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1. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus

Author

Conseil Régional du Centre-Val de Loire, Department of Energy (US), Kohler, Annegret [0000-0002-9575-9567], Sow, Mamadou Dia [0000-0002-2815-4939], Delaunay, Alain [0000-0002-2519-5380], Fauchery, Laure [0000-0002-2571-0274], Barry, Kerrie W. [0000-0002-8999-6785], Keymanesh, Keykhosrow [0000-0001-6019-9443], Singan, Vasanth [0000-0002-9983-5707], Grigoriev, Igor [0000-0002-3136-8903], Fichot, Régis [0000-0001-5527-4103], Conde, Daniel [0000-0001-8362-4190], Perales, Mariano [0000-0002-7351-8439], Tost, Jörg [0000-0002-2683-0817], Martin, Francis M. [0000-0002-4737-3715], Allona, Isabel [0000-0002-7012-2850], Strauss, Steven H. [0000-0001-9670-3082], Veneault-Fourrey, Claire [0000-0001-9778-2659], Maury, Stéphane 0000-0003-0481-0847], Vigneaud, Julien, Kohler, Annegret, Sow, Mamadou Dia, Delaunay, Alain, Fauchery, Laure, Guinet, Frederic, Daviaud, Christian, Barry, Kerrie W., Keymanesh, Keykhosrow, Johnson, Jenifer, Singan, Vasanth, Grigoriev, Igor, Fichot, Régis, Conde, Daniel, Perales, Mariano, Tost, Jörg, Martin, Francis M., Allona, Isabel, Strauss, Steven H., Veneault-Fourrey, Claire, Maury, Stéphane, Conseil Régional du Centre-Val de Loire, Department of Energy (US), Kohler, Annegret [0000-0002-9575-9567], Sow, Mamadou Dia [0000-0002-2815-4939], Delaunay, Alain [0000-0002-2519-5380], Fauchery, Laure [0000-0002-2571-0274], Barry, Kerrie W. [0000-0002-8999-6785], Keymanesh, Keykhosrow [0000-0001-6019-9443], Singan, Vasanth [0000-0002-9983-5707], Grigoriev, Igor [0000-0002-3136-8903], Fichot, Régis [0000-0001-5527-4103], Conde, Daniel [0000-0001-8362-4190], Perales, Mariano [0000-0002-7351-8439], Tost, Jörg [0000-0002-2683-0817], Martin, Francis M. [0000-0002-4737-3715], Allona, Isabel [0000-0002-7012-2850], Strauss, Steven H. [0000-0001-9670-3082], Veneault-Fourrey, Claire [0000-0001-9778-2659], Maury, Stéphane 0000-0003-0481-0847], Vigneaud, Julien, Kohler, Annegret, Sow, Mamadou Dia, Delaunay, Alain, Fauchery, Laure, Guinet, Frederic, Daviaud, Christian, Barry, Kerrie W., Keymanesh, Keykhosrow, Johnson, Jenifer, Singan, Vasanth, Grigoriev, Igor, Fichot, Régis, Conde, Daniel, Perales, Mariano, Tost, Jörg, Martin, Francis M., Allona, Isabel, Strauss, Steven H., Veneault-Fourrey, Claire, and Maury, Stéphane

Abstract

Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.

