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Su Y, Liu L, Deng Q, Lü Z, Wang Z, He Z, Wang T. Epigenetic architecture of Pseudotaxus chienii: Revealing the synergistic effects of climate and soil variables. Ecol Evol 2023; 13:e10511. [PMID: 37701023 PMCID: PMC10493196 DOI: 10.1002/ece3.10511] [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: 12/06/2022] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023] Open
Abstract
Whether conifers can withstand environmental changes especially temperature fluctuations has been controversial. Epigenetic analysis may provide new perspectives for solving the issue. Pseudotaxus chienii is an endangered gymnosperm species endemic to China. In this study, we have examined the genetic and epigenetic variations in its natural populations aiming to disentangle the synergistic effects of climate and soil on its population (epi)genetic differentiation by using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP) techniques. We identified 23 AFLP and 26, 7, and 5 MSAP outliers in P. chienii. Twenty-one of the putative adaptive AFLP loci were found associated with climate and/or soil variables including precipitation, temperature, K, Fe, Zn, and Cu, whereas 21, 7, and 4 MSAP outliers were significantly related to precipitation of wettest month (Bio13), precipitation driest of month (Bio14), percent tree cover (PTC), and soil Fe, Mn, and Cu compositions. Total precipitation and precipitation in the driest seasons were the most influential factors for genetic and epigenetic variation, respectively. In addition, a high full-methylation level and a strong correlation between genetic and epigenetic variation were detected in P. chienii. Climate is found of greater importance than soil in shaping adaptive (epi)genetic differentiation, and the synergistic effects of climate and climate-soil variables were also observed. The identified climate and soil variables should be considered when applying ex situ conservation.
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Affiliation(s)
- Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Li Liu
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Qi Deng
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- School of MedicineGuangxi University of Science and TechnologyLiuzhouChina
| | - Zhuyan Lü
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ziqing He
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ting Wang
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Thapliyal G, Bhandari MS, Vemanna RS, Pandey S, Meena RK, Barthwal S. Engineering traits through CRISPR/cas genome editing in woody species to improve forest diversity and yield. Crit Rev Biotechnol 2023; 43:884-903. [PMID: 35968912 DOI: 10.1080/07388551.2022.2092714] [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: 04/16/2021] [Revised: 04/27/2022] [Accepted: 05/14/2022] [Indexed: 11/03/2022]
Abstract
Dangers confronting forest ecosystems are many and the strength of these biological systems is deteriorating, thus substantially affecting tree physiology, phenology, and growth. The establishment of genetically engineered trees into degraded woodlands, which would be adaptive to changing climate, could help in subsiding ecological threats and bring new prospects. This should not be resisted due to the apprehension of transgene dispersal in forests. Consequently, it is important to have a deep insight into the genetic structure and phenotypic limits of the reproductive capability of tree stands/population(s) to endure tolerance and survival. Importantly, for a better understanding of genes and their functional mechanisms, gene editing (GeEd) technology is an excellent molecular tool to unravel adaptation progressions. Therefore, GeEd could be harnessed for resolving the allelic interactions for the creation of gene diversity, and transgene dispersal may be alleviated among the population or species in different bioclimatic zones around the globe. This review highlights the potential of the CRISPR/Cas tools in genomic, transcriptomic, and epigenomic-based assorted and programmable alterations of genes in trees that might be able to fix the trait-specific gene function. Also, we have discussed the application of diverse forms of GeEd to genetically improve several traits, such as wood density, phytochemical constituents, biotic and abiotic stress tolerance, and photosynthetic efficiency in trees. We believe that the technology encourages fundamental research in the forestry sector besides addressing key aspects, which might fasten tree breeding and germplasm improvement programs worldwide.
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Affiliation(s)
- Garima Thapliyal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
| | - Ramu S Vemanna
- Regional Center for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Forest Protection Division, Forest Research Institute, Dehradun, India
| | - Rajendra K Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
| | - Santan Barthwal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
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Férriz M, Martin-Benito D, Fernández-de-Simón MB, Conde M, García-Cervigón AI, Aranda I, Gea-Izquierdo G. Functional phenotypic plasticity mediated by water stress and [CO2] explains differences in drought tolerance of two phylogenetically close conifers. TREE PHYSIOLOGY 2023; 43:909-924. [PMID: 36809504 PMCID: PMC10255776 DOI: 10.1093/treephys/tpad021] [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: 12/12/2022] [Accepted: 02/15/2023] [Indexed: 06/11/2023]
Abstract
Forests are threatened globally by increased recurrence and intensity of hot droughts. Functionally close coexisting species may exhibit differences in drought vulnerability large enough to cause niche differentiation and affect forest dynamics. The effect of rising atmospheric [CO2], which could partly alleviate the negative effects of drought, may also differ between species. We analysed functional plasticity in seedlings of two taxonomically close pine species (Pinus pinaster Ait., Pinus pinea L.) under different [CO2] and water stress levels. The multidimensional functional trait variability was more influenced by water stress (preferentially xylem traits) and [CO2] (mostly leaf traits) than by differences between species. However, we observed differences between species in the strategies followed to coordinate their hydraulic and structural traits under stress. Leaf 13C discrimination decreased with water stress and increased under elevated [CO2]. Under water stress both species increased their sapwood area to leaf area ratios, tracheid density and xylem cavitation, whereas they reduced tracheid lumen area and xylem conductivity. Pinus pinea was more anisohydric than P. pinaster. Pinus pinaster produced larger conduits under well-watered conditions than P. pinea. Pinus pinea was more tolerant to water stress and more resistant to xylem cavitation under low water potentials. The higher xylem plasticity in P. pinea, particularly in tracheid lumen area, expressed a higher capacity of acclimation to water stress than P. pinaster. In contrast, P. pinaster coped with water stress comparatively more by increasing plasticity of leaf hydraulic traits. Despite the small differences observed in the functional response to water stress and drought tolerance between species, these interspecific differences agreed with ongoing substitution of P. pinaster by P. pinea in forests where both species co-occur. Increased [CO2] had little effect on the species-specific relative performance. Thus, a competitive advantage under moderate water stress of P. pinea compared with P. pinaster is expected to continue in the future.
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Affiliation(s)
- M Férriz
- ICIFOR-INIA, CSIC. Ctra La Coruña km 7.5, 28040 Madrid, Spain
| | - D Martin-Benito
- ICIFOR-INIA, CSIC. Ctra La Coruña km 7.5, 28040 Madrid, Spain
| | | | - M Conde
- ICIFOR-INIA, CSIC. Ctra La Coruña km 7.5, 28040 Madrid, Spain
| | - A I García-Cervigón
- Department of Biology and Geology, Physics and Inorganic Chemistry Rey Juan Carlos University, c/Tulipán s/n, 28933 Móstoles, Spain
| | - I Aranda
- ICIFOR-INIA, CSIC. Ctra La Coruña km 7.5, 28040 Madrid, Spain
| | - G Gea-Izquierdo
- ICIFOR-INIA, CSIC. Ctra La Coruña km 7.5, 28040 Madrid, Spain
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Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. FRONTIERS IN PLANT SCIENCE 2023; 14:1181039. [PMID: 37389288 PMCID: PMC10306282 DOI: 10.3389/fpls.2023.1181039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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Affiliation(s)
- Dolores Rita Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Biology Department, Ġ.F.Abela Junior College, Msida, Malta
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Evangelia Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Miroslav Baranek
- Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Elena Carneros
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Aleksandra Radanovic
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jean-Paul Ebejer
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Francesco Guarino
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vera Inácio
- BioISI – BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Michal Lieberman-Lazarovich
- Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel
| | | | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d’Orléans, Orléans, France
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Pilar S. Testillano
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Dimitar Todorov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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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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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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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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8
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Kordyum E, Dubyna D. The role of epigenetic regulation in adaptive phenotypic plasticity of plants. UKRAINIAN BOTANICAL JOURNAL 2021. [DOI: 10.15407/ukrbotj78.05.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In recent decades, knowledge about the role of epigenetic regulation of gene expression in plant responses to external stimuli and in adaptation of plants to adverse environmental fluctuations have extended significantly. DNA methylation is considered as the main molecular mechanism that provides genomic information and contributes to the understanding of the molecular basis of phenotypic variations based on epigenetic modifications. Unfortunately, the vast majority of research in this area has been performed on the model species Arabidopsis thaliana. The development of the methylation-sensitive amplified polymorphism (MSAP) method has made it possible to implement the large-scale detection of DNA methylation alterations in wild non-model and agricultural plants with large and highly repetitive genomes in natural and manipulated habitats. The article presents current information on DNA methylation in species of natural communities and crops and its importance in plant development and adaptive phenotypic plasticity, along with brief reviews of current ideas about adaptive phenotypic plasticity and epigenetic regulation of gene expression. The great potential of further studies of the epigenetic role in phenotypic plasticity of a wide range of non-model species in natural populations and agrocenoses for understanding the molecular mechanisms of plant existence in the changing environment in onto- and phylogeny, directly related to the key tasks of forecasting the effects of global warming and crop selection, is emphasized. Specific taxa of the Ukrainian flora, which, in authors’ opinion, are promising and interesting for this type of research, are recommended.
