenetics-mediated crop breeding (epibreeding), highlight its advances and limitations, outline currently available methodologies, and propose novel RNA-based strategies to modify the epigenome in a gene-specific and transgene-free manner.
Collapse
Affiliation(s)
- Athanasios Dalakouras
- Institute of Industrial and Forage Crops, HAO-DEMETER, 41335 Larissa, Greece
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, 57001 Thessaloniki, Greece
| | | |
Collapse
|
10
|
Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
Collapse
Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| |
Collapse
|
11
|
Quantitative Epigenetics: A New Avenue for Crop Improvement. EPIGENOMES 2020; 4:epigenomes4040025. [PMID: 34968304 PMCID: PMC8594725 DOI: 10.3390/epigenomes4040025] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/24/2020] [Accepted: 11/04/2020] [Indexed: 12/30/2022] Open
Abstract
Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Furthermore, the development of epigenetic recombinant inbred lines (epi-RILs) in model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Likewise, epigenome-wide association study (EWAS) and epi-genotyping by sequencing (epi-GBS) have revolutionized the field of epigenetics research in plants. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can potentially facilitate epigenetic based molecular breeding of important crop plants.
Collapse
|
12
|
Genitoni J, Vassaux D, Delaunay A, Citerne S, Portillo Lemus L, Etienne MP, Renault D, Stoeckel S, Barloy D, Maury S. Hypomethylation of the aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala mimics the adaptive transition into the terrestrial morphotype. PHYSIOLOGIA PLANTARUM 2020; 170:280-298. [PMID: 32623739 DOI: 10.1111/ppl.13162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Ongoing global changes affect ecosystems and open up new opportunities for biological invasion. The ability of invasive species to rapidly adapt to new environments represents a relevant model for studying short-term adaptation mechanisms. The aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala, is classified as harmful in European rivers. In French wet meadows, this species has shown a rapid transition from aquatic to terrestrial environments with emergence of two distinct morphotypes in 5 years. To understand the heritable mechanisms involved in adjustment to such a new environment, we investigate both genetic and epigenetic as possible sources of flexibility involved in this fast terrestrial transition. We found a low overall genetic differentiation between the two morphotypes arguing against the possibility that terrestrial morphotype emerged from a new adaptive genetic capacity. Artificial hypomethylation was induced on both morphotypes to assess the epigenetic hypothesis. We analyzed global DNA methylation, morphological changes, phytohormones and metabolite profiles of both morphotype responses in both aquatic and terrestrial conditions in shoot and root tissues. Hypomethylation significantly affected morphological variables, phytohormone levels and the amount of some metabolites. The effects of hypomethylation depended on morphotypes, conditions and plant tissues, which highlighted differences among the morphotypes and their plasticity. Using a correlative integrative approach, we showed that hypomethylation of the aquatic morphotype mimicked the characteristics of the terrestrial morphotype. Our data suggest that DNA methylation rather than a new adaptive genetic capacity is playing a key role in L. grandiflora subsp. hexapetala plasticity during its rapid aquatic to terrestrial transition.
Collapse
Affiliation(s)
- Julien Genitoni
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Danièle Vassaux
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Alain Delaunay
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Luis Portillo Lemus
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Marie-Pierre Etienne
- Institut Agro, CNRS, Université Rennes, IRMAR (Institut de Recherche Mathématique de Rennes) - UMR 6625, Rennes, F-35000, France
| | - David Renault
- UMR CNRS 6553 EcoBio, University of Rennes 1, Rennes, France
- Institut Universitaire de France, 1 rue Descartes, Paris, France
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université Rennes, Le Rheu, 35653, France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| |
Collapse
|
13
|
Corbin KR, Bolt B, Rodríguez López CM. Breeding for Beneficial Microbial Communities Using Epigenomics. Front Microbiol 2020; 11:937. [PMID: 32477316 PMCID: PMC7242621 DOI: 10.3389/fmicb.2020.00937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/20/2020] [Indexed: 02/03/2023] Open
Affiliation(s)
- Kendall R Corbin
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States.,Biosystems and Agricultural Engineering, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Bridget Bolt
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Carlos M Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| |
Collapse
|
14
|
Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings. G3-GENES GENOMES GENETICS 2020; 10:1019-1028. [PMID: 31941723 PMCID: PMC7056980 DOI: 10.1534/g3.119.400770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Epigenetic modifications such as DNA methylation, where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence plant response to changing environments. One way to test this impact is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree, Quercus lobata, with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that demethylation treatment led to 3–6% absolute reductions and 6.7–43.2% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings. We tested whether this result could be due to impact of the treatment on the soil microbiome and found minimal differences in the soil microbiome between two groups, although with limited sample size. We found no significant differences in leaf fluctuating asymmetry (i.e., deviations from bilateral symmetry), which has been found in other studies. Nonetheless, treated seedlings showed differential expression of a total of 23 genes. Overall, this study provides initial evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings and suggests that removal of DNA methylation affects plant development.