Published
2023

2. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Author

European Cooperation in Science and Technology, Agius, Dolores Rita [0000-0003-1819-2883], Kapazoglou, Aliki [0000-0002-7584-5994], Avramidou, Evangelia V. [0000-0002-5932-1189], Baránek, Miroslav [0000-0002-1583-3588], Carneros, Elena [0000-0003-2066-6320], Caro, Elena [0000-0002-1034-1621], Castiglione, Stefano [0000-0002-0632-4677], Cicatelli, Angela [0000-0001-6996-3495], Radanovic, Aleksandra [0000-0002-7467-9728], Ebejer, Jean Paul [0000-0003-0888-2637], Gackowski, Daniel [0000-0002-7259-1511], Guarino, Francesco [0000-0001-8536-4257], Gulyás, Andrea [0000-0001-6978-1341], Hidvégi, Norbert [0000-0003-3665-2724], Hoenicka, Hans [0000-0001-7226-3772], Inácio, Vera [0000-0002-5652-2540], Johannes, Frank [0000-0002-7962-2907], Karalija, Erna [0000-0001-7262-0645], Lieberman-Lazarovich, Michal [0000-0002-1776-8257], Martinelli, Federico [0000-0002-8502-767X], Maury, Stéphane [0000-0003-0481-0847], Mladenov, Velimir [0000-0002-2182-6579], Morais-Cecílio, Leonor [0000-0001-9313-2253], Pecinka, Ales [0000-0001-9277-1766], Tani, Eleni [0000-0001-6178-0459], Testillano, P. S. [0000-0003-4509-7646], Valledor, Luis [0000-0002-0636-365X], Vassileva, Valya [0000-0002-9055-8002], Agius, Dolores Rita, Kapazoglou, Aliki, Avramidou, Evangelia V., Baránek, Miroslav, Carneros, Elena, Caro, Elena, Castiglione, Stefano, Cicatelli, Angela, Radanovic, Aleksandra, Ebejer, Jean Paul, Gackowski, Daniel, Guarino, Francesco, Gulyás, Andrea, Hidvégi, Norbert, Hoenicka, Hans, Inácio, Vera, Johannes, Frank, Karalija, Erna, Lieberman-Lazarovich, Michal, Martinelli, Federico, Maury, Stéphane, Mladenov, Velimir, Morais-Cecílio, Leonor, Pecinka, Ales, Tani, Eleni, Testillano, Pilar S., Todorov, Dimitar, Valledor, Luis, Vassileva, Valya, European Cooperation in Science and Technology, Agius, Dolores Rita [0000-0003-1819-2883], Kapazoglou, Aliki [0000-0002-7584-5994], Avramidou, Evangelia V. [0000-0002-5932-1189], Baránek, Miroslav [0000-0002-1583-3588], Carneros, Elena [0000-0003-2066-6320], Caro, Elena [0000-0002-1034-1621], Castiglione, Stefano [0000-0002-0632-4677], Cicatelli, Angela [0000-0001-6996-3495], Radanovic, Aleksandra [0000-0002-7467-9728], Ebejer, Jean Paul [0000-0003-0888-2637], Gackowski, Daniel [0000-0002-7259-1511], Guarino, Francesco [0000-0001-8536-4257], Gulyás, Andrea [0000-0001-6978-1341], Hidvégi, Norbert [0000-0003-3665-2724], Hoenicka, Hans [0000-0001-7226-3772], Inácio, Vera [0000-0002-5652-2540], Johannes, Frank [0000-0002-7962-2907], Karalija, Erna [0000-0001-7262-0645], Lieberman-Lazarovich, Michal [0000-0002-1776-8257], Martinelli, Federico [0000-0002-8502-767X], Maury, Stéphane [0000-0003-0481-0847], Mladenov, Velimir [0000-0002-2182-6579], Morais-Cecílio, Leonor [0000-0001-9313-2253], Pecinka, Ales [0000-0001-9277-1766], Tani, Eleni [0000-0001-6178-0459], Testillano, P. S. [0000-0003-4509-7646], Valledor, Luis [0000-0002-0636-365X], Vassileva, Valya [0000-0002-9055-8002], Agius, Dolores Rita, Kapazoglou, Aliki, Avramidou, Evangelia V., Baránek, Miroslav, Carneros, Elena, Caro, Elena, Castiglione, Stefano, Cicatelli, Angela, Radanovic, Aleksandra, Ebejer, Jean Paul, Gackowski, Daniel, Guarino, Francesco, Gulyás, Andrea, Hidvégi, Norbert, Hoenicka, Hans, Inácio, Vera, Johannes, Frank, Karalija, Erna, Lieberman-Lazarovich, Michal, Martinelli, Federico, Maury, Stéphane, Mladenov, Velimir, Morais-Cecílio, Leonor, Pecinka, Ales, Tani, Eleni, Testillano, Pilar S., Todorov, Dimitar, Valledor, Luis, and Vassileva, Valya

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.