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Kubiak-Szymendera M, Pryszcz LP, Białas W, Celińska E. Epigenetic Response of Yarrowia lipolytica to Stress: Tracking Methylation Level and Search for Methylation Patterns via Whole-Genome Sequencing. Microorganisms 2021; 9:microorganisms9091798. [PMID: 34576693 PMCID: PMC8471669 DOI: 10.3390/microorganisms9091798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is a common, but not universal, epigenetic modification that plays an important role in multiple cellular processes. While definitely settled for numerous plant, mammalian, and bacterial species, the genome methylation in different fungal species, including widely studied and industrially-relevant yeast species, Yarrowia lipolytica, is still a matter of debate. In this paper, we report a differential DNA methylation level in the genome of Y. lipolytica subjected to sequential subculturing and to heat stress conditions. To this end, we adopted repeated batch bioreactor cultivations of Y. lipolytica subjected to thermal stress in specific time intervals. To analyze the variation in DNA methylation between stressed and control cultures, we (a) quantified the global DNA methylation status using an immuno-assay, and (b) studied DNA methylation patterns through whole-genome sequencing. Primarily, we demonstrated that 5 mC modification can be detected using a commercial immuno-assay, and that the modifications are present in Y. lipolytica’s genome at ~0.5% 5 mC frequency. On the other hand, we did not observe any changes in the epigenetic response of Y. lipolytica to heat shock (HS) treatment. Interestingly, we identified a general phenomenon of decreased 5 mC level in Y. lipolytica’s genome in the stationary phase of growth, when compared to a late-exponential epigenome. While this study provides an insight into the subculturing stress response and adaptation to the stress at epigenetic level by Y. lipolytica, it also leaves an open question of inability to detect any genomic DNA methylation level (either in CpG context or context-less) through whole-genome sequencing. The results of ONT sequencing, suggesting that 5 mC modification is either rare or non-existent in Y. lipolytica genome, are contradicted with the results of the immunoassay.
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Affiliation(s)
- Monika Kubiak-Szymendera
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Leszek P. Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
- Correspondence:
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Badad O, Lakhssassi N, Zaid N, El Baze A, Zaid Y, Meksem J, Lightfoot DA, Tombuloglu H, Zaid EH, Unver T, Meksem K. Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil. PLANTS 2021; 10:plants10071405. [PMID: 34371608 PMCID: PMC8309279 DOI: 10.3390/plants10071405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/31/2022]
Abstract
Secondary metabolites are particularly important to humans due to their pharmaceutical properties. Moreover, secondary metabolites are key compounds in climate change adaptation in long-living trees. Recently, it has been described that the domestication of Olea subspecies had no major selection signature on coding variants and was mainly related to changes in gene expression. In addition, the phenotypic plasticity in Olea subspecies was linked to the activation of transposable elements in the genes neighboring. Here, we investigated the imprint of DNA methylation in the unassigned fraction of the phenotypic plasticity of the Olea subspecies, using methylated DNA immuno-precipitation sequencing (MeDIP-seq) for a high-resolution genome-wide DNA methylation profiling of leaves and fruits during fruit development in wild and cultivated olives from Turkey. Notably, the methylation profiling showed a differential DNA methylation in secondary metabolism responsible for the sensory quality of olive oil. Here, we highlight for the first time the imprint of DNA methylation in modulating the activity of the Linoleate 9S lipoxygenase in the biosynthesis of volatile aromatic compounds. Unprecedently, the current study reveals the methylation status of the olive genome during fruit ripening.
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Affiliation(s)
- Oussama Badad
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
| | - Nabil Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
| | - Younes Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
- Research Center, Abulcasis University of Health Sciences, Rabat 10000, Morocco
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA;
| | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia;
| | - El Houcine Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
| | - Turgay Unver
- Ficus Biotechnology, Ostim OSB Mah, 100. Yil Blv, No:55, Yenimahalle, Ankara 06000, Turkey
- Correspondence: (T.U.); (K.M.)
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
- Correspondence: (T.U.); (K.M.)
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11
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Trontin JF, Raschke J, Rupps A. Tree 'memory': new insights on temperature-induced priming effects during early embryogenesis. TREE PHYSIOLOGY 2021; 41:906-911. [PMID: 33216135 DOI: 10.1093/treephys/tpaa150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/02/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Jean-François Trontin
- Biotechnology and Advanced Forestry Department, FCBA Technological Institute, 71, Route d'Arcachon, Pierroton, F-33610 Cestas, France
| | - Juliane Raschke
- Institute of Biology, Section Botany and Arboretum, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Andrea Rupps
- Institute of Biology, Section Botany and Arboretum, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
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12
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The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline. EPIGENOMES 2021; 5:epigenomes5020012. [PMID: 34968299 PMCID: PMC8594691 DOI: 10.3390/epigenomes5020012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022] Open
Abstract
Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use.
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13
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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14
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Varela A, Ibañez VN, Alonso R, Zavallo D, Asurmendi S, Gomez Talquenca S, Marfil CF, Berli FJ. Vineyard environments influence Malbec grapevine phenotypic traits and DNA methylation patterns in a clone-dependent way. PLANT CELL REPORTS 2021; 40:111-125. [PMID: 33068175 DOI: 10.1007/s00299-020-02617-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/30/2020] [Indexed: 05/14/2023]
Abstract
By studying three cv. Malbec clones cultivated in two vineyards with contrasting environmental conditions, we demonstrated that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent. Clonal selection and vegetative propagation determine low genetic variability in grapevine cultivars, although it is common to observe diverse phenotypes. Environmental signals may induce epigenetic changes altering gene expression and phenotype. The range of phenotypes that a genotype expresses in different environments is known as phenotypic plasticity. DNA methylation is the most studied epigenetic mechanism, but only few works evaluated this novel source of variability in grapevines. In the present study, we analyzed the effects on phenotypic traits and epigenome of three Vitis vinifera cv. Malbec clones cultivated in two contrasting vineyards of Mendoza, Argentina. Anonymous genome regions were analyzed using methylation-sensitive amplified polymorphism (MSAP) markers. Clone-dependent phenotypic and epigenetic variability between vineyards were found. The clone that presented the clearer MSAP differentiation between vineyards was selected and analyzed through reduced representation bisulfite sequencing. Twenty-nine differentially methylated regions between vineyards were identified and associated to genes and/or promoters. We discuss about a group of genes related to hormones homeostasis and sensing that could provide a hint of the epigenetic role in the determination of the different phenotypes observed between vineyards and conclude that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent.
