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Gelaw TA, Sanan-Mishra N. Molecular priming with H 2O 2 and proline triggers antioxidant enzyme signals in maize seedlings during drought stress. Biochim Biophys Acta Gen Subj 2024; 1868:130633. [PMID: 38762030 DOI: 10.1016/j.bbagen.2024.130633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Drought and water stress impose major limitations to crops, including Maize, as they affect the plant biology at multiple levels. Drought activates the cellular signalling machinery to maintain the osmotic and ROS homeostasis for controlling plant response and adaptation to stress. Molecular priming of seeds plays a significant role in imparting stress tolerance by helping plants to remember the stress, which improves their response when they encounter stress again. METHODS In this study, we examined the effect of priming maize seeds with H2O2 and proline, individually or in combination, on response to drought stress. We investigated the role of molecular priming on the physiological, biochemical and molecular response of maize seedlings during drought stress. RESULTS We observed that seed-priming played a significant role in mediating stress tolerance of seedlings under drought stress as indicated by changes in growth, biochemical properties, pigment and osmolyte accumulation, antioxidant enzyme activities, gas exchange parameters and gene expression. Seed-priming resulted in reduced expression of specific miRNAs to increase target transcripts associated with synthesis of osmolytes and maintenance of ROS homeostasis for reducing potential damage to the cellular components. CONCLUSIONS Seed-priming induced changes in the growth, biochemical properties, pigment and osmolyte accumulation, antioxidant enzyme activities, gas exchange parameters and gene expression, though the response was dependent on the genotype, as well as concentration and combination of the priming agents.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, 110067 New Delhi, India; Department of Biotechnology, College of Agriculture and Natural Resource Sciences, Debre Birhan University, 445 Debre Birhan, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, 110067 New Delhi, India.
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2
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Fossdal CG, Krokene P, Olsen JE, Strimbeck R, Viejo M, Yakovlev I, Mageroy MH. Epigenetic stress memory in gymnosperms. PLANT PHYSIOLOGY 2024; 195:1117-1133. [PMID: 38298164 PMCID: PMC11142372 DOI: 10.1093/plphys/kiae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/02/2024]
Abstract
Gymnosperms are long-lived, cone-bearing seed plants that include some of the most ancient extant plant species. These relict land plants have evolved to survive in habitats marked by chronic or episodic stress. Their ability to thrive in these environments is partly due to their phenotypic flexibility, and epigenetic regulation likely plays a crucial part in this plasticity. We review the current knowledge on abiotic and biotic stress memory in gymnosperms and the possible epigenetic mechanisms underlying long-term phenotypic adaptations. We also discuss recent technological improvements and new experimental possibilities that likely will advance our understanding of epigenetic regulation in these ancient and hard-to-study plants.
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Affiliation(s)
- Carl Gunnar Fossdal
- Division of Plant Health and Biotechnology, Norwegian Institute of Bioeconomy Research, Ås 1431, Norway
| | - Paal Krokene
- Division of Plant Health and Biotechnology, Norwegian Institute of Bioeconomy Research, Ås 1431, Norway
| | - Jorunn Elisabeth Olsen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås 1432, Norway
| | - Richard Strimbeck
- Department of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Marcos Viejo
- Department of Functional Biology, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Igor Yakovlev
- Division of Plant Health and Biotechnology, Norwegian Institute of Bioeconomy Research, Ås 1431, Norway
| | - Melissa H Mageroy
- Division of Plant Health and Biotechnology, Norwegian Institute of Bioeconomy Research, Ås 1431, Norway
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3
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Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
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4
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Viejo M, Tengs T, Yakovlev I, Cross H, Krokene P, Olsen JE, Fossdal CG. Epitype-inducing temperatures drive DNA methylation changes during somatic embryogenesis in the long-lived gymnosperm Norway spruce. FRONTIERS IN PLANT SCIENCE 2023; 14:1196806. [PMID: 37546277 PMCID: PMC10399239 DOI: 10.3389/fpls.2023.1196806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023]
Abstract
An epigenetic memory of the temperature sum experienced during embryogenesis is part of the climatic adaptation strategy of the long-lived gymnosperm Norway spruce. This memory has a lasting effect on the timing of bud phenology and frost tolerance in the resulting epitype trees. The epigenetic memory is well characterized phenotypically and at the transcriptome level, but to what extent DNA methylation changes are involved have not previously been determined. To address this, we analyzed somatic epitype embryos of Norway spruce clones produced at contrasting epitype-inducing conditions (18 and 28°C). We screened for differential DNA methylation in 2744 genes related mainly to the epigenetic machinery, circadian clock, and phenology. Of these genes, 68% displayed differential DNA methylation patterns between contrasting epitype embryos in at least one methylation context (CpG, CHG, CHH). Several genes related to the epigenetic machinery (e.g., DNA methyltransferases, ARGONAUTE) and the control of bud phenology (FTL genes) were differentially methylated. This indicates that the epitype-inducing temperature conditions induce an epigenetic memory involving specific DNA methylation changes in Norway spruce.