Collapse
|
15
|
Herrera CM, Medrano M, Pérez R, Bazaga P, Alonso C. Within-plant heterogeneity in fecundity and herbivory induced by localized DNA hypomethylation in the perennial herb Helleborus foetidus. AMERICAN JOURNAL OF BOTANY 2019; 106:798-806. [PMID: 31157419 DOI: 10.1002/ajb2.1291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Phenotypic heterogeneity of reiterated, homologous structures produced by individual plants has ecological consequences for plants and their animal consumers. This paper examines experimentally the epigenetic mosaicism hypothesis, which postulates that within-plant variation in traits of reiterated structures may partly arise from different parts of the same genetic individual differing in patterns or extent of genomic DNA methylation. METHODS Leaves of paired ramets borne by field-growing Helleborus foetidus plants were infiltrated periodically over the entire flowering period with either a water solution of the demethylating agent zebularine or just water as the control. The effects of the zebularine treatment were assessed by quantifying genome-wide DNA cytosine methylation in leaves and monitoring inflorescence growth and flower production, number of ovules per flower, pollination success, fruit set, seed set, seed size, and distribution of sap-feeding insects. RESULTS Genomic DNA from leaves in zebularine-treated ramets was significantly less methylated than DNA from leaves in control ones. Inflorescences in treated ramets grew smaller and produced fewer flowers, with fewer ovules and lower follicle and seed set, but did not differ from inflorescences in untreated ramets in pollination success or seed size. The zebularine treatment influenced the within-plant distribution of sap-feeding insects. CONCLUSIONS Experimental manipulation of genomic DNA methylation level in leaves of wild-growing H. foetidus plants induced considerable within-plant heterogeneity in phenotypic (inflorescences, flowers, fecundity) and ecologically relevant traits (herbivore distribution), which supports the hypothesis that epigenetic mosaicism may partly account for within-plant variation.
Collapse
Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| |
Collapse
|
16
|
|
17
|
Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare). EPIGENOMES 2018. [DOI: 10.3390/epigenomes2020012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
|
18
|
The DNA Methylome and Association of Differentially Methylated Regions with Differential Gene Expression during Heat Stress in Brassica rapa. Int J Mol Sci 2018; 19:ijms19051414. [PMID: 29747401 PMCID: PMC5983725 DOI: 10.3390/ijms19051414] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/16/2018] [Accepted: 04/29/2018] [Indexed: 01/04/2023] Open
Abstract
Cytosine DNA methylation is a critical epigenetic mechanism in the silencing of transposable elements, imprinting and regulating gene expression. However, little is known about the potential role of mC in response to heat stress. To determine and explore the functions of the dynamic DNA methylome during heat stress, we characterized single-base resolution methylome maps of Brassica rapa and assessed the dynamic changes of mC under heat stress using whole genome bisulfite sequencing. On average, the DNA methylation levels of CG, CHG and CHH are 39.3%, 15.38% and 5.24% in non-heading Chinese cabbage (NHCC), respectively. We found that the patterns of methylation are similar to other eudicot plants, but with higher CHH methylation levels. Further comparative analysis revealed varying patterns for three sequence contexts (mCG, mCHG and mCHH) under heat stress indicating context- and position-dependent methylation regulation. DNA methylation near the TSS and TES may be closely associated with methylation-dependent transcriptional silencing. Association analysis of differential methylation and differential gene expression revealed a different set of methDEGs involved at early and late stages under heat stress. The systemic characterization of the dynamic DNA methylome during heat stress will improve our understanding of the mechanism of epigenetic regulation under heat stress.
Collapse
|
19
|
Alonso C, Pérez R, Bazaga P, Medrano M, Herrera CM. Within-plant variation in seed size and inflorescence fecundity is associated with epigenetic mosaicism in the shrub Lavandula latifolia (Lamiaceae). ANNALS OF BOTANY 2018; 121:153-160. [PMID: 29186299 PMCID: PMC5786237 DOI: 10.1093/aob/mcx140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 11/02/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS Sub-individual variation in traits of homologous structures has multiple ecological consequences for individuals and populations. Assessing the evolutionary significance of such effects requires an improved knowledge of the mechanisms underlying within-plant phenotypic heterogeneity. The hypothesis that continuous within-plant variation in some phenotypic traits can be associated with epigenetic mosaicism was examined. METHODS Fifteen individuals of the long-lived, evergreen Mediterranean shrub Lavandula latifolia were studied. Five widely spaced 'modules', each consisting of a single inflorescence plus all its subtending basal leaves, were collected from each shrub. Genomic DNA was extracted from leaf samples and genome-wide cytosine methylation determined by reversed phase high-performance liquid chromatography (HPLC) with spectrofluorimetric detection. The number and mean mass of seeds produced were determined for each inflorescence. An assessment was made of whether (1) leaves from different modules in the same plant differed significantly in global DNA cytosine methylation, and (2) mosaicism in cytosine methylation contributed to explain variation across modules in number and size of seeds. KEY RESULTS Leaves from different modules in the same plant differed in global DNA cytosine methylation. The magnitude of epigenetic mosaicism was substantial, as the variance in DNA methylation among modules of the same shrub was greater than the variance between individuals. Number and mean mass of seeds produced by individual inflorescences varied within plants and were quadratically related to cytosine methylation of subtending leaves, with an optimum at an intermediate methylation level (approx. 25 %). CONCLUSIONS The results support a causal link between global cytosine methylation of leaves in a module and the size and numbers of seeds produced by the associated inflorescence. It is proposed that variation in global DNA methylation within L. latifolia shrubs may result from the concerted action of plant sectoriality and differential exposure of different plant parts to some environmental factor(s) with a capacity to induce durable epigenetic changes.