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Affiliation(s)
- Anabella Varela
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Verónica N Ibañez
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Rodrigo Alonso
- Catena Institute of Wine (CIW), Bodega Catena Zapata, Cobos w/n, M5509, Agrelo, Mendoza, Argentina
| | - Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Losos Reseros y N. Repetto w/n, Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Losos Reseros y N. Repetto w/n, Hurlingham B1686IGC, Buenos Aires, Argentina
| | | | - Carlos F Marfil
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina.
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina.
| | - Federico J Berli
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina.
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina.
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15
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García-García I, Méndez-Cea B, Martín-Gálvez D, Seco JI, Gallego FJ, Linares JC. Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline. FRONTIERS IN PLANT SCIENCE 2021; 12:797958. [PMID: 35058957 PMCID: PMC8764141 DOI: 10.3389/fpls.2021.797958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/13/2021] [Indexed: 05/14/2023]
Abstract
Forest tree species are highly vulnerable to the effects of climate change. As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough. However, the current lack of knowledge on this field is remarkable, due to many challenges that researchers face when studying this issue. Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change drives tree species epigenetic modifications. In spite of this challenging framework, some insights on the relationships among climate change-induced stress and epigenomics are coming. Advances in DNA sequencing technologies and an increasing number of studies dealing with this topic must boost our knowledge on tree adaptive capacity to changing environmental conditions. Here, we discuss challenges and perspectives in the epigenetics of climate change-induced forests decline, aiming to provide a general overview of the state of the art.
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Affiliation(s)
- Isabel García-García
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Isabel García-García,
| | - Belén Méndez-Cea
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- Belén Méndez-Cea,
| | - David Martín-Gálvez
- Departamento de Biodiversidad, Ecología y Evolución, UD Zoología, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - José Ignacio Seco
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
| | - Francisco Javier Gallego
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Carlos Linares
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
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16
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Vizcaíno-Palomar N, Fady B, Alía R, Raffin A, Mutke S, Benito Garzón M. The legacy of climate variability over the last century on populations' phenotypic variation in tree height. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141454. [PMID: 32814202 DOI: 10.1016/j.scitotenv.2020.141454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/21/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
Phenotypic plasticity and local adaptation are the two main processes underlying trait variability. Under rapid environmental change, phenotypic plasticity, if adaptive, could increase the odds for organisms to persist. However, little is known on how environmental variation has shaped plasticity across species ranges over time. Here, we assess whether the portion of phenotypic variation of tree populations linked to the environment is related to the inter-annual climate variability of the last century and how it varies among populations across species ranges and age. To this aim, we used 372,647 individual tree height measurements of three pine species found in low elevation forests in Europe: Pinus nigra Arnold, P. pinaster Aiton and P. pinea L. Measurements were taken in a network of 38 common gardens established in Europe and North Africa with 315 populations covering the distribution range of the species. We fitted linear mixed-effect models of tree height as a function of age, population, climate and competition effects. Models allowed us to estimate tree height response curves at the population level and indexes of populations' phenotypic variation, as a proxy of phenotypic plasticity, at 4, 8 and 16 years old, and relate these indexes to the inter-annual climate variability of the last century. We found that phenotypic variation in tree height was higher in young trees than in older ones. We also found that P. pinea showed the highest phenotypic variation in tree height compared with P. pinaster and P. nigra. Finally, phenotypic variation in tree height may be partly adaptive, and differently across species, as climate variability during the last century at the origin of the populations explained between 51 and 69% of the current phenotypic variation of P. nigra and P. pinea, almost twice of the levels of P. pinaster. MAIN CONCLUSIONS: Populations' phenotypic variation in tree height is largely explained by the climate variability that the populations experienced during the last century, which we attribute to the genetic diversity among populations.
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Affiliation(s)
| | - Bruno Fady
- INRAE, Unité de Recherches Ecologie des Forêts Méditerranéennes (URFM), Avignon, France.
| | - Ricardo Alía
- INIA, Forest Research Centre & iuFOR UVa-INIA, Ctra La Coruña km 7.5, 28040 Madrid, Spain.
| | - Annie Raffin
- INRAE, Unité Expérimentale Forêt Pierroton (UEFP), 33610 Cestas, France.
| | - Sven Mutke
- INIA, Forest Research Centre & iuFOR UVa-INIA, Ctra La Coruña km 7.5, 28040 Madrid, Spain.
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17
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Jaramillo-Correa JP, Bagnoli F, Grivet D, Fady B, Aravanopoulos FA, Vendramin GG, González-Martínez SC. Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse. Mol Ecol 2020; 29:4797-4811. [PMID: 33063352 DOI: 10.1111/mec.15684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022]
Abstract
Severe bottlenecks significantly diminish the amount of genetic diversity and the speed at which it accumulates (i.e., evolutionary rate). They further compromise the efficiency of natural selection to eliminate deleterious variants, which may reach fixation in the surviving populations. Consequently, expanding and adapting to new environments may pose a significant challenge when strong bottlenecks result in genetic pauperization. Herein, we surveyed the patterns of nucleotide diversity, molecular adaptation and genetic load across 177 gene-loci in a circum-Mediterranean conifer (Pinus pinea L.) that represents one of the most extreme cases of genetic pauperization in widespread outbreeding taxa. We found very little genetic variation in both hypervariable nuclear microsatellites (SSRs) and gene-loci, which translated into genetic diversity estimates one order of magnitude lower than those previously reported for pines. Such values were consistent with a strong population decline that began some ~1 Ma. Comparisons with the related and parapatric maritime pine (Pinus pinaster Ait.) revealed reduced rates of adaptive evolution (α and ωa ) and a significant accumulation of genetic load. It is unlikely that these are the result from differences in mutation rate or linkage disequilibrium between the two species; instead they are the presumable outcome of contrasting demographic histories affecting both the speed at which these taxa accumulate genetic diversity, and the global efficacy of selection. Future studies, and programs for conservation and management, should thus start testing for the effects of genetic load on fitness, and integrating such effects into predictive models.
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Affiliation(s)
- Juan P Jaramillo-Correa
- Department of Evolutionary Ecology, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Francesca Bagnoli
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain
| | - Bruno Fady
- INRAE, Unité de Recherche Écologie des Forêts Méditerranéennes (URFM), Avignon, France
| | - Filippos A Aravanopoulos
- Laboratory of Forest Genetics and Tree Breeding, Department of Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Giovanni G Vendramin
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
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18
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Kalinka A, Achrem M. The distribution pattern of 5-methylcytosine in rye (Secale L.) chromosomes. PLoS One 2020; 15:e0240869. [PMID: 33057421 PMCID: PMC7561101 DOI: 10.1371/journal.pone.0240869] [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: 06/23/2020] [Accepted: 10/04/2020] [Indexed: 12/02/2022] Open
Abstract
The rye (Secale L.) genome is large, and it contains many classes of repetitive sequences. Secale species differ in terms of genome size, heterochromatin content, and global methylation level; however, the organization of individual types of sequences in chromosomes is relatively similar. The content of the abundant subtelomeric heterochromatin fraction in rye do not correlate with the global level of cytosine methylation, hence immunofluorescence detection of 5-methylcytosine (5-mC) distribution in metaphase chromosomes was performed. The distribution patterns of 5-methylcytosine in the chromosomes of Secale species/subspecies were generally similar. 5-methylcytosine signals were dispersed along the entire length of the chromosome arms of all chromosomes, indicating high levels of methylation, especially at retrotransposon sequences. 5-mC signals were absent in the centromeric and telomeric regions, as well as in subtelomeric blocks of constitutive heterochromatin, in each of the taxa studied. Pericentromeric domains were methylated, however, there was a certain level of polymorphism in these areas, as was the case with the nucleolus organizer region. Sequence methylation within the region of the heterochromatin intercalary bands were also demonstrated to be heterogenous. Unexpectedly, there was a lack of methylation in rye subtelomeres, indicating that heterochromatin is a very diverse fraction of chromatin, and its epigenetic regulation or potential influence on adjacent regions can be more complex than has conventionally been thought. Like telomeres and centromeres, subtelomeric heterochromatin can has a specific role, and the absence of 5-mC is required to maintain the heterochromatin state.