Published
2023

3. Deciphering the epigenetic alphabet involved in transgenerational stress memory in crops

Author

European Cooperation in Science and Technology, Mladenov, Velimir [0000-0002-2182-6579], Fotopoulos, Vasileios [0000-0003-1205-2070], Kaiserli, Eirini [0000-0003-1517-4591], Karalija, Erna [0000-0001-7262-0645], Maury, Stéphane [0000-0003-0481-0847], Baránek, Miroslav [0000-0002-1583-3588], Segal, Na’ama [0000-0002-4133-6411, Testillano, P. S. [0000-0003-4509-7646], Vassileva, Valya [0000-0002-9055-8002], Pinto, Glória [0000-0001-7735-5131], Nagel, Manuela [0000-0003-0396-0333], Hoenicka, Hans [0000-0001-7226-3772], Miladinovic, Dragana [0000-0001-9555-9162], Gallusci, Philippe [0000-0003-1163-8299], Vergata, Chiara [0000-0003-2727-7977], Kapazoglou, Aliki [0000-0002-7584-5994], Abraham, Eleni [0000-0003-4032-5830], Tani, Eleni [0000-0001-6178-0459], Sarri, Efi [0000-0003-4816-2167], Avramidou, Evangelia V. [0000-0002-5932-1189], Gašparović, Mateo [0000-0003-2345-7882], Martinelli, Federico [0000-0002-8502-767X], Mladenov, Velimir, Fotopoulos, Vasileios, Kaiserli, Eirini, Karalija, Erna, Maury, Stéphane, Baránek, Miroslav, Segal, Na’ama, Testillano, Pilar S., Vassileva, Valya, Pinto, Glória, Nagel, Manuela, Hoenicka, Hans, Miladinovic, Dragana, Gallusci, Philippe, Vergata, Chiara, Kapazoglou, Aliki, Abraham, Eleni, Tani, Eleni, Gerakari, Maria, Sarri, Efi, Avramidou, Evangelia V., Gašparović, Mateo, Martinelli, Federico, European Cooperation in Science and Technology, Mladenov, Velimir [0000-0002-2182-6579], Fotopoulos, Vasileios [0000-0003-1205-2070], Kaiserli, Eirini [0000-0003-1517-4591], Karalija, Erna [0000-0001-7262-0645], Maury, Stéphane [0000-0003-0481-0847], Baránek, Miroslav [0000-0002-1583-3588], Segal, Na’ama [0000-0002-4133-6411, Testillano, P. S. [0000-0003-4509-7646], Vassileva, Valya [0000-0002-9055-8002], Pinto, Glória [0000-0001-7735-5131], Nagel, Manuela [0000-0003-0396-0333], Hoenicka, Hans [0000-0001-7226-3772], Miladinovic, Dragana [0000-0001-9555-9162], Gallusci, Philippe [0000-0003-1163-8299], Vergata, Chiara [0000-0003-2727-7977], Kapazoglou, Aliki [0000-0002-7584-5994], Abraham, Eleni [0000-0003-4032-5830], Tani, Eleni [0000-0001-6178-0459], Sarri, Efi [0000-0003-4816-2167], Avramidou, Evangelia V. [0000-0002-5932-1189], Gašparović, Mateo [0000-0003-2345-7882], Martinelli, Federico [0000-0002-8502-767X], Mladenov, Velimir, Fotopoulos, Vasileios, Kaiserli, Eirini, Karalija, Erna, Maury, Stéphane, Baránek, Miroslav, Segal, Na’ama, Testillano, Pilar S., Vassileva, Valya, Pinto, Glória, Nagel, Manuela, Hoenicka, Hans, Miladinovic, Dragana, Gallusci, Philippe, Vergata, Chiara, Kapazoglou, Aliki, Abraham, Eleni, Tani, Eleni, Gerakari, Maria, Sarri, Efi, Avramidou, Evangelia V., Gašparović, Mateo, and Martinelli, Federico