Collapse
Affiliation(s)
- Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, CSIC-US, Avda. Américo Vespucio, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | - Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| |
Collapse
|
20
|
|
21
|
Yao Y, Kovalchuk I. Exposure to zebularine and 5-azaC triggers microsatellite instability in the exposed Arabidopsis thaliana plants and their progeny. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2017.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
22
|
Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
23
|
Puy J, Dvořáková H, Carmona CP, de Bello F, Hiiesalu I, Latzel V. Improved demethylation in ecological epigenetic experiments: Testing a simple and harmless foliar demethylation application. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12903] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Javier Puy
- Department of BotanyFaculty of ScienceUniversity of South Bohemia České Budějovice Czech Republic
| | - Hana Dvořáková
- Department of BotanyFaculty of ScienceUniversity of South Bohemia České Budějovice Czech Republic
| | - Carlos P. Carmona
- Department of BotanyFaculty of ScienceUniversity of South Bohemia České Budějovice Czech Republic
- Institute of Ecology and Earth SciencesDepartment of BotanyUniversity of Tartu Tartu Estonia
| | - Francesco de Bello
- Department of BotanyFaculty of ScienceUniversity of South Bohemia České Budějovice Czech Republic
- Institute of BotanyCzech Academy of Science Třeboň Czech Republic
| | - Inga Hiiesalu
- Institute of Ecology and Earth SciencesDepartment of BotanyUniversity of Tartu Tartu Estonia
| | - Vít Latzel
- Institute of BotanyCzech Academy of Sciences Průhonice Czech Republic
| |
Collapse
|
24
|
Fortes AM, Gallusci P. Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:82. [PMID: 28220131 PMCID: PMC5292615 DOI: 10.3389/fpls.2017.00082] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/16/2017] [Indexed: 05/20/2023]
Abstract
Epigenetic marks include Histone Post-Translational Modifications and DNA methylation which are known to participate in the programming of gene expression in plants and animals. These epigenetic marks may be subjected to dynamic changes in response to endogenous and/or external stimuli and can have an impact on phenotypic plasticity. Studying how plant genomes can be epigenetically shaped under stressed conditions has become an essential issue in order to better understand the molecular mechanisms underlying plant stress responses and enabling epigenetic in addition to genetic factors to be considered when breeding crop plants. In this perspective, we discuss the contribution of epigenetic mechanisms to our understanding of plant responses to biotic and abiotic stresses. This regulation of gene expression in response to environment raises important biological questions for perennial species such as grapevine which is asexually propagated and grown worldwide in contrasting terroirs and environmental conditions. However, most species used for epigenomic studies are annual herbaceous plants, and epigenome dynamics has been poorly investigated in perennial woody plants, including grapevine. In this context, we propose grape as an essential model for epigenetic and epigenomic studies in perennial woody plants of agricultural importance.
Collapse
Affiliation(s)
- Ana M. Fortes
- Faculdade de Ciências, Instituto de Biossistemas e Ciências Integrativas, Universidade de LisboaLisboa, Portugal
| | - Philippe Gallusci
- UMR EGFV, Université de Bordeaux, Institut national de la recherche agronomique, Institut des Sciences de la Vigne et du VinVillenave-d’Ornon, France
| |
Collapse
|
25
|
Xie H, Konate M, Sai N, Tesfamicael KG, Cavagnaro T, Gilliham M, Breen J, Metcalfe A, Stephen JR, De Bei R, Collins C, Lopez CMR. Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine ( Vitis vinifera cv. Shiraz). FRONTIERS IN PLANT SCIENCE 2017; 8:1860. [PMID: 29163587 PMCID: PMC5670326 DOI: 10.3389/fpls.2017.01860] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/11/2017] [Indexed: 05/21/2023]
Abstract
Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant's phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia. Methylation sensitive amplified polymorphisms (MSAPs) were used to obtain global patterns of DNA methylation. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Pairwise epigenetic distances between vineyards indicate that the main contributor (23-24%) to the detected variability is associated to the distribution of the vineyards on the N-S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive genotyping by sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique gene ontology terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.