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Affiliation(s)
- Anna Kalinka
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
- * E-mail:
| | - Magdalena Achrem
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
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19
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The assessment of epigenetic diversity, differentiation, and structure in the 'Fuji' mutation line implicates roles of epigenetic modification in the occurrence of different mutant groups as well as spontaneous mutants. PLoS One 2020; 15:e0235073. [PMID: 32584862 PMCID: PMC7316255 DOI: 10.1371/journal.pone.0235073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/07/2020] [Indexed: 01/01/2023] Open
Abstract
The ‘Fuji’ line includes many varieties with a similar genetic background and consistent inducement factors with epigenetic occurrence, thus it may be considered an ideal candidate for epigenetic research. In this study, 91 bud mutations of ‘Fuji’ apple were used as the test materials. Using the genetic variation within ‘Fuji’ as the control, the characteristics of epigenetic variation at different levels in both varieties and mutant groups were examined. The results showed that: (1) the global genomic DNA methylation level of the 91 bud mutants of ‘Fuji’ ranged from 29.120%-45.084%, with an average of 35.910%. Internal cytosine methylation was the main DNA methylation pattern. Regarding the variation of methylation patterns of ‘Fuji’ mutants, the vast majority of loci maintained the original methylation pattern existed in ‘Fuji’. CHG methylation variation was the main type of variation; (2) the variation in methylation patterns between the mutant groups was greater than that of methylation levels. Among these patterns, the variation in CHG methylation patterns (including CHG hypermethylation and CHG demethylation) was expected to be dominant. The observed variation in methylation levels was more important in the Color mutant group; however, the variation in methylation patterns was more obvious in both the early maturation and Spur mutant groups. Moreover, the range of variation in the Early-maturation group was much wider than that in the Spur mutant group; (3) epigenetic diversity and genetic diversity were both low between the mutant groups. In the ‘Fuji’ mutant groups, there was few correlation between genetic and epigenetic variation, and epigenetic differentiation resulted in more loci with moderate or greater differentiation; (4) the purifying selection seemed to play a major role in the differentiation of different groups of ‘Fuji’ mutants (65.618%), but epigenetic diversity selection still occurred at nearly 35% of loci. Sixteen epigenetic outlier loci were detected.
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20
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Abstract
Climate change leads to global drought-induced stress and increased plant mortality. Tree species living in rapidly changing climate conditions are exposed to danger and must adapt to new climate conditions to survive. Trees respond to changes in the environment in numerous ways. Physiological modulation at the seed stage, germination strategy and further development are influenced by many different factors. We review forest abiotic threats (such as drought and heat), including biochemical responses of plants to stress, and biotic threats (pathogens and insects) related to global warming. We then discus the varied adaptations of tree species to changing climate conditions such as seed resistance to environmental stress, improved by an increase in temperature, affinity to specific fungal symbionts, a wide range of tolerance to abiotic environmental conditions in the offspring of populations occurring in continental climate, and germination strategies closely linked to the ecological niche of the species. The existing studies do not clearly indicate whether tree adaptations are shaped by epigenetics or phenology and do not define the role of phenotypic plasticity in tree development. We have created a juxtaposition of literature that is useful in identifying the factors that play key roles in these processes. We compare scientific evidence that species distribution and survival are possible due to phenotypic plasticity and thermal memory with studies that testify that trees’ phenology depends on phylogenesis, but this issue is still open. It is possible that studies in the near future will bring us closer to understanding the mechanisms through which trees adapt to stressful conditions, especially in the context of epigenetic memory in long-lived organisms, and allow us to minimize the harmful effects of climatic events by predicting tree species’ responses or by developing solutions such as assisted migration to mitigate the consequences of these phenomena.
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21
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Smith‐Ferguson J, Beekman M. Can't see the colony for the bees: behavioural perspectives of biological individuality. Biol Rev Camb Philos Soc 2019; 94:1935-1946. [DOI: 10.1111/brv.12542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Jules Smith‐Ferguson
- School of Life and Environmental SciencesUniversity of Sydney Sydney New South Wales 2006 Australia
| | - Madeleine Beekman
- School of Life and Environmental SciencesUniversity of Sydney Sydney New South Wales 2006 Australia
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22
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Climate Change Impacts on Pinus pinea L. Silvicultural System for Cone Production and Ways to Contour Those Impacts: A Review Complemented with Data from Permanent Plots. FORESTS 2019. [DOI: 10.3390/f10020169] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Umbrella pine (Pinus pinea L.) cones take three years to develop. With the increasing frequency of extreme droughts, water available for trees has decreased—climate change is a reality. The cone’s survival in its first two years of development and the average cone weight during its last year of maturation is affected, thus, reducing kernel quantity and quality. Climate change has resulted in forest fires becoming an inescapable issue in forest management planning. A literature review was carried out, focusing, on one hand, the predicted climatic changes for the Mediterranean basin and, on the other hand, the umbrella pine silvicultural mechanisms at tree, stand, and landscape levels that may help to face these constraints. Finally, the Portuguese case was focused, describing the management practices that are being adopted to achieve, even when the period of cone formation and growth include dry years, one to six tons of cones per hectare per year in adult stands.
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23
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Thiebaut F, Hemerly AS, Ferreira PCG. A Role for Epigenetic Regulation in the Adaptation and Stress Responses of Non-model Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:246. [PMID: 30881369 PMCID: PMC6405435 DOI: 10.3389/fpls.2019.00246] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 02/13/2019] [Indexed: 05/21/2023]
Abstract
In recent years enormous progress has been made in understanding the role of epigenetic regulation response to environmental stimuli, especially in response to stresses. Molecular mechanisms involved in chromatin dynamics and silencing have been explained, leading to an appreciation of how new phenotypes can be generated quickly in response to environmental modifications. In some cases, it has also been shown that epigenetic modifications can be stably transmitted to the next generations. Despite this, the vast majority of studies have been carried out with model plants, particularly with Arabidopsis, and very little is known on how native plants in their natural habitat react to changes in their environment. Climate change has been affecting, sometimes drastically, the conditions of numerous ecosystems around the world, forcing populations of native species to adapt quickly. Although part of the adaptation can be explained by the preexisting genetic variation in the populations, recent studies have shown that new stable phenotypes can be generated through epigenetic modifications in few generations, contributing to the stability and survival of the plants in their natural habitat. Here, we review the recent data that suggest that epigenetic variation can help natural populations to cope to with change in their environments.
