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Mladenov V, Fotopoulos V, Kaiserli E, Karalija E, Maury S, Baranek M, Segal N, Testillano PS, Vassileva V, Pinto G, Nagel M, Hoenicka H, Miladinović D, Gallusci P, Vergata C, Kapazoglou A, Abraham E, Tani E, Gerakari M, Sarri E, Avramidou E, Gašparović M, Martinelli F. Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops. Int J Mol Sci 2021; 22:7118. [PMID: 34281171 PMCID: PMC8268041 DOI: 10.3390/ijms22137118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/27/2021] [Indexed: 12/11/2022] Open
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.
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Affiliation(s)
- Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology & Food Science, Cyprus University of Technology, Lemesos 3036, Cyprus;
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Erna Karalija
- Laboratory for Plant Physiology, Department for Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Stephane Maury
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France;
| | - Miroslav Baranek
- Mendeleum—Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Naama Segal
- Israel Oceanographic and Limnological Research, The National Center for Mariculture (NCM), P.O.B. 1212, Eilat 88112, Israel;
| | - Pilar S. Testillano
- Center of Biological Research Margarita Salas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Glória Pinto
- Centre for Environmental and Marine Studies (CESAM), Biology Department, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Manuela Nagel
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany;
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany;
| | - Dragana Miladinović
- Laboratory for Biotechnology, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—CS5000833882 Villenave d’Ornon, 33076 Bordeaux, France;
| | - Chiara Vergata
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-Dimitra (HAO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Eleni Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Evaggelia Avramidou
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, 10000 Zagreb, Croatia;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
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Allegra A, Gallotta A, Carimi F, Mercati F, Inglese P, Martinelli F. Metabolic Profiling and Post-harvest Behavior of "Dottato" Fig ( Ficus carica L.) Fruit Covered With an Edible Coating From O. ficus-indica. FRONTIERS IN PLANT SCIENCE 2018; 9:1321. [PMID: 30233636 PMCID: PMC6134321 DOI: 10.3389/fpls.2018.01321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
Fig fruits are usually highly sensitive to some physiopathological disorders during post-harvest life, such as softening and skin cracking. Indeed, the use of edible coating (EC) has been evaluated in several fruit crops to reduce fruit post-harvest transpiration and to maintain fruit visual quality. The aim of this study was to determine the post-harvest metabolic response of breba figs treated with mucilage extract from O puntia ficus-indica cladodes, using an untargeted metabolomic approach. Coated and non-coated (control) fruit were sealed in plastic bags, and stored at 4°C for 7 days. The effect of the ECs on their quality fruit during cold storage and qualitative attributes were evaluated by analyzing the fruit primary metabolism and other qualitative parameters such as total soluble solids (TSS) content, titratable acidity (TA), fresh weight loss and firmness. Results underlined that EC was effective in maintaining fruit fresh weight, and fruit firmness. Stepwise discriminant analysis was able to discriminate fruit conditions. Alanine, xylulose, aspartic acid, glutamic, acid and 2,5-dihydroxypyrazine showed a significant role on discriminating edible coated fruit from untreated ones. Principal component analysis (PCA) was able to highlight clear differences in the overall metabolism changes between untreated and treated fruit. The application of EC significantly mitigated the decrease of most of the aminoacid content during cold storage. EC treatment caused the changes of several organic acids in comparison to untreated control, increasing the amount of carbohydrates and other key metabolites, such as beta-sitosterol, glycerol, and uracil. These results clearly showed the drastic effects of EC on fig metabolism during post-harvest and shed light on the beneficial mechanisms of this treatment.