Collapse
Affiliation(s)
- Huahan Xie
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Moumouni Konate
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Na Sai
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - Kiflu G. Tesfamicael
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Timothy Cavagnaro
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Gilliham
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - James Breen
- Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Andrew Metcalfe
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - John R. Stephen
- Plant Genomics Centre, Australian Genome Research Facility Ltd., Adelaide, SA, Australia
| | - Roberta De Bei
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Cassandra Collins
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Carlos M. R. Lopez
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Carlos M. R. Lopez,
| |
Collapse
|
26
|
Kellenberger RT, Schlüter PM, Schiestl FP. Herbivore-Induced DNA Demethylation Changes Floral Signalling and Attractiveness to Pollinators in Brassica rapa. PLoS One 2016; 11:e0166646. [PMID: 27870873 PMCID: PMC5117703 DOI: 10.1371/journal.pone.0166646] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/01/2016] [Indexed: 12/27/2022] Open
Abstract
Plants have to fine-tune their signals to optimise the trade-off between herbivore deterrence and pollinator attraction. An important mechanism in mediating plant-insect interactions is the regulation of gene expression via DNA methylation. However, the effect of herbivore-induced DNA methylation changes on pollinator-relevant plant signalling has not been systematically investigated. Here, we assessed the impact of foliar herbivory on DNA methylation and floral traits in the model crop plant Brassica rapa. Methylation-sensitive amplified fragment length polymorphism (MSAP) analysis showed that leaf damage by the caterpillar Pieris brassicae was associated with genome-wide methylation changes in both leaves and flowers of B. rapa as well as a downturn in flower number, morphology and scent. A comparison to plants with jasmonic acid-induced defence showed similar demethylation patterns in leaves, but both the floral methylome and phenotype differed significantly from P. brassicae infested plants. Standardised genome-wide demethylation with 5-azacytidine in five different B. rapa full-sib groups further resulted in a genotype-specific downturn of floral morphology and scent, which significantly reduced the attractiveness of the plants to the pollinator bee Bombus terrestris. These results suggest that DNA methylation plays an important role in adjusting plant signalling in response to changing insect communities.
Collapse
Affiliation(s)
- Roman T. Kellenberger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Florian P. Schiestl
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| |
Collapse
|
27
|
Xu J, Tanino KK, Horner KN, Robinson SJ. Quantitative trait variation is revealed in a novel hypomethylated population of woodland strawberry (Fragaria vesca). BMC PLANT BIOLOGY 2016; 16:240. [PMID: 27809774 PMCID: PMC5095969 DOI: 10.1186/s12870-016-0936-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/27/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Phenotypic variation is determined by a combination of genotype, environment and their interactions. The realization that allelic diversity can be both genetic and epigenetic allows the environmental component to be further separated. Partitioning phenotypic variation observed among inbred lines with an altered epigenome can allow the epigenetic component controlling quantitative traits to be estimated. To assess the contribution of epialleles on phenotypic variation and determine the fidelity with which epialleles are inherited, we have developed a novel hypomethylated population of strawberry (2n = 2x = 14) using 5-azacytidine from which individuals with altered phenotypes can be identified, selected and characterized. RESULTS The hypomethylated population was generated using an inbred strawberry population in the F. vesca ssp. vesca accession Hawaii 4. Analysis of whole genome sequence data from control and hypomethylated lines indicate that 5-azacytidine exposure does not increase SNP above background levels. The populations contained only Hawaii 4 alleles, removing introgression of alternate F. vesca alleles as a potential source of variation. Although genome sequencing and genetic marker data are unable to rule out 5-azacytidine induced chromosomal rearrangements as a potential source of the trait variation observed, none were detected in our survey. Quantitative trait variation focusing on flowering time and rosette diameter was scored in control and treated populations where expanded levels of variation were observed among the hypomethylated lines. Methylation sensitive molecular markers indicated that 5-azacytidine induced alterations in DNA methylation patterns and inheritance of methylation patterns were confirmed by bisulfite sequencing of targeted regions. It is possible that methylation polymorphisms might underlie or have induced genetic changes underlying the observable differences in quantitative phenotypes. CONCLUSIONS This population developed in a uniform genetic background provides a resource for the discovery of new variation controlling quantitative traits. Genome sequence analysis indicates that 5-azacytidine did not induce point mutations and the induced variation is largely restricted to DNA methylation. Using this resource, we have identified new variation and demonstrated the inheritance of both variant trait and methylation patterns. Although direct associations remain to be determined, these data suggest epigenetic variation might be subject to selection.
Collapse
Affiliation(s)
- Jihua Xu
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan Canada
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan Canada
| | - Karen K. Tanino
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan Canada
| | - Kyla N. Horner
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan Canada
| | - Stephen J. Robinson
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan Canada
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan Canada
| |
Collapse
|
28
|
Consuegra S, Rodríguez López CM. Epigenetic-induced alterations in sex-ratios in response to climate change: An epigenetic trap? Bioessays 2016; 38:950-8. [PMID: 27548838 DOI: 10.1002/bies.201600058] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We hypothesize that under the predicted scenario of climate change epigenetically mediated environmental sex determination could become an epigenetic trap. Epigenetically regulated environmental sex determination is a mechanism by which species can modulate their breeding strategies to accommodate environmental change. Growing evidence suggests that epigenetic mechanisms may play a key role in phenotypic plasticity and in the rapid adaptation of species to environmental change, through the capacity of organisms to maintain a non-genetic plastic memory of the environmental and ecological conditions experienced by their parents. However, inherited epigenetic variation could also be maladaptive, becoming an epigenetic trap. This is because environmental sex determination can alter sex ratios by increasing the survival of one of the sexes at the expense of negative fitness consequences for the other, which could lead not only to the collapse of natural populations, but also have an impact in farmed animal and plant species.