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24
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Mutke S, Vendramin GG, Fady B, Bagnoli F, González-Martínez SC. Molecular and Quantitative Genetics of Stone Pine (Pinus pinea). SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2019. [DOI: 10.1007/978-3-319-96454-6_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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25
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Yoshida T, Tarutani Y, Kakutani T, Kawabe A. DNA Methylation Diversification at the Integrated Organellar DNA-Like Sequence. Genes (Basel) 2018; 9:genes9120602. [PMID: 30513997 PMCID: PMC6316516 DOI: 10.3390/genes9120602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/20/2018] [Accepted: 11/28/2018] [Indexed: 12/29/2022] Open
Abstract
Plants have a lot of diversity in epigenetic modifications such as DNA methylation in their natural populations or cultivars. Although many studies observing the epigenetic diversity within and among species have been reported, the mechanisms how these variations are generated are still not clear. In addition to the de novo spontaneous epi-mutation, the intra- and inter-specific crossing can also cause a change of epigenetic modifications in their progenies. Here we report an example of diversification of DNA methylation by crossing and succeeding selfing. We traced the inheritance pattern of epigenetic modification during the crossing experiment between two natural strains Columbia (Col), and Landsberg electa (Ler) in model plant Arabidopsis thaliana to observe the inheritance of DNA methylation in two organellar DNA-like sequence regions in the nuclear genome. Because organellar DNA integration to the nuclear genome is common in flowering plants and these sequences are occasionally methylated, such DNA could be the novel source of plant genome evolution. The amplicon sequencing, using bisulfite-converted DNA and a next-generation auto-sequencer, was able to efficiently track the heredity of DNA methylation in F1 and F2 populations. One region showed hypomethylation in the F1 population and succeeding elevation of DNA methylation with large variance in the F2 population. The methylation level of Col and Ler alleles in F2 heterozygotes showed a significant positive correlation, implying the trans-chromosomal effect on DNA methylation. The results may suggest the possible mechanism causing the natural epigenetic diversity within plant populations.
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Affiliation(s)
- Takanori Yoshida
- Faculty of Life Science, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.
| | - Yoshiaki Tarutani
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan.
| | - Tetsuji Kakutani
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan.
- Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Akira Kawabe
- Faculty of Life Science, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.
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26
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Parasyri A, Papazi A, Stamatis N, Zerveas S, Avramidou EV, Doulis AG, Pirintsos S, Kotzabasis K. Lichen as Micro-Ecosystem: Extremophilic Behavior with Astrobiotechnological Applications. ASTROBIOLOGY 2018; 18:1528-1542. [PMID: 30383392 DOI: 10.1089/ast.2017.1789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This work demonstrates the tolerance of lichen Pleurosticta acetabulum under extreme conditions similar to those encountered in extraterrestrial environments. Specifically, the impact of three extreme Mars-like conditions-complete dehydration, extremely low temperature (-196°C/77K), and oxygen depletion-on lichens was investigated. The symbiosis of mycobiont and photobiont partners creates a micro-ecosystem that ensures viability of both symbiotic partners under prolonged desiccation and extremely low temperatures without any cultivation care. Changes in the molecular structure and function of the photosynthetic apparatus, in the level of chlorophylls, polyamines, fatty acids, carbohydrates, ergosterol, efflux of K+, and DNA methylation ensure the ecological integrity of the system and offer resistance of lichens to above-mentioned extreme environmental conditions. For the first time, we also demonstrate that the unprecedented polyextremophilic characteristic of lichens could be linked to biotechnological applications, following exposure to these extreme conditions, such that their ability to produce a high yield of hydrogen was unchanged. All these support that lichens are (a) ideal model systems for a space mission to inhabit other planets, supporting also the aspect that the panspermia theory could be extended to incorporate in the traveling entities not only single organisms but micro-ecosystems like lichens, and (b) ideal model systems for astrobiotechnological applications (hydrogen production), such as in the development of bioregeneration systems for extraterrestrial environments.
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Affiliation(s)
- Athina Parasyri
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
| | - Aikaterini Papazi
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
| | | | - Sotirios Zerveas
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
| | | | | | - Stergios Pirintsos
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
- 3 Botanical Garden, University of Crete , Gallos Campus, Rethymnon, Greece
| | - Kiriakos Kotzabasis
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
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27
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Cossu RM, Casola C, Giacomello S, Vidalis A, Scofield DG, Zuccolo A. LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes. Genome Biol Evol 2018; 9:3449-3462. [PMID: 29228262 PMCID: PMC5751070 DOI: 10.1093/gbe/evx260] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 12/29/2022] Open
Abstract
The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read-based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.
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Affiliation(s)
- Rosa Maria Cossu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University
| | - Stefania Giacomello
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Amaryllis Vidalis
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Section of Population Epigenetics and Epigenomics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Douglas G Scofield
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Sweden
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Istituto di Genomica Applicata, Udine, Italy
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28
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Heer K, Ullrich KK, Hiss M, Liepelt S, Schulze Brüning R, Zhou J, Opgenoorth L, Rensing SA. Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing. Ecol Evol 2018; 8:9672-9682. [PMID: 30386566 PMCID: PMC6202725 DOI: 10.1002/ece3.4374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 12/24/2022] Open
Abstract
Epigenetic mechanisms represent a possible mechanism for achieving a rapid response of long-lived trees to changing environmental conditions. However, our knowledge on plant epigenetics is largely limited to a few model species. With increasing availability of genomic resources for many tree species, it is now possible to adopt approaches from model species that permit to obtain single-base pair resolution data on methylation at a reasonable cost. Here, we used targeted bisulfite sequencing (TBS) to study methylation patterns in the conifer species Norway spruce (Picea abies). To circumvent the challenge of disentangling epigenetic and genetic differences, we focused on four clone pairs, where clone members were growing in different climatic conditions for 24 years. We targeted >26.000 genes using TBS and determined the performance and reproducibility of this approach. We characterized gene body methylation and compared methylation patterns between environments. We found highly comparable capture efficiency and coverage across libraries. Methylation levels were relatively constant across gene bodies, with 21.3 ± 0.3%, 11.0 ± 0.4% and 1.3 ± 0.2% in the CG, CHG, and CHH context, respectively. The variance in methylation profiles did not reveal consistent changes between environments, yet we could identify 334 differentially methylated positions (DMPs) between environments. This supports that changes in methylation patterns are a possible pathway for a plant to respond to environmental change. After this successful application of TBS in Norway spruce, we are confident that this approach can contribute to broaden our knowledge of methylation patterns in natural tree populations.
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Affiliation(s)
- Katrin Heer
- Conservation BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
- Department of EcologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | - Kristian K. Ullrich
- Plant Cell BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
- Department of Evolutionary GeneticsMax Planck Institute for Evolutionary BiologyPloenGermany
| | - Manuel Hiss
- Plant Cell BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | - Sascha Liepelt
- Conservation BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | | | - Jiabin Zhou
- College of Life SciencesShaanxi Normal UniversityXi'anChina
- State Key Laboratory of Grassland Agro‐EcosystemsSchool of Life SciencesLanzhou UniversityLanzhouChina
| | - Lars Opgenoorth
- Department of EcologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | - Stefan A. Rensing
- Plant Cell BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
- BIOSS Biological Signaling StudiesUniversity of FreiburgFreiburgGermany
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29
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Hao DC, Xiao PG. Deep in shadows: Epigenetic and epigenomic regulations of medicinal plants. CHINESE HERBAL MEDICINES 2018. [DOI: 10.1016/j.chmed.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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30
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Liu L, Pei C, Liu S, Guo X, Du N, Guo W. Genetic and epigenetic changes during the invasion of a cosmopolitan species ( Phragmites australis). Ecol Evol 2018; 8:6615-6624. [PMID: 30038761 PMCID: PMC6053550 DOI: 10.1002/ece3.4144] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 02/24/2018] [Accepted: 03/29/2018] [Indexed: 12/25/2022] Open
Abstract
While many introduced invasive species can increase genetic diversity through multiple introductions and/or hybridization to colonize successfully in new environments, others with low genetic diversity have to persist by alternative mechanisms such as epigenetic variation. Given that Phragmites australis is a cosmopolitan reed growing in a wide range of habitats and its invasion history, especially in North America, has been relatively well studied, it provides an ideal system for studying the role and relationship of genetic and epigenetic variation in biological invasions. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive (MS) AFLP methods to evaluate genetic and epigenetic diversity and structure in groups of the common reed across its range in the world. Evidence from analysis of molecular variance (AMOVA) based on AFLP and MS-AFLP data supported the previous conclusion that the invasive introduced populations of P. australis in North America were from European and Mediterranean regions. In the Gulf Coast region, the introduced group harbored a high level of genetic variation relative to originating group from its native location, and it showed epigenetic diversity equal to that of the native group, if not higher, while the introduced group held lower genetic diversity than the native. In the Great Lakes region, the native group displayed very low genetic and epigenetic variation, and the introduced one showed slightly lower genetic and epigenetic diversity than the original one. Unexpectedly, AMOVA and principal component analysis did not demonstrate any epigenetic convergence between native and introduced groups before genetic convergence. Our results suggested that intertwined changes in genetic and epigenetic variation were involved in the invasion success in North America. Although our study did not provide strong evidence proving the importance of epigenetic variation prior to genetic, it implied the similar role of stable epigenetic diversity to genetic diversity in the adaptation of P. australis to local environment.