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Affiliation(s)
- Marcos Viejo
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Department of Functional Biology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Torstein Tengs
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
- Department of Breeding and Genetics, Norwegian Institute of Food, Fisheries and Aquaculture Research (NOFIMA), Ås, Norway
| | - Igor Yakovlev
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Hugh Cross
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
- Department of Science, National Ecological Observatory Network, Boulder, CO, United States
| | - Paal Krokene
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Jorunn E. Olsen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Carl Gunnar Fossdal
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
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5
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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Vicente TFL, Félix C, Félix R, Valentão P, Lemos MFL. Seaweed as a Natural Source against Phytopathogenic Bacteria. Mar Drugs 2022; 21:23. [PMID: 36662196 PMCID: PMC9867177 DOI: 10.3390/md21010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Plant bacterial pathogens can be devastating and compromise entire crops of fruit and vegetables worldwide. The consequences of bacterial plant infections represent not only relevant economical losses, but also the reduction of food availability. Synthetic bactericides have been the most used tool to control bacterial diseases, representing an expensive investment for the producers, since cyclic applications are usually necessary, and are a potential threat to the environment. The development of greener methodologies is of paramount importance, and some options are already available in the market, usually related to genetic manipulation or plant community modulation, as in the case of biocontrol. Seaweeds are one of the richest sources of bioactive compounds, already being used in different industries such as cosmetics, food, medicine, pharmaceutical investigation, and agriculture, among others. They also arise as an eco-friendly alternative to synthetic bactericides. Several studies have already demonstrated their inhibitory activity over relevant bacterial phytopathogens, some of these compounds are known for their eliciting ability to trigger priming defense mechanisms. The present work aims to gather the available information regarding seaweed extracts/compounds with antibacterial activity and eliciting potential to control bacterial phytopathogens, highlighting the extracts from brown algae with protective properties against microbial attack.
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Affiliation(s)
- Tânia F. L. Vicente
- MARE-Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network Associated Laboratory, ESTM, Polytechnic of Leiria, 2520-641 Peniche, Portugal
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Carina Félix
- MARE-Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network Associated Laboratory, ESTM, Polytechnic of Leiria, 2520-641 Peniche, Portugal
| | - Rafael Félix
- MARE-Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network Associated Laboratory, ESTM, Polytechnic of Leiria, 2520-641 Peniche, Portugal
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Patrícia Valentão
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Marco F. L. Lemos
- MARE-Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network Associated Laboratory, ESTM, Polytechnic of Leiria, 2520-641 Peniche, Portugal
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7
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Liu H, Able AJ, Able JA. Priming crops for the future: rewiring stress memory. TRENDS IN PLANT SCIENCE 2022; 27:699-716. [PMID: 34906381 DOI: 10.1016/j.tplants.2021.11.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 05/12/2023]
Abstract
The agricultural sector must produce resilient and climate-smart crops to meet the increasing needs of global food production. Recent advancements in elucidating the mechanistic basis of plant stress memory have provided new opportunities for crop improvement. Stress memory-coordinated changes at the organismal, cellular, and various omics levels prepare plants to be more responsive to reoccurring stress within or across generation(s). The exposure to a primary stress, or stress priming, can also elicit a beneficial impact when encountering a secondary abiotic or biotic stress through the convergence of synergistic signalling pathways, referred to as cross-stress tolerance. 'Rewired plants' with stress memory provide a new means to stimulate adaptable stress responses, safeguard crop reproduction, and engineer climate-smart crops for the future.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia
| | - Amanda J Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia
| | - Jason A Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia.