Abstract

Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics

Published
2021

4. Epigenetics for crop improvement in times of global change

Author

European Cooperation in Science and Technology, Kakoulidou, Ioanna [0000-0002-0502-2466], Avramidou, Evangelia V. [0000-0002-5932-1189], Baránek, Miroslav [0000-0002-1583-3588], Brunel-Muguet, Sophie [0000-0001-6940-4618], Farrona, Sara [0000-0002-6855-2237], Johannes, Frank [0000-0002-7962-2907], Kaiserli, Eirini [0000-0003-1517-4591], Lieberman-Lazarovich, Michal [0000-0002-1776-8257], Martinelli, Federico [0000-0002-8502-767X], Mladenov, Velimir [0000-0002-2182-6579], Testillano, P. S. [0000-0003-4509-7646], Vassileva, Valya [0000-0002-9055-8002], Maury, Stéphane [0000-0003-0481-0847], Kakoulidou, Ioanna, Avramidou, Evangelia V., Baránek, Miroslav, Brunel-Muguet, Sophie, Farrona, Sara, Johannes, Frank, Kaiserli, Eirini, Lieberman-Lazarovich, Michal, Martinelli, Federico, Mladenov, Velimir, Testillano, Pilar S., Vassileva, Valya, Maury, Stéphane, European Cooperation in Science and Technology, Kakoulidou, Ioanna [0000-0002-0502-2466], Avramidou, Evangelia V. [0000-0002-5932-1189], Baránek, Miroslav [0000-0002-1583-3588], Brunel-Muguet, Sophie [0000-0001-6940-4618], Farrona, Sara [0000-0002-6855-2237], Johannes, Frank [0000-0002-7962-2907], Kaiserli, Eirini [0000-0003-1517-4591], Lieberman-Lazarovich, Michal [0000-0002-1776-8257], Martinelli, Federico [0000-0002-8502-767X], Mladenov, Velimir [0000-0002-2182-6579], Testillano, P. S. [0000-0003-4509-7646], Vassileva, Valya [0000-0002-9055-8002], Maury, Stéphane [0000-0003-0481-0847], Kakoulidou, Ioanna, Avramidou, Evangelia V., Baránek, Miroslav, Brunel-Muguet, Sophie, Farrona, Sara, Johannes, Frank, Kaiserli, Eirini, Lieberman-Lazarovich, Michal, Martinelli, Federico, Mladenov, Velimir, Testillano, Pilar S., Vassileva, Valya, and Maury, Stéphane

Abstract

Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity—naturally, genetically, chemically, or environmentally induced—can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.

Published
2021

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

Author

Guevara, M Ángeles [0000-0001-7399-3136], Abarca, Dolores [0000-0003-3877-0767], Maury, Stéphane [0000-0003-0481-0847], Cervera, María Teresa [0000-0001-6797-2347], Bräutigam, K., Vining, K. J., Lafon-Placette, C., Fossdal, C. G., Mirouze, M., Marcos, J. G., Fluch, S., Fraga, Mario F., Guevara, M Ángeles, Abarca, Dolores, Johnsen, O., Maury, Stéphane, Strauss, Steven H., Campbell, M. M., Rohde, A., Díaz-Sala, Carmen, Cervera, María Teresa, Guevara, M Ángeles [0000-0001-7399-3136], Abarca, Dolores [0000-0003-3877-0767], Maury, Stéphane [0000-0003-0481-0847], Cervera, María Teresa [0000-0001-6797-2347], Bräutigam, K., Vining, K. J., Lafon-Placette, C., Fossdal, C. G., Mirouze, M., Marcos, J. G., Fluch, S., Fraga, Mario F., Guevara, M Ángeles, Abarca, Dolores, Johnsen, O., Maury, Stéphane, Strauss, Steven H., Campbell, M. M., Rohde, A., Díaz-Sala, Carmen, and Cervera, María Teresa

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. © 2013 The Authors. Published by Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Published
2013

6. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus

Author

Julien Vigneaud, Annegret Kohler, Mamadou Dia Sow, Alain Delaunay, Laure Fauchery, Frederic Guinet, Christian Daviaud, Kerrie W. Barry, Keykhosrow Keymanesh, Jenifer Johnson, Vasanth Singan, Igor Grigoriev, Régis Fichot, Daniel Conde, Mariano Perales, Jörg Tost, Francis M. Martin, Isabel Allona, Steven H. Strauss, Claire Veneault‐Fourrey, Stéphane Maury, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Oregon State University (OSU), Conseil Régional Région Centre Val de Loire, Department of Energy (US), Kohler, Annegret, Sow, Mamadou Dia, Delaunay, Alain, Fauchery, Laure, Barry, Kerrie W., Keymanesh, Keykhosrow, Singan, Vasanth, Grigoriev, Igor, Fichot, Régis, Conde, Daniel, Perales, Mariano, Tost, Jörg, Martin, Francis M., Allona, Isabel, Strauss, Steven H., Veneault-Fourrey, Claire, and Maury, Stéphane 0000-0003-0481-0847]