Collapse
Affiliation(s)
- Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Swansea, UK.
| | - Carlos M Rodríguez López
- Environmental Epigenetics and Genetics Group, School of Agriculture, University of Adelaide, Glen Osmond, South Australia, Australia.
| |
Collapse
|
29
|
Adu-Gyamfi R, Wetten A, Marcelino Rodríguez López C. Effect of Cryopreservation and Post-Cryopreservation Somatic Embryogenesis on the Epigenetic Fidelity of Cocoa (Theobroma cacao L.). PLoS One 2016; 11:e0158857. [PMID: 27403857 PMCID: PMC4942035 DOI: 10.1371/journal.pone.0158857] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/22/2016] [Indexed: 11/24/2022] Open
Abstract
UNLABELLED While cocoa plants regenerated from cryopreserved somatic embryos can demonstrate high levels of phenotypic variability, little is known about the sources of the observed variability. Previous studies have shown that the encapsulation-dehydration cryopreservation methodology imposes no significant extra mutational load since embryos carrying high levels of genetic variability are selected against during protracted culture. Also, the use of secondary rather than primary somatic embryos has been shown to further reduce the incidence of genetic somaclonal variation. Here, the effect of in vitro conservation, cryopreservation and post-cryopreservation generation of somatic embryos on the appearance of epigenetic somaclonal variation were comparatively assessed. To achieve this we compared the epigenetic profiles, generated using Methylation Sensitive Amplified Polymorphisms, of leaves collected from the ortet tree and from cocoa somatic embryos derived from three in vitro conditions: somatic embryos, somatic embryos cryopreserved in liquid nitrogen and somatic embryos generated from cryoproserved somatic embryos. Somatic embryos accumulated epigenetic changes but these were less extensive than in those regenerated after storage in LN. Furthermore, the passage of cryopreserved embryos through another embryogenic stage led to further increase in variation. Interestingly, this detected variability appears to be in some measure reversible. The outcome of this study indicates that the cryopreservation induced phenotypic variability could be, at least partially, due to DNA methylation changes. KEY MESSAGE Phenotypic variability observed in cryostored cocoa somatic-embryos is epigenetic in nature. This variability is partially reversible, not stochastic in nature but a directed response to the in-vitro culture and cryopreservation.
Collapse
Affiliation(s)
- Raphael Adu-Gyamfi
- Faculty of Agriculture, University for Development Studies, P.O. Box TL 1882, Tamale, Ghana
| | - Andy Wetten
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, Berks, RG6 6AS, United Kingdom
| | - Carlos Marcelino Rodríguez López
- Environmental Epigenetics and Genetics Group, Plant Research Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| |
Collapse
|
30
|
Taudt A, Colomé-Tatché M, Johannes F. Genetic sources of population epigenomic variation. Nat Rev Genet 2016; 17:319-32. [DOI: 10.1038/nrg.2016.45] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
31
|
Xu J, Tanino KK, Robinson SJ. Stable Epigenetic Variants Selected from an Induced Hypomethylated Fragaria vesca Population. FRONTIERS IN PLANT SCIENCE 2016; 7:1768. [PMID: 27965682 PMCID: PMC5126047 DOI: 10.3389/fpls.2016.01768] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/09/2016] [Indexed: 05/05/2023]
Abstract
Epigenetic inheritance was transmitted through selection over five generations of extreme early, but not late flowering time phenotypic lines in Fragaria vesca. Epigenetic variation was initially artificially induced using the DNA demethylation reagent 5-azacytidine (5-azaC). It is the first report to explore epigenetic variant selection and phenotypic trait inheritance in strawberry. Transmission frequency of these traits was determined across generations. The early flowering (EF4) and late stolon (LS) phenotypic traits were successfully transmitted across five and three generations through meiosis, respectively. Stable mitotic transmission of the early flowering phenotype was also demonstrated using clonal daughters derived from the 4th Generation (S4) mother plant. In order to further explore the DNA methylation patterns underlying the early flowering trait, the standard MSAP method using isoschizomers Hpa II/Msp I, and newly modified MSAP method using isoschizomers Tfi I/Pfe I which detected DNA methylation at CG, CHG, CHH sites were used in two early flowering lines, EF lines 1 (P2) and EF lines 2 (P3), and control lines (P1). A significant reduction in the number of fully-methylated bands was detected in P2 and P3 when compared to P1 using the novel MSAP method. In the standard MSAP, the symmetric CG and CHG methylation was maintained over generations in the early flowering lines based on the clustering in P2 and P3, the novel MSAP approach revealed the asymmetric CHH methylation pattern was not maintained over generations. This study provides evidence of stable selection of phenotypic traits, particularly early flowering through both meiosis and mitosis, which is meaningful to both breeding programs and commercial horticulture. The maintenance in CG and CHG methylation over generations suggests the early flowering phenotype might be related to DNA methylation alterations at the CG or CHG sites. Finally, this work provides a new approach for studying the role of epigenetics on complex quantitative trait improvement in strawberry, as well as providing a tool to expand phenotypic diversity and expedite potential new horticulture cultivar releases through either seed or vegetative propagation.