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Affiliation(s)
- Lele Liu
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Cuiping Pei
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Shuna Liu
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Xiao Guo
- College of Landscape Architecture and ForestryQingdao Agricultural UniversityQingdaoChina
| | - Ning Du
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Weihua Guo
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
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31
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Groot MP, Wagemaker N, Ouborg NJ, Verhoeven KJF, Vergeer P. Epigenetic population differentiation in field- and common garden-grown Scabiosa columbaria plants. Ecol Evol 2018; 8:3505-3517. [PMID: 29607042 PMCID: PMC5869358 DOI: 10.1002/ece3.3931] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/27/2017] [Accepted: 12/06/2017] [Indexed: 12/12/2022] Open
Abstract
Populations often differ in phenotype and these differences can be caused by adaptation by natural selection, random neutral processes, and environmental responses. The most straightforward way to divide mechanisms that influence phenotypic variation is heritable variation and environmental‐induced variation (e.g., plasticity). While genetic variation is responsible for most heritable phenotypic variation, part of this is also caused by nongenetic inheritance. Epigenetic processes may be one of the underlying mechanisms of plasticity and nongenetic inheritance and can therefore possibly contribute to heritable differences through drift and selection. Epigenetic variation may be influenced directly by the environment, and part of this variation can be transmitted to next generations. Field screenings combined with common garden experiments will add valuable insights into epigenetic differentiation, epigenetic memory and can help to reveal part of the relative importance of epigenetics in explaining trait variation. We explored both genetic and epigenetic diversity, structure and differentiation in the field and a common garden for five British and five French Scabiosa columbaria populations. Genetic and epigenetic variation was subsequently correlated with trait variation. Populations showed significant epigenetic differentiation between populations and countries in the field, but also when grown in a common garden. By comparing the epigenetic variation between field and common garden‐grown plants, we showed that a considerable part of the epigenetic memory differed from the field‐grown plants and was presumably environmentally induced. The memory component can consist of heritable variation in methylation that is not sensitive to environments and possibly genetically based, or environmentally induced variation that is heritable, or a combination of both. Additionally, random epimutations might be responsible for some differences as well. By comparing epigenetic variation in both the field and common environment, our study provides useful insight into the environmental and genetic components of epigenetic variation.
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Affiliation(s)
- Maartje P Groot
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands
| | - Niels Wagemaker
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands
| | - N Joop Ouborg
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO-KNAW) Wageningen The Netherlands
| | - Philippine Vergeer
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands.,Plant Ecology and Nature Conservation Group Wageningen The Netherlands
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32
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Monja-Mio KM, Quiroz-Moreno A, Herrera-Herrera G, Montero-Muñoz JL, Sánchez-Teyer F, Robert ML. Analysis of Two Clonal Lines (Embryogenic and Non-Embryogenic) of <i>Agave fourcroydes</i> Using AFLP and MSAP. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/ajps.2018.94059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Shi W, Chen X, Gao L, Xu CY, Ou X, Bossdorf O, Yang J, Geng Y. Transient Stability of Epigenetic Population Differentiation in a Clonal Invader. FRONTIERS IN PLANT SCIENCE 2018; 9:1851. [PMID: 30881370 PMCID: PMC6405520 DOI: 10.3389/fpls.2018.01851] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/29/2018] [Indexed: 05/02/2023]
Abstract
Epigenetic variation may play an important role in how plants cope with novel environments. While significant epigenetic differences among plants from contrasting habitats have often been observed in the field, the stability of these differences remains little understood. Here, we combined field monitoring with a multi-generation common garden approach to study the dynamics of DNA methylation variation in invasive Chinese populations of the clonal alligator weed (Alternanthera philoxeroides). Using AFLP and MSAP markers, we found little variation in DNA sequence but substantial epigenetic population differentiation. In the field, these differences remained stable across multiple years, whereas in a common environment they were maintained at first but then progressively eroded. However, some epigenetic differentiation remained even after 10 asexual generations. Our data indicate that epigenetic variation in alligator weed most likely results from a combination of environmental induction and spontaneous epimutation, and that much of it is neither rapidly reversible (phenotypic plasticity) nor long-term stable, but instead displays an intermediate level of stability. Such transient epigenetic stability could be a beneficial mechanism in novel and heterogeneous environments, particularly in a genetically impoverished invader.
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Affiliation(s)
- Wen Shi
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Institute of Ecology and Geobotany, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Plant Disease & Pest, School of Life Sciences, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Crop Disease & Pest, School of Life Sciences, Yunnan University, Kunming, China
| | - Xiaojie Chen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Institute of Ecology and Geobotany, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Lexuan Gao
- Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education, Fudan University, Shanghai, China
| | - Cheng-Yuan Xu
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, QLD, Australia
| | - Xiaokun Ou
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Institute of Ecology and Geobotany, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Ji Yang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education, Fudan University, Shanghai, China
- *Correspondence: Ji Yang, Yupeng Geng, ;
| | - Yupeng Geng
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Institute of Ecology and Geobotany, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- *Correspondence: Ji Yang, Yupeng Geng, ;
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34
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Vanden Broeck A, Cox K, Brys R, Castiglione S, Cicatelli A, Guarino F, Heinze B, Steenackers M, Vander Mijnsbrugge K. Variability in DNA Methylation and Generational Plasticity in the Lombardy Poplar, a Single Genotype Worldwide Distributed Since the Eighteenth Century. FRONTIERS IN PLANT SCIENCE 2018; 9:1635. [PMID: 30483290 PMCID: PMC6242946 DOI: 10.3389/fpls.2018.01635] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 10/22/2018] [Indexed: 05/21/2023]
Abstract
In the absence of genetic diversity, plants rely on the capacity of phenotypic plasticity to cope with shifts in environmental conditions. Understanding the mechanisms behind phenotypic plasticity and how local phenotypic adjustments are transferred to clonal offspring, will provide insight into its ecological and evolutionary significance. Epigenetic changes have recently been proposed to play a crucial role in rapid environmental adaptation. While the contribution of epigenetic changes to phenotypic plasticity has been extensively studied in sexual reproducing model organisms, little work has been done on vegetative generations of asexual reproducing plant species. We studied the variability of DNA methylation and bud set phenology of the Lombardy poplar (Populus nigra cv. Italica Duroi), a cultivated tree representing a single genotype worldwide distributed since the eighteenth century. Bud set observations and CpG methyl polymorphisms were studied on vegetative offspring resulting from cuttings grown for one season in a common glasshouse environment. The cuttings were collected from 60 adult Lombardy poplars growing in different environments. The physiological condition of the cuttings was determined by measuring weight and nutrient condition. Methylation sensitive amplified polymorphisms were used to obtain global patterns of DNA methylation. Using logistic regression models, we investigated correlations among epigenotype, bud phenology, and the climate at the home site of the donor trees, while accounting for physiological effects. We found significant epigenetic variation as well as significant variation in bud phenology, in the absence of genetic variation. Remarkably, phenology of bud set observed at the end of the growing season in the common environment was significantly correlated with climate variables at the home site of the mother trees, specifically the average temperature of January and monthly potential evapotranspiration. Although we could not directly detect significant effects of epigenetic variation on phenology, our results suggest that, in the Lombardy poplar, epigenetic marks contribute to the variation of phenotypic response that can be transferred onto asexually reproduced offspring resulting in locally adapted ecotypes. This contributes to the growing evidence that epigenetic-based transgenerational inheritance might be relevant for adaptation and evolution in contrasting or rapidly changing environments.