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Affiliation(s)
- Alessio Allegra
- Department of Agricultural, Food and Forest Sciences – Università degli Studi di Palermo, Palermo, Italy
| | - Alessandra Gallotta
- Department of Soil, Plants and Food Science (DiSSPA), University of Bari, Bari, Italy
| | - Francesco Carimi
- Institute of Biosciences and BioResources, Division of Palermo, National Research Council, Palermo, Italy
| | - Francesco Mercati
- Institute of Biosciences and BioResources, Division of Palermo, National Research Council, Palermo, Italy
| | - Paolo Inglese
- Department of Agricultural, Food and Forest Sciences – Università degli Studi di Palermo, Palermo, Italy
| | - Federico Martinelli
- Department of Agricultural, Food and Forest Sciences – Università degli Studi di Palermo, Palermo, Italy
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Martinelli F, Marchese A, Giovino A, Marra FP, Della Noce I, Caruso T, Dandekar AM. In-Field and Early Detection of Xylella fastidiosa Infections in Olive Using a Portable Instrument. FRONTIERS IN PLANT SCIENCE 2018; 9:2007. [PMID: 30713547 PMCID: PMC6345699 DOI: 10.3389/fpls.2018.02007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 12/31/2018] [Indexed: 05/04/2023]
Affiliation(s)
- Federico Martinelli
- Department of Agricultural Food Forest Sciences, University of Palermo, Palermo, Italy
- *Correspondence: Federico Martinelli
| | - Annalisa Marchese
- Department of Agricultural Food Forest Sciences, University of Palermo, Palermo, Italy
| | - Antonio Giovino
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Bagheria, Italy
| | - Francesco Paolo Marra
- Department of Agricultural Food Forest Sciences, University of Palermo, Palermo, Italy
| | | | - Tiziano Caruso
- Department of Agricultural Food Forest Sciences, University of Palermo, Palermo, Italy
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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Ibáñez AM, Martinelli F, Reagan RL, Uratsu SL, Vo A, Tinoco MA, Phu ML, Chen Y, Rocke DM, Dandekar AM. Transcriptome and metabolome analysis of citrus fruit to elucidate puffing disorder. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 217-218:87-98. [PMID: 24467900 DOI: 10.1016/j.plantsci.2013.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/31/2013] [Accepted: 12/06/2013] [Indexed: 05/09/2023]
Abstract
A systems-level analysis reveals details of molecular mechanisms underlying puffing disorder in Citrus fruit. Flavedo, albedo and juice sac tissues of normal fruits and fruits displaying symptoms of puffing disorder were studied using metabolomics at three developmental stages. Microarrays were used to compare normal and puffed fruits for each of the three tissues. A protein-protein interaction network inferred from previous work on Arabidopsis identified hub proteins whose transcripts show significant changes in expression. Glycolysis, the backbone of primary metabolism, appeared to be severely affected by the disorder, based on both transcriptomic and metabolomic results. Significantly less citric acid was observed consistently in puffed fruits. Gene set enrichment analysis suggested that glycolysis and carbohydrate metabolism were significantly altered in puffed samples in both albedo and flavedo. Expression of invertases and genes for sucrose export, amylose-starch and starch-maltose conversion was higher in puffed fruits. These changes may significantly alter source-sink communications. Genes associated with gibberellin and cytokinin signaling were downregulated in symptomatic albedo tissues, suggesting that these hormones play key roles in the disorder. Findings may be applied toward the development of early diagnostic methods based on host response genes and metabolites (i.e. citric acid), and toward therapeutics based on hormones.
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Affiliation(s)
- Ana M Ibáñez
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA
| | - Federico Martinelli
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA; Department of Agricultural and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy; I.E.M.E.S.T. Istituto Euro Mediterraneo di Scienza e Tecnologia, Via Emerico Amari, 123, 90139 Palermo, Italy
| | - Russell L Reagan
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA
| | - Sandra L Uratsu
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA
| | - Anna Vo
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA
| | - Mario A Tinoco
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA
| | - My L Phu
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA
| | - Ying Chen
- Division of Biostatistics, Med Sci 1C, Room 146, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - David M Rocke
- Division of Biostatistics, Med Sci 1C, Room 146, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 4, Davis, CA 95616, USA.
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Martinelli F, Reagan RL, Uratsu SL, Phu ML, Albrecht U, Zhao W, Davis CE, Bowman KD, Dandekar AM. Gene regulatory networks elucidating huanglongbing disease mechanisms. PLoS One 2013; 8:e74256. [PMID: 24086326 PMCID: PMC3783430 DOI: 10.1371/journal.pone.0074256] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/29/2013] [Indexed: 12/02/2022] Open
Abstract
Next-generation sequencing was exploited to gain deeper insight into the response to infection by Candidatus liberibacter asiaticus (CaLas), especially the immune disregulation and metabolic dysfunction caused by source-sink disruption. Previous fruit transcriptome data were compared with additional RNA-Seq data in three tissues: immature fruit, and young and mature leaves. Four categories of orchard trees were studied: symptomatic, asymptomatic, apparently healthy, and healthy. Principal component analysis found distinct expression patterns between immature and mature fruits and leaf samples for all four categories of trees. A predicted protein - protein interaction network identified HLB-regulated genes for sugar transporters playing key roles in the overall plant responses. Gene set and pathway enrichment analyses highlight the role of sucrose and starch metabolism in disease symptom development in all tissues. HLB-regulated genes (glucose-phosphate-transporter, invertase, starch-related genes) would likely determine the source-sink relationship disruption. In infected leaves, transcriptomic changes were observed for light reactions genes (downregulation), sucrose metabolism (upregulation), and starch biosynthesis (upregulation). In parallel, symptomatic fruits over-expressed genes involved in photosynthesis, sucrose and raffinose metabolism, and downregulated starch biosynthesis. We visualized gene networks between tissues inducing a source-sink shift. CaLas alters the hormone crosstalk, resulting in weak and ineffective tissue-specific plant immune responses necessary for bacterial clearance. Accordingly, expression of WRKYs (including WRKY70) was higher in fruits than in leaves. Systemic acquired responses were inadequately activated in young leaves, generally considered the sites where most new infections occur.