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8
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
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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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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Gao Y, Cui Y, Zhao R, Chen X, Zhang J, Zhao J, Kong L. Cryo-Treatment Enhances the Embryogenicity of Mature Somatic Embryos via the lncRNA-miRNA-mRNA Network in White Spruce. Int J Mol Sci 2022; 23:ijms23031111. [PMID: 35163033 PMCID: PMC8834816 DOI: 10.3390/ijms23031111] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/09/2022] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
In conifers, somatic embryogenesis is uniquely initiated from immature embryos in a narrow time window, which is considerably hindered by the difficulty to induce embryogenic tissue (ET) from other tissues, including mature somatic embryos. In this study, the embryogenic ability of newly induced ET and DNA methylation levels was detected, and whole-transcriptome sequencing analyses were carried out. The results showed that ultra-low temperature treatment significantly enhanced ET induction from mature somatic embryos, with the induction rate from 0.4% to 15.5%, but the underlying mechanisms remain unclear. The newly induced ET showed higher capability in generating mature embryos than the original ET. DNA methylation levels fluctuated during the ET induction process. Here, WGCNA analysis revealed that OPT4, TIP1-1, Chi I, GASA5, GST, LAX3, WRKY7, MYBS3, LRR-RLK, PBL7, and WIN1 genes are involved in stress response and auxin signal transduction. Through co-expression analysis, lncRNAs MSTRG.505746.1, MSTRG.1070680.1, and MSTRG.33602.1 might bind to pre-novel_miR_339 to promote the expression of WRKY7 genes for stress response; LAX3 could be protected by lncRNAs MSTRG.1070680.1 and MSTRG.33602.1 via serving as sponges for novel_miR_495 to initiate auxin signal transduction; lncRNAs MSTRG.505746.1, MSTRG.1070680.1, and MSTRG.33602.1 might serve as sponges for novel_miR_527 to enhance the expression of Chi I for early somatic embryo development. This study provides new insight into the area of stress-enhanced early somatic embryogenesis in conifers, which is also attributable to practical applications.
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Affiliation(s)
- Ying Gao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Ying Cui
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Ruirui Zhao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Xiaoyi Chen
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Jinfeng Zhang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Jian Zhao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
- Correspondence: (J.Z.); (L.K.)
| | - Lisheng Kong
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
- Correspondence: (J.Z.); (L.K.)
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10
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Sow MD, Le Gac AL, Fichot R, Lanciano S, Delaunay A, Le Jan I, Lesage-Descauses MC, Citerne S, Caius J, Brunaud V, Soubigou-Taconnat L, Cochard H, Segura V, Chaparro C, Grunau C, Daviaud C, Tost J, Brignolas F, Strauss SH, Mirouze M, Maury S. RNAi suppression of DNA methylation affects the drought stress response and genome integrity in transgenic poplar. THE NEW PHYTOLOGIST 2021; 232:80-97. [PMID: 34128549 DOI: 10.1111/nph.17555] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/08/2021] [Indexed: 05/27/2023]
Abstract
Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via downregulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula × Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit. We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.