Collapse
Affiliation(s)
- Jihua Xu
- Department of Plant Sciences, University of Saskatchewan Saskatoon, SK, Canada
| | - Karen K Tanino
- Department of Plant Sciences, University of Saskatchewan Saskatoon, SK, Canada
| | - Stephen J Robinson
- Department of Plant Sciences, University of SaskatchewanSaskatoon, SK, Canada; Agriculture and Agri-Food Canada, Saskatoon Research CentreSaskatoon, SK, Canada
| |
Collapse
|
32
|
Alonso C, Pérez R, Bazaga P, Medrano M, Herrera CM. MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild-growing species. Mol Ecol Resour 2015; 16:80-90. [PMID: 25944158 DOI: 10.1111/1755-0998.12426] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 12/28/2022]
Abstract
Methylation of DNA cytosines affects whether transposons are silenced and genes are expressed, and is a major epigenetic mechanism whereby plants respond to environmental change. Analyses of methylation-sensitive amplification polymorphism (MS-AFLP or MSAP) have been often used to assess methyl-cytosine changes in response to stress treatments and, more recently, in ecological studies of wild plant populations. MSAP technique does not require a sequenced reference genome and provides many anonymous loci randomly distributed over the genome for which the methylation status can be ascertained. Scoring of MSAP data, however, is not straightforward, and efforts are still required to standardize this step to make use of the potential to distinguish between methylation at different nucleotide contexts. Furthermore, it is not known how accurately MSAP infers genome-wide cytosine methylation levels in plants. Here, we analyse the relationship between MSAP results and the percentage of global cytosine methylation in genomic DNA obtained by HPLC analysis. A screening of literature revealed that methylation of cytosines at cleavage sites assayed by MSAP was greater than genome-wide estimates obtained by HPLC, and percentages of methylation at different nucleotide contexts varied within and across species. Concurrent HPLC and MSAP analyses of DNA from 200 individuals of the perennial herb Helleborus foetidus confirmed that methyl-cytosine was more frequent in CCGG contexts than in the genome as a whole. In this species, global methylation was unrelated to methylation at the inner CG site. We suggest that global HPLC and context-specific MSAP methylation estimates provide complementary information whose combination can improve our current understanding of methylation-based epigenetic processes in nonmodel plants.
Collapse
Affiliation(s)
- Conchita Alonso
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, CSIC-US, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Carlos M Herrera
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
| |
Collapse
|
33
|
Witzel K, Neugart S, Ruppel S, Schreiner M, Wiesner M, Baldermann S. Recent progress in the use of 'omics technologies in brassicaceous vegetables. FRONTIERS IN PLANT SCIENCE 2015; 6:244. [PMID: 25926843 PMCID: PMC4396356 DOI: 10.3389/fpls.2015.00244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/26/2015] [Indexed: 05/21/2023]
Abstract
Continuing advances in 'omics methodologies and instrumentation is enhancing the understanding of how plants cope with the dynamic nature of their growing environment. 'Omics platforms have been only recently extended to cover horticultural crop species. Many of the most widely cultivated vegetable crops belong to the genus Brassica: these include plants grown for their root (turnip, rutabaga/swede), their swollen stem base (kohlrabi), their leaves (cabbage, kale, pak choi) and their inflorescence (cauliflower, broccoli). Characterization at the genome, transcript, protein and metabolite levels has illustrated the complexity of the cellular response to a whole series of environmental stresses, including nutrient deficiency, pathogen attack, heavy metal toxicity, cold acclimation, and excessive and sub-optimal irradiation. This review covers recent applications of 'omics technologies to the brassicaceous vegetables, and discusses future scenarios in achieving improvements in crop end-use quality.