Subjects
DNA METHYLATION 1, corrhizas, DNA demethylatione, Mycorrhizas, poplar, Physiology, [SDV]Life Sciences [q-bio], Plant Science, DEMETER, Laccaria bicolormy, Laccaria bicolor, pigenetic
Abstract

17 Pág., Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism., MDS and JV received PhD grants from the MRES and Conseil Régional Région Centre Val de Loire, respectively. The LBLGC and the LEE/CNRGH benefit from the support of the ANR EPITREE (ANR-17-CE32-0009-01, https://www6.inrae.fr/epitree-project_eng/) to SM and JT. We thank RTP3E CNRS and IHPE for the access to the bioinformatic platform (http://galaxy.univ-perp.fr/, Christian Chaparro, France). CVF, AK, FM, FG, and LF benefit from the support of the Genomic Science Program (project ‘Plant-Microbe Interface’), US Department of Energy, Office of Science, Biological and Environmental Research under the contract DE-AC05-00OR22725 and the Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE; grant ANR-11-LABX-0002-01). The work (proposal: 10.46936/10.25585/60001022) conducted by the US Department of Energy JGI (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy operated under Contract no. DE-AC02-05CH11231.

Published
2023
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7. Epigenetics for crop improvement in times of global change

Author

Eirini Kaiserli, Federico Martinelli, Frank Johannes, Sophie Brunel-Muguet, Sara Farrona, Ioanna Kakoulidou, Stéphane Maury, Michal Lieberman-Lazarovich, Miroslav Baránek, Evangelia V. Avramidou, Pilar S. Testillano, Valya Vassileva, Velimir Mladenov, European Cooperation in Science and Technology, Kakoulidou, Ioanna [0000-0002-0502-2466], Avramidou, Evangelia V. [0000-0002-5932-1189], Baránek, Miroslav [0000-0002-1583-3588], Brunel-Muguet, Sophie [0000-0001-6940-4618], Farrona, Sara [0000-0002-6855-2237], Johannes, Frank [0000-0002-7962-2907], Kaiserli, Eirini [0000-0003-1517-4591], Lieberman-Lazarovich, Michal [0000-0002-1776-8257], Martinelli, Federico [0000-0002-8502-767X], Mladenov, Velimir [0000-0002-2182-6579], Testillano, P. S. [0000-0003-4509-7646], Vassileva, Valya [0000-0002-9055-8002], Maury, Stéphane [0000-0003-0481-0847], Kakoulidou, Ioanna, Avramidou, Evangelia V., Baránek, Miroslav, Brunel-Muguet, Sophie, Farrona, Sara, Johannes, Frank, Kaiserli, Eirini, Lieberman-Lazarovich, Michal, Martinelli, Federico, Mladenov, Velimir, Testillano, P. S., Vassileva, Valya, and Maury, Stéphane

Subjects
Epigenomics, QH301-705.5, Climate change, Context (language use), Review, Biology, Breeding, Prediction models, General Biochemistry, Genetics and Molecular Biology, Memory, Epigenetics, Biology (General), Regeneration (ecology), DNA methylation, General Immunology and Microbiology, business.industry, fungi, food and beverages, Epigenome, Plant epigenetics, Priming, Evolutionary biology, Agriculture, Adaptation, General Agricultural and Biological Sciences, business
Abstract

46 p.-3 fig.-1 tab., Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity—naturally, genetically, chemically, or environmentally induced—can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change., This research was supported by COST action (European Cooperation in Science and Technology) EPIgenetic mechanisms of Crop Adaptation To Climate cHange (EPICATCH)—grant number CA19125.