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Affiliation(s)
- Mamadou D Sow
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Anne-Laure Le Gac
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Sophie Lanciano
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Isabelle Le Jan
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | | | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Jose Caius
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Hervé Cochard
- Université Clermont Auvergne, INRAE, PIAF, Clermont-Ferrand, 63000, France
| | - Vincent Segura
- BioForA, INRAE, ONF, UMR 0588, Orléans, 45075, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Montpellier SupAgro, UMR 1334, Montpellier, F-34398, France
| | | | - Christoph Grunau
- UMR 5244, IHPE, Université de Perpignan, Perpignan, 66100, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Franck Brignolas
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Marie Mirouze
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
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11
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Liu JJ, Schoettle AW, Sniezko RA, Williams H, Zamany A, Rancourt B. Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family. BMC Genomics 2021; 22:567. [PMID: 34294045 PMCID: PMC8299668 DOI: 10.1186/s12864-021-07885-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/29/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains (NLR) make up one of most important resistance (R) families for plants to resist attacks from various pathogens and pests. The available transcriptomes of limber pine (Pinus flexilis) allow us to characterize NLR genes and related resistance gene analogs (RGAs) in host resistance against Cronartium ribicola, the causal fungal pathogen of white pine blister rust (WPBR) on five-needle pines throughout the world. We previously mapped a limber pine major gene locus (Cr4) that confers complete resistance to C. ribicola on the Pinus consensus linkage group 8 (LG-8). However, genetic distribution of NLR genes as well as their divergence between resistant and susceptible alleles are still unknown. RESULTS To identify NLR genes at the Cr4 locus, the present study re-sequenced a total of 480 RGAs using targeted sequencing in a Cr4-segregated seed family. Following a call of single nucleotide polymorphisms (SNPs) and genetic mapping, a total of 541 SNPs from 155 genes were mapped across 12 LGs. Three putative NLR genes were newly mapped in the Cr4 region, including one that co-segregated with Cr4. The tight linkage of NLRs with Cr4-controlled phenotypes was further confirmed by bulked segregation analysis (BSA) using extreme-phenotype genome-wide association study (XP-GWAS) for significance test. Local tandem duplication in the Cr4 region was further supported by syntenic analysis using the sugar pine genome sequence. Significant gene divergences have been observed in the NLR family, revealing that diversifying selection pressures are relatively higher in local duplicated genes. Most genes showed similar expression patterns at low levels, but some were affected by genetic background related to disease resistance. Evidence from fine genetic dissection, evolutionary analysis, and expression profiling suggests that two NLR genes are the most promising candidates for Cr4 against WPBR. CONCLUSION This study provides fundamental insights into genetic architecture of the Cr4 locus as well as a set of NLR variants for marker-assisted selection in limber pine breeding. Novel NLR genes were identified at the Cr4 locus and the Cr4 candidates will aid deployment of this R gene in combination with other major/minor genes in the limber pine breeding program.