Collapse
Affiliation(s)
- Katja Witzel
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Susanne Neugart
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Silke Ruppel
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Monika Schreiner
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Melanie Wiesner
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Susanne Baldermann
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
- Institute of Nutritional Science, University of PotsdamNuthetal, Germany
| |
Collapse
|
34
|
Kalischuk ML, Johnson D, Kawchuk LM. Priming with a double-stranded DNA virus alters Brassica rapa seed architecture and facilitates a defense response. Gene 2015; 557:130-7. [DOI: 10.1016/j.gene.2014.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 12/06/2014] [Accepted: 12/09/2014] [Indexed: 01/11/2023]
|
35
|
Rodríguez López CM, Wilkinson MJ. Epi-fingerprinting and epi-interventions for improved crop production and food quality. FRONTIERS IN PLANT SCIENCE 2015; 6:397. [PMID: 26097484 PMCID: PMC4456566 DOI: 10.3389/fpls.2015.00397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/18/2015] [Indexed: 05/05/2023]
Abstract
Increasing crop production at a time of rapid climate change represents the greatest challenge facing contemporary agricultural research. Our understanding of the genetic control of yield derives from controlled field experiments designed to minimize environmental variance. In spite of these efforts there is substantial residual variability among plants attributable to Genotype × Environment interactions. Recent advances in the field of epigenetics have revealed a plethora of gene control mechanisms that could account for much of this unassigned variation. These systems act as a regulatory interface between the perception of the environment and associated alterations in gene expression. Direct intervention of epigenetic control systems hold the enticing promise of creating new sources of variability that could enhance crop performance. Equally, understanding the relationship between various epigenetic states and responses of the crop to specific aspects of the growing environment (epigenetic fingerprinting) could allow for a more tailored approach to plant agronomy. In this review, we explore the many ways in which epigenetic interventions and epigenetic fingerprinting can be deployed for the improvement of crop production and quality.
Collapse
Affiliation(s)
- Carlos M. Rodríguez López
- *Correspondence: Carlos M. Rodríguez López, Plant Research Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, Adelaide, SA 5064, Australia
| | | |
Collapse
|
36
|
Bilichak A, Ilnytskyy Y, Wóycicki R, Kepeshchuk N, Fogen D, Kovalchuk I. The elucidation of stress memory inheritance in Brassica rapa plants. FRONTIERS IN PLANT SCIENCE 2015; 6:5. [PMID: 25653665 PMCID: PMC4300914 DOI: 10.3389/fpls.2015.00005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/05/2015] [Indexed: 05/05/2023]
Abstract
Plants are able to maintain the memory of stress exposure throughout their ontogenesis and faithfully propagate it into the next generation. Recent evidence argues for the epigenetic nature of this phenomenon. Small RNAs (smRNAs) are one of the vital epigenetic factors because they can both affect gene expression at the place of their generation and maintain non-cell-autonomous gene regulation. Here, we have made an attempt to decipher the contribution of smRNAs to the heat-shock-induced transgenerational inheritance in Brassica rapa plants using sequencing technology. To do this, we have generated comprehensive profiles of a transcriptome and a small RNAome (smRNAome) from somatic and reproductive tissues of stressed plants and their untreated progeny. We have demonstrated that the highest tissue-specific alterations in the transcriptome and smRNAome profile are detected in tissues that were not directly exposed to stress, namely, in the endosperm and pollen. Importantly, we have revealed that the progeny of stressed plants exhibit the highest fluctuations at the smRNAome level but not at the transcriptome level. Additionally, we have uncovered the existence of heat-inducible and transgenerationally transmitted tRNA-derived small RNA fragments in plants. Finally, we suggest that miR168 and braAGO1 are involved in the stress-induced transgenerational inheritance in plants.
Collapse
Affiliation(s)
- Andriy Bilichak
- Lethbridge Research Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
| | - Rafal Wóycicki
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
| | - Nina Kepeshchuk
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
| | - Dawson Fogen
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
- *Correspondence: Igor Kovalchuk, Department of Biological Sciences, University of Lethbridge, University Drive 4401, Lethbridge, AB, T1K 3M4, Canada e-mail:
| |
Collapse
|
37
|
Medrano M, Herrera CM, Bazaga P. Epigenetic variation predicts regional and local intraspecific functional diversity in a perennial herb. Mol Ecol 2014; 23:4926-38. [DOI: 10.1111/mec.12911] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/19/2014] [Accepted: 09/04/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Mónica Medrano
- Estación Biológica de Doñana; Consejo Superior de Investigaciones Científicas (CSIC); Avenida Américo Vespucio s/n Isla de La Cartuja Sevilla 41092 Spain
| | - Carlos M. Herrera
- Estación Biológica de Doñana; Consejo Superior de Investigaciones Científicas (CSIC); Avenida Américo Vespucio s/n Isla de La Cartuja Sevilla 41092 Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana; Consejo Superior de Investigaciones Científicas (CSIC); Avenida Américo Vespucio s/n Isla de La Cartuja Sevilla 41092 Spain
| |
Collapse
|
38
|
Bloomfield JA, Rose TJ, King GJ. Sustainable harvest: managing plasticity for resilient crops. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:517-33. [PMID: 24891039 PMCID: PMC4207195 DOI: 10.1111/pbi.12198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/14/2014] [Indexed: 05/18/2023]
Abstract
Maintaining crop production to feed a growing world population is a major challenge for this period of rapid global climate change. No consistent conceptual or experimental framework for crop plants integrates information at the levels of genome regulation, metabolism, physiology and response to growing environment. An important role for plasticity in plants is assisting in homeostasis in response to variable environmental conditions. Here, we outline how plant plasticity is facilitated by epigenetic processes that modulate chromatin through dynamic changes in DNA methylation, histone variants, small RNAs and transposable elements. We present examples of plant plasticity in the context of epigenetic regulation of developmental phases and transitions and map these onto the key stages of crop establishment, growth, floral initiation, pollination, seed set and maturation of harvestable product. In particular, we consider how feedback loops of environmental signals and plant nutrition affect plant ontogeny. Recent advances in understanding epigenetic processes enable us to take a fresh look at the crosstalk between regulatory systems that confer plasticity in the context of crop development. We propose that these insights into genotype × environment (G × E) interaction should underpin development of new crop management strategies, both in terms of information-led agronomy and in recognizing the role of epigenetic variation in crop breeding.