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Affiliation(s)
- Federico Martinelli
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- Dipartimento di Sistemi Agro-ambientali, Università degli Studi di Palermo, Palermo, Italy
| | - Russell L. Reagan
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Sandra L. Uratsu
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - My L. Phu
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Ute Albrecht
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, United States of America
| | - Weixiang Zhao
- Department of Mechanical and Aerospace Engineering, University of California Davis, Davis, California, United States of America
| | - Cristina E. Davis
- Department of Mechanical and Aerospace Engineering, University of California Davis, Davis, California, United States of America
| | - Kim D. Bowman
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, United States of America
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
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Barros PM, Gonçalves N, Saibo NJM, Oliveira MM. Functional characterization of two almond C-repeat-binding factors involved in cold response. TREE PHYSIOLOGY 2012; 32:1113-28. [PMID: 22832014 DOI: 10.1093/treephys/tps067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Low temperature plays a crucial role in seasonal development of woody plants and may directly impact crop production, more particularly in temperate fruit trees. Given its high genetic variability and adaptability to different climatic conditions, almond (Prunus dulcis Mill.) is an interesting model to understand the mechanisms regulating low temperature sensing in fruit trees. In this paper, we report the cloning and characterization of two genes (PdCBF1 and PdCBF2) belonging to the C-repeat-binding factor (CBF) family of transcription factors. Southern blotting analysis showed that this family is composed of at least five members. In almond shoots propagated in vitro, transcription of these genes was rapidly induced by low temperature, suggesting an involvement in cold acclimation. Transactivation assays showed that PdCBF1 and PdCBF2 could bind to dehydration responsive element/C-repeat containing sequences, as activators of gene expression. In addition, induction of both PdCBFs by cold was higher towards the end of the day, which agreed with the expression pattern of PdDehydrin1, a predicted CBF target gene. Furthermore, PdCBF1 and PdCBF2 were also transiently induced by abscisic acid and drought treatments. Considering the bin mapping analysis that correlated PdCBFs and PdDHN1 (respectively in linkage groups 5 and 7) with two different quantitative trait locicontrolling blooming time, it is relevant to perform further association studies that may validate their effect on this trait.
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Affiliation(s)
- Pedro M Barros
- Genomics of Plant Stress Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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Weiss J, Egea-Cortines M. Transcriptomic analysis of cold response in tomato fruits identifies dehydrin as a marker of cold stress. J Appl Genet 2010; 50:311-9. [PMID: 19875881 DOI: 10.1007/bf03195689] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tomato is sensitive to cold during vegetative growth, fruit set, development, and ripening. We have characterized the effect of cold stress (6xC for up to 48 h) on the transcriptome of Micro-Tom tomato fruits during ripening by subtractive PCR. The cold stress caused modifications in gene expression of housekeeping genes. From a total of 38 genes up-regulated by cold, only one clone - a dehydrin homologue - was related to previously identified cold-stress genes. Phylogenetic analysis showed its clustering with other cold-induced dehydrins, and increased distances from dehydrins activated by abscisic acid. Quantitative expression analysis of tomato dehydrin showed it was activated by cold treatment in leaves and fruits. As dehydrin is a member of the Sl-CBF1 regulon from tomato, we analyzed the cold-responsive transcription factor Sl-CBF1 in mature leaves and ripening fruits stored at 6xC. Leaves of Micro-Tom showed high basal levels of the transcription factor Sl-CBF1, compared to fruits. Cold treatment caused increased levels of Sl-CBF1 expression in leaves but not in fruits of Micro-Tom and Demisem (a commercial cultivar). Tomato dehydrin can be used as a transcriptional marker of cold stress in leaves and ripening fruits. However, our results indicate that the cold response activation of dehydrin gene in tomato fruits is the consequence of an alternative pathway, different from the Sl-CBF1 regulon.
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Affiliation(s)
- J Weiss
- Institute of Plant Biotechnology, Technical University of Cartagena (UPCT), Department of Agricultural Science and Technology, ETSIA, Cartagena, Spain
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Pulla RK, Kim YJ, Kim MK, Senthil KS, In JG, Yang DC. Isolation of a novel dehydrin gene from Codonopsis lanceolata and analysis of its response to abiotic stresses. BMB Rep 2008; 41:338-43. [DOI: 10.5483/bmbrep.2008.41.4.338] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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