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Affiliation(s)
- Jun-Jun Liu
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Anna W. Schoettle
- USDA Forest Service, Rocky Mountain Research Station, 240 West Prospect Road, Fort Collins, CO 80526 USA
| | - Richard A. Sniezko
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, Oregon, 97424 USA
| | - Holly Williams
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Arezoo Zamany
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Benjamin Rancourt
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
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12
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Trontin JF, Raschke J, Rupps A. Tree 'memory': new insights on temperature-induced priming effects during early embryogenesis. TREE PHYSIOLOGY 2021; 41:906-911. [PMID: 33216135 DOI: 10.1093/treephys/tpaa150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/02/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Jean-François Trontin
- Biotechnology and Advanced Forestry Department, FCBA Technological Institute, 71, Route d'Arcachon, Pierroton, F-33610 Cestas, France
| | - Juliane Raschke
- Institute of Biology, Section Botany and Arboretum, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Andrea Rupps
- Institute of Biology, Section Botany and Arboretum, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
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Sankaranarayanan R, Palani SN, Tamilmaran N, Punitha Selvakumar AS, Chandra Sekar P, Tennyson J. Novel approaches on identification of conserved miRNAs for broad-spectrum Potyvirus control measures. Mol Biol Rep 2021; 48:2377-2388. [PMID: 33743120 DOI: 10.1007/s11033-021-06271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
Potyviridae comprises more than 200 ssRNA viruses, many of which have a broad host range and geographical distributions. Potyvirids (members of Potyviridae) infect several economically important plants such as saffron, cardamom, cucumber, pepper, potato, tomato, yam, etc. Cumulatively, potyvirids cause a substantial economic loss. The major bottleneck in developing an efficient antiviral strategy is that viruses quickly evade host immunity owing to their higher mutation and recombination rates. Due to this reason, the emergence of newer and improved broad-spectrum approaches to combat viral infections is essential. The use of microRNA's (miRNA) to circumvent viral infection against animal viruses has been successfully employed. Fewer studies reported the development of efficient miRNA-based antivirus resistant strategies against plant viruses and none focused on multiple virus resistance. We focused on potyviruses since studies are limited and identification of conserved miRNAs among various host plants would be an initiative to design broad-spectrum antivirus strategies. In this study, we predicted evolutionarily conserved miRNAs by BLAST searching of reported miRNAs from 15 plants against the GSS and EST sequences of banana. A total of nine miRNAs were predicted and screened in nine diverse potyvirids' hosts (Banana, Tomato, Green gram, Jasmine, Chilli, Coriander, Onion, Rose and Colocasia) belonging to eight different orders (Zingiberales, Solanales, Fabales, Lamiales, Apiales, Asperagales, Rosales and Alismatales). Results suggested that miR168 and miR162 are conserved among all the selected plants. This comprehensive study laid the foundations to design broad-spectrum antivirus resistance using miRNAs. To conclude miR168 and miR162 are conserved among many plants and play a crucial role in evading virus infection which could be used as a potential candidate for developing antiviral strategies against potyvirid infections.
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Perdiguero P, Rodrigues AS, Chaves I, Costa B, Alves A, de María N, Vélez MD, Díaz-Sala C, Cervera MT, Miguel CM. Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability. PLANT, CELL & ENVIRONMENT 2021; 44:706-728. [PMID: 33314160 DOI: 10.1111/pce.13976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
An increasing number of microRNAs (miRNAs) and miRNA-related sequences produced during miRNA biogenesis, comprising the isomiRome, have been recently highlighted in different species as critical mediators of environmental stress responses. Conifers have some of the largest known genomes but an extensive characterization of the isomiRome from any conifer species has been lacking. We provide here a comprehensive overview of the Pinus pinaster isomiRome expressed in roots, stem and needles under well-watered and drought conditions. From the 13,441 unique small RNA sequences identified, 2,980 were annotated as canonical miRNAs or miRNA* and the remaining were classified as isomiRNA or miRNA-like sequences. A survey of their expression patterns highlighted roots as the most responsive organ under drought, where specific sequences of which a 24-nt novel miRNA stood out, were strongly down-regulated. Given the putative roles of the miRNA-targeted transcripts validated specifically in root tissues, some of the miRNAs, conserved and novel, are shortlisted as potential regulators of drought response. These results provide a valuable resource for comparative studies between gymnosperms and angiosperms. Furthermore, it evidences high transferability of the isomiRome between pine species being a useful basis for further molecular regulation and physiological studies, and especially those focused on adaptation to drought conditions.
