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      Epigenetic regulation of adaptive responses of forest tree species to the environment

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          Abstract

          Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular “memory”. Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change.

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          Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

          Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences. Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels. However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.
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            Plant phenotypic plasticity in a changing climate.

            Climate change is altering the availability of resources and the conditions that are crucial to plant performance. One way plants will respond to these changes is through environmentally induced shifts in phenotype (phenotypic plasticity). Understanding plastic responses is crucial for predicting and managing the effects of climate change on native species as well as crop plants. Here, we provide a toolbox with definitions of key theoretical elements and a synthesis of the current understanding of the molecular and genetic mechanisms underlying plasticity relevant to climate change. By bringing ecological, evolutionary, physiological and molecular perspectives together, we hope to provide clear directives for future research and stimulate cross-disciplinary dialogue on the relevance of phenotypic plasticity under climate change. Copyright © 2010 Elsevier Ltd. All rights reserved.
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              A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening.

              A major component in the regulatory network controlling fruit ripening is likely to be the gene at the tomato Colorless non-ripening (Cnr) locus. The Cnr mutation results in colorless fruits with a substantial loss of cell-to-cell adhesion. The nature of the mutation and the identity of the Cnr gene were previously unknown. Using positional cloning and virus-induced gene silencing, here we demonstrate that an SBP-box (SQUAMOSA promoter binding protein-like) gene resides at the Cnr locus. Furthermore, the Cnr phenotype results from a spontaneous epigenetic change in the SBP-box promoter. The discovery that Cnr is an epimutation was unexpected, as very few spontaneous epimutations have been described in plants. This study demonstrates that an SBP-box gene is critical for normal ripening and highlights the likely importance of epialleles in plant development and the generation of natural variation.
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                Author and article information

                Journal
                Ecol Evol
                Ecol Evol
                ece3
                Ecology and Evolution
                Blackwell Publishing Ltd
                2045-7758
                2045-7758
                February 2013
                17 January 2013
                : 3
                : 2
                : 399-415
                Affiliations
                [1 ]Centre for the Analysis of Genome Evolution and Function, Department of Cell & Systems Biology, University of Toronto Toronto, ON, M5S 3B2, Canada
                [2 ]Department of Forest Ecosystems and Society, Oregon State University Corvallis, OR, 97331-5752, USA
                [3 ]UFR-Faculté des Sciences, UPRES EA 1207 ‘Laboratoire de Biologie des Ligneux et des Grandes Cultures’ (LBLGC), INRA, USC1328 ‘Arbres et Réponses aux Contraintes Hydrique et Environnementales’ (ARCHE), University of Orléans Rue de Chartres, BP 6759, F-45067, Orléans, France
                [4 ]Department of Biology and Environment, Norwegian Forest and Landscape Institute PO Box 115, N-1431, Aas, Norway
                [5 ]Epigenetic Regulations and Seed Development, Institut de Recherche pour le Développement, UMR232 ERL5300 CNRS-IRD 911 Av. Agropolis, 34394, Montpellier, France
                [6 ]School of Life Sciences, University of Warwick Wellesbourne, Warkwick, CV35 9EF, United Kingdom
                [7 ]Platform for Integrated Clone Management (PICME), Health & Environment Department, AIT Austrian Institute of Technology GmbH Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
                [8 ]Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA–HUCA), University of Oviedo Spain
                [9 ]Dpt. of Forest Ecology and Genetics, Forest Genomics and Ecophysiology group, Forest Research Centre (CIFOR). INIA Crta. La Coruña km 7,5, 28040, Madrid, Spain
                [10 ]Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPM Madrid, Spain
                [11 ]Department of Life Sciences, University of Alcalá Ctra. Madrid-Barcelona Km. 33,600, 28871, Alcalá de Henares, Madrid, Spain
                [12 ]Department of Plant and Environmental Sciences, Norwegian University of Life Sciences PO Box 5003, N-1432, Ås, Norway
                [13 ]Department of Biological Sciences, University of Toronto Scarborough, University of Toronto 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
                [14 ]Department Plant Growth & Development, Institute of Agriculture and Fisheries Research Caritasstraat 21, 9090, Melle, Belgium
                Author notes
                María-Teresa Cervera, INIA. Forest Research Centre. Department of Forest Ecology and Genetics, Forest Genomics and Ecophysiology group. Crta. La Coruña km 7,5. 28040 Madrid, Spain. Tel: +(34) 91 347 6798; Fax: +(34) 91 347 6767; E-mail: cervera@ 123456inia.es

                Funding information The preparation of this review was supported by funding from the FP7 UE projects FoResTTraC (2440096-FP7) and ProCoGen (289841-FP7).

                Article
                10.1002/ece3.461
                3586649
                23467802
                09e08e95-cd18-4b18-8dae-dae7d8412d29
                © 2013 Published by Blackwell Publishing Ltd.

                Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.

                History
                : 07 August 2012
                : 19 November 2012
                : 27 November 2012
                Categories
                Original Research

                Evolutionary Biology
                adaptive response,environmental stress,epigenetic memory of stressful conditions,epigenetics,forest trees,phenotypic plasticity

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