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1. 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

2. 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

3. 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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