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Affiliation(s)
- Pedro Perdiguero
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Centro de Investigación en Sanidad Animal (CISA-INIA), Madrid, Spain
| | - Andreia Santos Rodrigues
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês Chaves
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Bruno Costa
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Alves
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Nuria de María
- Departamento de Ecología y Genética Forestal, INIA-CIFOR, Madrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - María Dolores Vélez
- Departamento de Ecología y Genética Forestal, INIA-CIFOR, Madrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Carmen Díaz-Sala
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Madrid, Spain
| | - María Teresa Cervera
- Departamento de Ecología y Genética Forestal, INIA-CIFOR, Madrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Célia Maria Miguel
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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15
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Castander-Olarieta A, Pereira C, Montalbán IA, Mendes VM, Correia S, Suárez-Álvarez S, Manadas B, Canhoto J, Moncaleán P. Proteome-Wide Analysis of Heat-Stress in Pinus radiata Somatic Embryos Reveals a Combined Response of Sugar Metabolism and Translational Regulation Mechanisms. FRONTIERS IN PLANT SCIENCE 2021; 12:631239. [PMID: 33912202 PMCID: PMC8072280 DOI: 10.3389/fpls.2021.631239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/22/2021] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis is the process by which bipolar structures with no vascular connection with the surrounding tissue are formed from a single or a group of vegetative cells, and in conifers it can be divided into five different steps: initiation, proliferation, maturation, germination and acclimatization. Somatic embryogenesis has long been used as a model to study the mechanisms regulating stress response in plants, and recent research carried out in our laboratory has demonstrated that high temperatures during initial stages of conifer somatic embryogenesis modify subsequent phases of the process, as well as the behavior of the resulting plants ex vitro. The development of high-throughput techniques has facilitated the study of the molecular response of plants to numerous stress factors. Proteomics offers a reliable image of the cell status and is known to be extremely susceptible to environmental changes. In this study, the proteome of radiata pine somatic embryos was analyzed by LC-MS after the application of high temperatures during initiation of embryonal masses [(23°C, control; 40°C (4 h); 60°C (5 min)]. At the same time, the content of specific soluble sugars and sugar alcohols was analyzed by HPLC. Results confirmed a significant decrease in the initiation rate of embryonal masses under 40°C treatments (from 44 to 30.5%) and an increasing tendency in the production of somatic embryos (from 121.87 to 170.83 somatic embryos per gram of embryogenic tissue). Besides, heat provoked a long-term readjustment of the protein synthesis machinery: a great number of structural constituents of ribosomes were increased under high temperatures, together with the down-regulation of the enzyme methionine-tRNA ligase. Heat led to higher contents of heat shock proteins and chaperones, transmembrane transport proteins, proteins related with post-transcriptional regulation (ARGONAUTE 1D) and enzymes involved in the synthesis of fatty acids, specific compatible sugars (myo-inositol) and cell-wall carbohydrates. On the other hand, the protein adenosylhomocysteinase and enzymes linked with the glycolytic pathway, nitrogen assimilation and oxidative stress response were found at lower levels.
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Affiliation(s)
| | - Cátia Pereira
- Department of Forestry Science, NEIKER, Arkaute, Spain
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Vera M. Mendes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Sandra Correia
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Jorge Canhoto
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Paloma Moncaleán
- Department of Forestry Science, NEIKER, Arkaute, Spain
- *Correspondence: Paloma Moncaleán,
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16
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Chang CYY, Bräutigam K, Hüner NPA, Ensminger I. Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers. THE NEW PHYTOLOGIST 2021; 229:675-691. [PMID: 32869329 DOI: 10.1111/nph.16904] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.
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Affiliation(s)
- Christine Yao-Yun Chang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Norman P A Hüner
- Department of Biology and The Biotron Experimental Climate Change Research Centre, Western University, London, ON, N6A5B7, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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17
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Cao H, Zhang X, Ruan Y, Zhang L, Cui Z, Li X, Jia B. miRNA expression profiling and zeatin dynamic changes in a new model system of in vivo indirect regeneration of tomato. PLoS One 2020; 15:e0237690. [PMID: 33332392 PMCID: PMC7745965 DOI: 10.1371/journal.pone.0237690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/27/2020] [Indexed: 01/15/2023] Open
Abstract
Callus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression during in vivo regeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role in in vivo regeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato during in vivo regeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation during in vivo regeneration of tomato provide novel insights into the regulation of regeneration in higher plants.
