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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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Garosi C, Ferrante R, Vettori C, Paffetti D. Meta-Analysis as a Tool to Identify Candidate Genes Involved in the Fagus sylvatica L. Abiotic Stress Response. Forests 2022; 13:159. [DOI: 10.3390/f13020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, we aimed to evaluate whether candidate genes for abiotic stresses in Fagus sylvatica L. are also candidate genes for herbaceous plants, with the purpose of better defining the abiotic stress response model of F. sylvatica. Therefore, a meta-analysis was performed on published papers related to abiotic stress. Firstly, we carried out a systematic review regarding the activity of 24 candidate genes selected for F. sylvatica under abiotic stress reported in 503 articles. After choosing the inclusion criteria, 73 articles out of 503, regarding 12 candidate genes, were included in this analysis. We performed an exploratory meta-analysis based on the random-effect model and the combined effect-size approach (Cohen’s d). The results obtained through Forest and Funnel plots indicate that the candidate genes for F. sylvatica are considered to be candidate genes in other herbaceous species. These results allowed us to set up models of plants’ response to abiotic stresses implementing the stress models in forest species. The results of this study will serve to bridge knowledge gaps regarding the pathways of response to abiotic stresses in trees based on the meta-analysis. The study approach used could be extended to observe larger gene databases and different species.
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Abstract
Turnover of species composition through time is frequently observed in ecosystems. It is often interpreted as indicating the impact of changes in the environment. Continuous turnover due solely to ecological dynamics-species interactions and dispersal-is also known to be theoretically possible; however the prevalence of such autonomous turnover in natural communities remains unclear. Here we demonstrate that observed patterns of compositional turnover and other important macroecological phenomena can be reproduced in large spatially explicit model ecosystems, without external forcing such as environmental change or the invasion of new species into the model. We find that autonomous turnover is triggered by the onset of ecological structural instability-the mechanism that also limits local biodiversity. These results imply that the potential role of autonomous turnover as a widespread and important natural process is underappreciated, challenging assumptions implicit in many observation and management tools. Quantifying the baseline level of compositional change would greatly improve ecological status assessments.
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Affiliation(s)
- Jacob D O'Sullivan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
| | - J Christopher D Terry
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Axel G Rossberg
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Snell Taylor S, Coyle JR, White EP, Hurlbert AH. A simulation study of the use of temporal occupancy for identifying core and transient species. PLoS One 2020; 15:e0241198. [PMID: 33095844 PMCID: PMC7584212 DOI: 10.1371/journal.pone.0241198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/09/2020] [Indexed: 11/18/2022] Open
Abstract
Transient species, which do not maintain self-sustaining populations in a system where they are observed, are ubiquitous in nature and their presence often impacts the interpretation of ecological patterns and processes. Identifying transient species from temporal occupancy, the proportion of time a species is observed at a given site over a time series, is subject to classification errors as a result of imperfect detection and source-sink dynamics. We use a simulation-based approach to assess how often errors in detection or classification occur in order to validate the use of temporal occupancy as a metric for inferring whether a species is a core or transient member of a community. We found that low detection increases error in the classification of core species, while high habitat heterogeneity and high detection increase error in classification of transient species. These findings confirm that temporal occupancy is a valid metric for inferring whether a species can maintain a self-sustaining population, but imperfect detection, low abundance, and highly heterogeneous landscapes may yield high misclassification rates.
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Affiliation(s)
- Sara Snell Taylor
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Jessica R. Coyle
- Department of Biology, Saint Mary’s College of California, Moraga, California, United States of America
| | - Ethan P. White
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America
- Informatics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Allen H. Hurlbert
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Curriculum for the Environment and Ecology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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