Published
2021

8. Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops

Author

Evangelia V. Avramidou, Stéphane Maury, Philippe Gallusci, Efi Sarri, Federico Martinelli, Eleni M. Abraham, Maria Gerakari, Eleni Tani, Na'ama Segal, Chiara Vergata, Mateo Gašparović, Valya Vassileva, Pilar S. Testillano, Glória Pinto, Eirini Kaiserli, Vasileios Fotopoulos, Miroslav Baránek, Hans Hoenicka, Erna Karalija, Dragana Miladinović, Aliki Kapazoglou, Velimir Mladenov, Manuela Nagel, European Cooperation in Science and Technology, Mladenov, Velimir, Fotopoulos, Vasileios, Kaiserli, Eirini, Karalija, Erna, Maury, Stéphane, Baránek, Miroslav, Segal, Na’ama, Testillano, P. S., Vassileva, Valya, Pinto, Glória, Nagel, Manuela, Hoenicka, Hans, Miladinovic, Dragana, Gallusci, Philippe, Vergata, Chiara, Kapazoglou, Aliki, Abraham, Eleni, Tani, Eleni, Sarri, Efi, Avramidou, Evangelia V., Gašparović, Mateo, Martinelli, Federico, Mladenov, Velimir [0000-0002-2182-6579], Fotopoulos, Vasileios [0000-0003-1205-2070], Kaiserli, Eirini [0000-0003-1517-4591], Karalija, Erna [0000-0001-7262-0645], Maury, Stéphane [0000-0003-0481-0847], Baránek, Miroslav [0000-0002-1583-3588], Segal, Na’ama [0000-0002-4133-6411, Testillano, P. S. [0000-0003-4509-7646], Vassileva, Valya [0000-0002-9055-8002], Pinto, Glória [0000-0001-7735-5131], Nagel, Manuela [0000-0003-0396-0333], Hoenicka, Hans [0000-0001-7226-3772], Miladinovic, Dragana [0000-0001-9555-9162], Gallusci, Philippe [0000-0003-1163-8299], Vergata, Chiara [0000-0003-2727-7977], Kapazoglou, Aliki [0000-0002-7584-5994], Abraham, Eleni [0000-0003-4032-5830], Tani, Eleni [0000-0001-6178-0459], Sarri, Efi [0000-0003-4816-2167], Avramidou, Evangelia V. [0000-0002-5932-1189], Gašparović, Mateo [0000-0003-2345-7882], Martinelli, Federico [0000-0002-8502-767X], University of Novi Sad, Cyprus University of Technology, University of Glasgow, University of Sarajevo, UNIVERZITET U SARAJEVU, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mendel University in Brno (MENDELU), National Center for Mariculture, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Bulgarian Academy of Sciences (BAS), Universidade de Aveiro, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Thünen Institute of Forest Genetics, Institute of Field and Vegetable Crops [Novi Sad], Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute for Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organisation 'DEMETER', Aristotle University of Thessaloniki, Agricultural University of Athens, and University of Zagreb

Subjects
Epigenomics, 0106 biological sciences, 0301 basic medicine, Acclimatization, Inheritance Patterns, Review, 01 natural sciences, Epigenesis, Genetic, Biotic stress, Gene Expression Regulation, Plant, Biology (General), Stress memory, Spectroscopy, 2. Zero hunger, Agricultural Sciences, Epigenetic, food and beverages, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Adaptation, Physiological, Computer Science Applications, Chemistry, Identification (biology), abiotic stress, biotic stress, epigenetic, methodology, stress memory, transgenerational memory, Crops, Agricultural, QH301-705.5, Biology, Catalysis, Inorganic Chemistry, 03 medical and health sciences, Transgenerational epigenetics, Stress, Physiological, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Epigenetics, Physical and Theoretical Chemistry, QD1-999, Molecular Biology, Abiotic stress, fungi, Organic Chemistry, Methodology, Agriculture Forestry and Fisheries, Transgenerational memory, DNA Methylation, Plant Breeding, 030104 developmental biology, 13. Climate action, Evolutionary biology, Alphabet, Adaptation, 010606 plant biology & botany
Abstract

20 p.-3 fig., Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics, This finalization of the review was funded by COST Action CA19125—EPIgenetic mechanisms of Crop Adaptation to Climate cHange.

Published
2021
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