Collapse
Affiliation(s)
- Justin A Bloomfield
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Terry J Rose
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| |
Collapse
|
39
|
Mirouze M, Vitte C. Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2801-12. [PMID: 24744427 DOI: 10.1093/jxb/eru120] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In the past decade, plant biologists and breeders have developed a growing interest in the field of epigenetics, which is defined as the study of heritable changes in gene expression that cannot be explained by changes in the DNA sequence. Epigenetic marks can be responsive to the environment, and evolve faster than genetic changes. Therefore, epigenetic diversity may represent an unexplored resource of natural variation that could be used in plant breeding programmes. On the other hand, crop genomes are largely populated with transposable elements (TEs) that are efficiently targeted by epigenetic marks, and part of the epigenetic diversity observed might be explained by TE polymorphisms. Characterizing the degree to which TEs influence epigenetic variation in crops is therefore a major goal to better use epigenetic variation. To date, epigenetic analyses have been mainly focused on the model plant Arabidopsis thaliana, and have provided clues on epigenome features, components that silence pathways, and effects of silencing impairment. But to what extent can Arabidopsis be used as a model for the epigenomics of crops? In this review, we discuss the similarities and differences between the epigenomes of Arabidopsis and crops. We explore the relationship between TEs and epigenomes, focusing on TE silencing control and escape, and the impact of TE mobility on epigenomic variation. Finally, we provide insights into challenges to tackle, and future directions to take in the route towards using epigenetic diversity in plant breeding programmes.
Collapse
Affiliation(s)
- Marie Mirouze
- Institut de Recherche pour le Développement, UMR232 DIADE Diversité Adaptation et Développement des Plantes, Université Montpellier 2, 911 avenue Agropolis F-34394 Montpellier, France
| | - Clémentine Vitte
- CNRS, UMR de Génétique Végétale, Chemin de Moulon, F-91190 Gif sur Yvette, France
| |
Collapse
|
40
|
Osabe K, Clement JD, Bedon F, Pettolino FA, Ziolkowski L, Llewellyn DJ, Finnegan EJ, Wilson IW. Genetic and DNA methylation changes in cotton (Gossypium) genotypes and tissues. PLoS One 2014; 9:e86049. [PMID: 24465864 PMCID: PMC3896429 DOI: 10.1371/journal.pone.0086049] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 12/05/2013] [Indexed: 12/19/2022] Open
Abstract
In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP) assays including a methylation insensitive enzyme (BsiSI), and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC). DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation) in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.
Collapse
|
41
|
Hou PQ, Lee YI, Hsu KT, Lin YT, Wu WZ, Lin JY, Nam TN, Fu SF. Functional characterization of Nicotiana benthamiana chromomethylase 3 in developmental programs by virus-induced gene silencing. PHYSIOLOGIA PLANTARUM 2014; 150:119-32. [PMID: 23683172 DOI: 10.1111/ppl.12071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 05/02/2013] [Accepted: 05/03/2013] [Indexed: 05/11/2023]
Abstract
DNA methylation is essential for normal developmental processes and genome stability. DNA methyltransferases are key enzymes catalyzing DNA methylation. Chromomethylase (CMT) genes are specific to the plant kingdom and encode chromodomain-containing methyltransferases. However, the function of CMT genes in plants remains elusive. In this study, we isolated and characterized a CMT gene from Nicotiana benthamiana, designated NbCMT3. Alignment of the NbCMT3 amino acid sequence with other plant CMT3s showed conservation of bromo-adjacent-homology and methyltransferase catalytic domains. We investigated the expression patterns of NbCMT3 and its function in developmental programs. NbCMT3 was expressed predominately in proliferating tissues such as apical shoots and young leaves. NbCMT3 protein showed a nuclear location, which could be related to its putative cellular functions. Knocking down NbCMT3 expression by virus-induced gene silencing revealed its vital role(s) in leaf morphogenesis. The formation of palisade cells was defective in NbCMT3-silenced plants as compared with controls. NbCMT3 has a role in developmental programs.
Collapse
Affiliation(s)
- Pin-Quan Hou
- Department of Biology, National Chunghua University of Education, No.1, Jin-De Road, 500, Changhua, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|