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Affiliation(s)
- An Vanden Broeck
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
- *Correspondence: An Vanden Broeck
| | - Karen Cox
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Rein Brys
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Stefano Castiglione
- Department of Chemistry and Biology A. Zambelli, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology A. Zambelli, University of Salerno, Fisciano, Italy
| | - Francesco Guarino
- Department of Chemistry and Biology A. Zambelli, University of Salerno, Fisciano, Italy
| | - Berthold Heinze
- Department of Forest Genetics, Austrian Federal Research Centre for Forests (BFW), Vienna, Austria
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35
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Balao F, Paun O, Alonso C. Uncovering the contribution of epigenetics to plant phenotypic variation in Mediterranean ecosystems. PLANT BIOLOGY (STUTTGART, GERMANY) 2018. [PMID: 28637098 DOI: 10.1111/plb.12594] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Epigenetic signals can affect plant phenotype and fitness and be stably inherited across multiple generations. Epigenetic regulation plays a key role in the mechanisms of plant response to the environment, without altering DNA sequence. As plants cannot adapt behaviourally or migrate instantly, such dynamic epigenetic responses may be particularly crucial for survival of plants within changing and challenging environments, such as the Mediterranean-Type Ecosystems (MTEs). These ecosystems suffer recurrent stressful events (warm and dry summers with associated fire regimes) that have selected for plants with similar phenotypic complex traits, resulting in similar vegetation growth forms. However, the potential role of epigenetics in plant adaptation to recurrent stressful environments such as the MTEs has generally been ignored. To understand the full spectrum of adaptive processes in such contexts, it is imperative to prompt study of the causes and consequences of epigenetic variation in natural populations. With this purpose, we review here current knowledge on epigenetic variation in natural populations and the genetic and epigenetic basis of some key traits for plants in the MTEs, namely those traits involved in adaptation to drought, fire and oligotrophic soils. We conclude there is still much to be learned about 'plant epigenetics in the wild' and, thus, we propose future research steps in the study of natural epigenetic variation of key traits in the MTEs at different scales.
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Affiliation(s)
- F Balao
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - C Alonso
- Estación Biológica de Doñana, CSIC, Sevilla, Spain
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36
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He S, Xu W, Li F, Wang Y, Liu A. Intraspecific DNA methylation polymorphism in the non-edible oilseed plant castor bean. PLANT DIVERSITY 2017; 39:300-307. [PMID: 30159523 PMCID: PMC6112301 DOI: 10.1016/j.pld.2017.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/25/2017] [Accepted: 05/27/2017] [Indexed: 05/05/2023]
Abstract
Investigation of the relationships of phenotypic and epigenetic variations might be a good way to dissect the genetic or molecular basis of phenotypic variation and plasticity in plants. Castor bean (Ricinus communis L.), an important non-edible oilseed crop, is a mono-species genus plant in the family Euphorbiaceae. Since it displays rich phenotypic variations with low genetic diversity, castor bean is a good model to investigate the molecular basis of phenotypic and epigenetic variations. Cytosine DNA methylation represents a major molecular mechanism of epigenetic occurrence. In this study, epigenetic diversity of sixty landrace accessions collected worldwide was investigated using the methylation-sensitive amplification polymorphism (MSAP) technique. Results showed that the epigenetic diversity (based on the polymorphism of DNA methylated loci) exhibited a medium variation (Ne = 1.395, He = 0.242, I = 0.366) at the population level though the variation was great, ranging from 3.80% to 34.31% among accessions. Both population structure analysis and the phylogenetic construction (using the neighbor-joining criteria) revealed that the two main clades were identified, but they did not display a distinct geographic structure. After inspecting the location of polymorphic methylated loci on genome we identified that the polymorphic methylated loci occur widely in nuclear and organelle genomes. This study provides new data to understand phenotypic and epigenetic variations in castor bean.
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Affiliation(s)
- Shan He
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fei Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yue Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Aizhong Liu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Zogli P, Libault M. Plant response to biotic stress: Is there a common epigenetic response during plant-pathogenic and symbiotic interactions? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:89-93. [PMID: 28818387 DOI: 10.1016/j.plantsci.2017.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 05/26/2023]
Abstract
Plants constantly interact with pathogenic and symbiotic microorganisms. Recent studies have revealed several regulatory mechanisms controlling these interactions. Among them, the plant defense system is activated not only in response to pathogenic, but also in response to symbiotic microbes. Interestingly, shortly after symbiotic microbial recognition, the plant defense system is suppressed to promote plant infection by symbionts. Research studies have demonstrated the influence of the plant epigenome in modulating both pathogenic and symbiotic plant-microbe interactions, thereby influencing plant survival, adaptation and evolution of the plant response to microbial infections. It is however unclear if plant pathogenic and symbiotic responses share similar epigenomic profiles or if epigenomic changes differentially regulate plant-microbe symbiosis and pathogenesis. In this mini-review, we provide an update of the current knowledge of epigenomic control on plant immune responses and symbiosis, with a special attention being paid to knowledge gap and potential strategies to fill-in the missing links.
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Affiliation(s)
- Prince Zogli
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Marc Libault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
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Guevara MÁ, de María N, Sáez-Laguna E, Vélez MD, Cervera MT, Cabezas JA. Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP). Methods Mol Biol 2017; 1456:99-112. [PMID: 27770361 DOI: 10.1007/978-1-4899-7708-3_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.
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Affiliation(s)
- María Ángeles Guevara
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - Nuria de María
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - Enrique Sáez-Laguna
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - María Dolores Vélez
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - María Teresa Cervera
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain.
| | - José Antonio Cabezas
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain.
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Baránek M, Čechová J, Kovacs T, Eichmeier A, Wang S, Raddová J, Nečas T, Ye X. Use of Combined MSAP and NGS Techniques to Identify Differentially Methylated Regions in Somaclones: A Case Study of Two Stable Somatic Wheat Mutants. PLoS One 2016; 11:e0165749. [PMID: 27792769 PMCID: PMC5085084 DOI: 10.1371/journal.pone.0165749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/16/2016] [Indexed: 12/22/2022] Open
Abstract
The appearance of somaclonal variability induced by in vitro cultivation is relatively frequent and can, in some cases, provide a valuable source of new genetic variation for crop improvement. The cause of this phenomenon remains unknown; however, there are a number of reports suggesting that epigenetics, including DNA methylations, are an important factor. In addition to the non-heritable DNA methylation changes caused by transient and reversible stress-responsive gene regulation, recent evidence supports the existence of mitotically and meiotically inherited changes. The induction of phenotypes via stable DNA methylation changes has occasionally great economical value; however, very little is known about the genetic or molecular basis of these phenotypes. We used a novel approach consisting of a standard MSAP analysis followed by deep amplicon sequencing to better understand this phenomenon. Our models included two wheat genotypes, and their somaclones induced using in vitro cultivation with a changed heritable phenotype (shortened stem height and silenced high molecular weight glutenin). Using this novel procedure, we obtained information on the dissimilarity of DNA methylation landscapes between the standard cultivar and its respective somaclones, and we extracted the sequences and genome regions that were differentially methylated between subjects. Transposable elements were identified as the most likely factor for producing changes in somaclone properties. In summary, the novel approach of combining MSAP and NGS is relatively easy and widely applicable, which is a rather unique feature compared with the currently available techniques in the epigenetics field.