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Affiliation(s)
- Huiying Cao
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Xinyue Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Yanye Ruan
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
- * E-mail: (YR); (LZ)
| | - Lijun Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
- * E-mail: (YR); (LZ)
| | - Zhenhai Cui
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Xuxiao Li
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Bing Jia
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
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18
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Castander-Olarieta A, Pereira C, Sales E, Meijón M, Arrillaga I, Cañal MJ, Goicoa T, Ugarte MD, Moncaleán P, Montalbán IA. Induction of Radiata Pine Somatic Embryogenesis at High Temperatures Provokes a Long-Term Decrease in DNA Methylation/Hydroxymethylation and Differential Expression of Stress-Related Genes. PLANTS 2020; 9:plants9121762. [PMID: 33322106 PMCID: PMC7762990 DOI: 10.3390/plants9121762] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Based on the hypothesis that embryo development is a crucial stage for the formation of stable epigenetic marks that could modulate the behaviour of the resulting plants, in this study, radiata pine somatic embryogenesis was induced at high temperatures (23 °C, eight weeks, control; 40 °C, 4 h; 60 °C, 5 min) and the global methylation and hydroxymethylation levels of emerging embryonal masses and somatic plants were analysed using LC-ESI-MS/ MS-MRM. In this context, the expression pattern of six genes previously described as stress-mediators was studied throughout the embryogenic process until plant level to assess whether the observed epigenetic changes could have provoked a sustained alteration of the transcriptome. Results indicated that the highest temperatures led to hypomethylation of both embryonal masses and somatic plants. Moreover, we detected for the first time in a pine species the presence of 5-hydroxymethylcytosine, and revealed its tissue specificity and potential involvement in heat-stress responses. Additionally, a heat shock protein-coding gene showed a down-regulation tendency along the process, with a special emphasis given to embryonal masses at first subculture and ex vitro somatic plants. Likewise, the transcripts of several proteins related with translation, oxidative stress response, and drought resilience were differentially expressed.
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Affiliation(s)
| | - Cátia Pereira
- Department of Forestry Science, NEIKER, 01192 Arkaute, Spain; (A.C.-O.); (C.P.)
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Ester Sales
- Departament of Ciencias Agrarias y del Medio Natural, Instituto Universitario de Ciencias Ambientales, Universidad de Zaragoza, Escuela Politécnica Superior, 22071 Huesca, Spain;
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, 33006 Oviedo, Spain; (M.M.); (M.J.C.)
| | - Isabel Arrillaga
- Departamento de Biología Vegetal, Facultad de Farmacia, Instituto BiotecMed, Universidad de Valencia, 46100 Burjassot, Spain;
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, 33006 Oviedo, Spain; (M.M.); (M.J.C.)
| | - Tomás Goicoa
- Department of Statistics, Computer Science and Mathematics, Universidad Pública de Navarra, 31006 Pamplona, Spain; (T.G.); (M.D.U.)
- INAMAT2 (Institute for Advanced Materials and Mathematics), Universidad Pública de Navarra, 31006 Pamplona, Spain
| | - María Dolores Ugarte
- Department of Statistics, Computer Science and Mathematics, Universidad Pública de Navarra, 31006 Pamplona, Spain; (T.G.); (M.D.U.)
- INAMAT2 (Institute for Advanced Materials and Mathematics), Universidad Pública de Navarra, 31006 Pamplona, Spain
| | - Paloma Moncaleán
- Department of Forestry Science, NEIKER, 01192 Arkaute, Spain; (A.C.-O.); (C.P.)
- Correspondence: (P.M.); (I.A.M.)
| | - Itziar A. Montalbán
- Department of Forestry Science, NEIKER, 01192 Arkaute, Spain; (A.C.-O.); (C.P.)
