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      An Epigenetic Alphabet of Crop Adaptation to Climate Change

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          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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          Regulation of chromatin by histone modifications.

          Chromatin is not an inert structure, but rather an instructive DNA scaffold that can respond to external cues to regulate the many uses of DNA. A principle component of chromatin that plays a key role in this regulation is the modification of histones. There is an ever-growing list of these modifications and the complexity of their action is only just beginning to be understood. However, it is clear that histone modifications play fundamental roles in most biological processes that are involved in the manipulation and expression of DNA. Here, we describe the known histone modifications, define where they are found genomically and discuss some of their functional consequences, concentrating mostly on transcription where the majority of characterisation has taken place.
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            Establishing, maintaining and modifying DNA methylation patterns in plants and animals.

            Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation. Recent findings in plants and animals have greatly increased our understanding of the pathways used to accurately target, maintain and modify patterns of DNA methylation and have revealed unanticipated mechanistic similarities between these organisms. Key roles have emerged for small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these processes. Drawing on insights from both plants and animals should deepen our understanding of the regulation and biological significance of DNA methylation.
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              Dynamics and function of DNA methylation in plants

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                Author and article information

                Contributors
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                Journal
                Front Genet
                Front Genet
                Front. Genet.
                Frontiers in Genetics
                Frontiers Media S.A.
                1664-8021
                16 February 2022
                2022
                : 13
                : 818727
                Affiliations
                [1] 1 Dipartimento di Chimica e Biologia “A. Zambelli” , Università Degli Studi di Salerno , Salerno, Italy
                [2] 2 Centre of Molecular Medicine and Biobanking , University of Malta , Msida, Malta
                [3] 3 Bayramic Vocational College , Canakkale Onsekiz Mart University , Canakkale, Turkey
                [4] 4 Department of Molecular and Cell Biology of Plants , Goethe University , Frankfurt, Germany
                [5] 5 CIRAD , UMR AGAP , Montpellier, France
                [6] 6 AGAP , Univ Montpellier , CIRAD, INRA, Institut Agro , Montpellier, France
                [7] 7 Centre for Agricultural Genomics and Biotechnology , FAFSEM, University of Debrecen , Debrecen, Hungary
                [8] 8 Institute of Molecular , Cell and Systems Biology , College of Medical , Veterinary and Life Sciences , University of Glasgow , Glasgow, United Kingdom
                [9] 9 Plant Sciences Institute , Agricultural Research Organization Volcani Center , Rishon LeZion, Israel
                [10] 10 Department of Chemistry and Biotechnology , Tallinn University of Technology , Tallinn, Estonia
                [11] 11 Institute of Biosciences and Bioresources (IBBR) , National Research Council (CNR) , Sesto Fiorentino, Italy
                [12] 12 Department of Agriculture , Food, Environment and Forestry (DAGRI) , University of Florence , Florence, Italy
                [13] 13 Department of Clinical Medicine , Public Health, Life and Environmental Sciences , University of L’Aquila , Aquila, Italy
                [14] 14 Institute of Molecular Biology and Biotechnology , Foundation for Research and Technology—Hellas , Heraklion, Greece
                [15] 15 Department of Biology , University of Crete , Heraklion, Greece
                [16] 16 Department of Plant Biology , Uppsala BioCenter , Swedish University of Agricultural Sciences and Linnean Center for Plant Biology , Uppsala, Sweden
                [17] 17 Chair of Photogrammetry and Remote Sensing , Faculty of Geodesy , University of Zagreb , Zagreb, Croatia
                [18] 18 Department of Horticultural Science , Bu-Ali Sina University , Hamedan, Iran
                [19] 19 Department of Biology , University of Florence , Sesto Fiorentino, Italy
                [20] 20 UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne , Université de Bordeaux , INRAE, Bordeaux Science Agro , Bordeaux, France
                [21] 21 Institute of Field and Vegetable Crops , National Institute of Republic of Serbia , Novi Sad, Serbia
                Author notes

                Edited by: Vijay Gahlaut, Institute of Himalayan Bioresource Technology (CSIR), India

                Reviewed by: Rajeev Ranjan, Purdue University, United States

                Namisha Sharma, National Institute of Plant Genome Research (NIPGR), India

                *Correspondence: Dragana Miladinović, draganavas@ 123456yahoo.com ; Federico Martinelli, federico.martinelli@ 123456unifi.it

                This article was submitted to Plant Genomics, a section of the journal Frontiers in Genetics

                Article
                818727
                10.3389/fgene.2022.818727
                8888914
                186751ba-33c6-4b21-94ce-590284014310
                Copyright © 2022 Guarino, Cicatelli, Castiglione, Agius, Orhun, Fragkostefanakis, Leclercq, Dobránszki, Kaiserli, Lieberman-Lazarovich, Sõmera, Sarmiento, Vettori, Paffetti, Poma, Moschou, Gašparović, Yousefi, Vergata, Berger, Gallusci, Miladinović and Martinelli.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 19 November 2021
                : 28 January 2022
                Categories
                Genetics
                Review

                Genetics
                abiotic stresses,adaptation,climate change,epigenetics,environmental stresses,epigenetic code
                Genetics
                abiotic stresses, adaptation, climate change, epigenetics, environmental stresses, epigenetic code

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