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Affiliation(s)
- Miroslav Baránek
- Mendeleum–Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
- * E-mail:
| | - Jana Čechová
- Mendeleum–Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | | | - Aleš Eichmeier
- Mendeleum–Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Shunli Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jana Raddová
- Mendeleum–Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Tomáš Nečas
- Department of Fruit Growing, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Whipple AV, Holeski LM. Epigenetic Inheritance across the Landscape. Front Genet 2016; 7:189. [PMID: 27826318 PMCID: PMC5079072 DOI: 10.3389/fgene.2016.00189] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/10/2016] [Indexed: 12/12/2022] Open
Abstract
The study of epigenomic variation at the landscape-level in plants may add important insight to studies of adaptive variation. A major goal of landscape genomic studies is to identify genomic regions contributing to adaptive variation across the landscape. Heritable variation in epigenetic marks, resulting in transgenerational plasticity, can influence fitness-related traits. Epigenetic marks are influenced by the genome, the environment, and their interaction, and can be inherited independently of the genome. Thus, epigenomic variation likely influences the heritability of many adaptive traits, but the extent of this influence remains largely unknown. Here, we summarize the relevance of epigenetic inheritance to ecological and evolutionary processes, and review the literature on landscape-level patterns of epigenetic variation. Landscape-level patterns of epigenomic variation in plants generally show greater levels of isolation by distance and isolation by environment then is found for the genome, but the causes of these patterns are not yet clear. Linkage between the environment and epigenomic variation has been clearly shown within a single generation, but demonstrating transgenerational inheritance requires more complex breeding and/or experimental designs. Transgenerational epigenetic variation may alter the interpretation of landscape genomic studies that rely upon phenotypic analyses, but should have less influence on landscape genomic approaches that rely upon outlier analyses or genome–environment associations. We suggest that multi-generation common garden experiments conducted across multiple environments will allow researchers to understand which parts of the epigenome are inherited, as well as to parse out the relative contribution of heritable epigenetic variation to the phenotype.
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Affiliation(s)
- Amy V Whipple
- Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University Flagstaff, AZ, USA
| | - Liza M Holeski
- Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University Flagstaff, AZ, USA
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Comparison of molecular genetic utilities of TD, AFLP, and MSAP among the accessions of japonica, indica, and Tongil of Oryza sativa L. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0426-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Vannier N, Mony C, Bittebière AK, Vandenkoornhuyse P. Epigenetic Mechanisms and Microbiota as a Toolbox for Plant Phenotypic Adjustment to Environment. FRONTIERS IN PLANT SCIENCE 2015; 6:1159. [PMID: 26779191 PMCID: PMC4688372 DOI: 10.3389/fpls.2015.01159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/07/2015] [Indexed: 05/24/2023]
Abstract
The classic understanding of organisms focuses on genes as the main source of species evolution and diversification. The recent concept of genetic accommodation questions this gene centric view by emphasizing the importance of phenotypic plasticity on evolutionary trajectories. Recent discoveries on epigenetics and symbiotic microbiota demonstrated their deep impact on plant survival, adaptation and evolution thus suggesting a novel comprehension of the plant phenotype. In addition, interplays between these two phenomena controlling plant plasticity can be suggested. Because epigenetic and plant-associated (micro-) organisms are both key sources of phenotypic variation allowing environmental adjustments, we argue that they must be considered in terms of evolution. This 'non-conventional' set of mediators of phenotypic variation can be seen as a toolbox for plant adaptation to environment over short, medium and long time-scales.
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Affiliation(s)
- Nathan Vannier
- Université de Rennes 1, CNRS, UMR6553 EcoBioRennes, France
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR6553 EcoBioRennes, France
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Baránek M, Čechová J, Raddová J, Holleinová V, Ondrušíková E, Pidra M. Dynamics and Reversibility of the DNA Methylation Landscape of Grapevine Plants (Vitis vinifera) Stressed by In Vitro Cultivation and Thermotherapy. PLoS One 2015; 10:e0126638. [PMID: 25973746 PMCID: PMC4431845 DOI: 10.1371/journal.pone.0126638] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/05/2015] [Indexed: 11/19/2022] Open
Abstract
There is relatively little information concerning long-term alterations in DNA methylation following exposure of plants to environmental stress. As little is known about the ratio of non-heritable changes in DNA methylation and mitotically-inherited methylation changes, dynamics and reversibility of the DNA methylation states were investigated in grapevine plants (Vitis vinifera) stressed by in vitro cultivation. It was observed that significant part of induced epigenetic changes could be repeatedly established by exposure to particular planting and stress conditions. However, once stress conditions were discontinued, many methylation changes gradually reverted and plants returned to epigenetic states similar to those of maternal plants. In fact, in the period of one to three years after in vitro cultivation it was difficult to distinguish the epigenetic states of somaclones and maternal plants. Forty percent of the observed epigenetic changes disappeared within a year subsequent to termination of stress conditions ending and these probably reflect changes caused by transient and reversible stress-responsive acclimation mechanisms. However, sixty percent of DNA methylation diversity remained after 1 year and probably represents mitotically-inherited epimutations. Sequencing of regions remaining variable between maternal and regenerant plants revealed that 29.3% of sequences corresponded to non-coding regions of grapevine genome. Eight sequences (19.5%) corresponded to previously identified genes and the remaining ones (51.2%) were annotated as "hypothetical proteins" based on their similarity to genes described in other species, including genes likely to undergo methylation changes following exposure to stress (V. vinifera gypsy-type retrotransposon Gret1, auxin-responsive transcription factor 6-like, SAM-dependent carboxyl methyltransferase).
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Affiliation(s)
- Miroslav Baránek
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Jana Čechová
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Jana Raddová
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Věra Holleinová
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Eva Ondrušíková
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Miroslav Pidra
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
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Determination of epigenetic inheritance, genetic inheritance, and estimation of genome DNA methylation in a full-sib family of Cupressus sempervirens L. Gene 2015; 562:180-7. [DOI: 10.1016/j.gene.2015.02.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 02/01/2023]
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46
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Pan J, Wang B, Pei ZY, Zhao W, Gao J, Mao JF, Wang XR. Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers. Mol Ecol Resour 2014; 15:711-22. [DOI: 10.1111/1755-0998.12342] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Jin Pan
- Department of Ecology and Environmental Science; Umeå University; Umeå SE-90187 Sweden
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Baosheng Wang
- Department of Ecology and Environmental Science; Umeå University; Umeå SE-90187 Sweden
| | - Zhi-Yong Pei
- Beijing Computing Centre; Beijing 100094 China
- Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 China
| | - Wei Zhao
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Jie Gao
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Menglun Yunnan 666303 China
| | - Jian-Feng Mao
- National Engineering Laboratory for Forest Tree Breeding; Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education; Beijing Forestry University; Beijing 100083 China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science; Umeå University; Umeå SE-90187 Sweden
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