- Correspondence: (P.M.); (I.A.M.)
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Abstract
The importance of tree genetic variability in the ability of forests to respond and adapt to environmental changes is crucial in forest management and conservation. Along with genetics, recent advances have highlighted “epigenetics” as an emerging and promising field of research for the understanding of tree phenotypic plasticity and adaptive responses. In this paper, we review recent advances in this emerging field and their potential applications for tree researchers and breeders, as well as for forest managers. First, we present the basics of epigenetics in plants before discussing its potential for trees. We then propose a bibliometric and overview of the literature on epigenetics in trees, including recent advances on tree priming. Lastly, we outline the promises of epigenetics for forest research and management, along with current gaps and future challenges. Research in epigenetics could use highly diverse paths to help forests adapt to global change by eliciting different innovative silvicultural approaches for natural- and artificial-based forest management.
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20
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Rehman M, Tanti B. Understanding epigenetic modifications in response to abiotic stresses in plants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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21
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Wójcik AM. Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis. Int J Mol Sci 2020; 21:E4969. [PMID: 32674459 PMCID: PMC7420248 DOI: 10.3390/ijms21144969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.
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Affiliation(s)
- Anna Maria Wójcik
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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22
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Smoczynska A, Pacak AM, Nuc P, Swida-Barteczka A, Kruszka K, Karlowski WM, Jarmolowski A, Szweykowska-Kulinska Z. A Functional Network of Novel Barley MicroRNAs and Their Targets in Response to Drought. Genes (Basel) 2020; 11:genes11050488. [PMID: 32365647 PMCID: PMC7290300 DOI: 10.3390/genes11050488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/27/2022] Open
Abstract
The regulation of mRNA (messenger RNA) levels by microRNA-mediated activity is especially important in plant responses to environmental stresses. In this work, we report six novel barley microRNAs, including two processed from the same precursor that are severely downregulated under drought conditions. For all analyzed microRNAs, we found target genes that were upregulated under drought conditions and that were known to be involved in a plethora of processes from disease resistance to chromatin–protein complex formation and the regulation of transcription in mitochondria. Targets for novel barley microRNAs were confirmed through degradome data analysis and RT-qPCR using primers flanking microRNA-recognition site. Our results show a broad transcriptional response of barley to water deficiency conditions through microRNA-mediated gene regulation and facilitate further research on drought tolerance in crops.
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Affiliation(s)
- Aleksandra Smoczynska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Andrzej M. Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Przemysław Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Wojciech M. Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-712 Poznan, Poland;
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
- Correspondence: ; Tel.: +48-61-829-5950
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23
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Liu H, Able AJ, Able JA. Transgenerational Effects of Water-Deficit and Heat Stress on Germination and Seedling Vigour-New Insights from Durum Wheat microRNAs. PLANTS (BASEL, SWITZERLAND) 2020; 9:E189. [PMID: 32033017 PMCID: PMC7076468 DOI: 10.3390/plants9020189] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 11/18/2022]
Abstract
Water deficiency and heat stress can severely limit crop production and quality. Stress imposed on the parents during reproduction could have transgenerational effects on their progeny. Seeds with different origins can vary significantly in their germination and early growth. Here, we investigated how water-deficit and heat stress on parental durum wheat plants affected seedling establishment of the subsequent generation. One stress-tolerant and one stress-sensitive Australian durum genotype were used. Seeds were collected from parents with or without exposure to stress during reproduction. Generally, stress on the previous generation negatively affected seed germination and seedling vigour, but to a lesser extent in the tolerant variety. Small RNA sequencing utilising the new durum genome assembly revealed significant differences in microRNA (miRNA) expression in the two genotypes. A bioinformatics approach was used to identify multiple miRNA targets which have critical molecular functions in stress adaptation and plant development and could therefore contribute to the phenotypic differences observed. Our data provide the first confirmation of the transgenerational effects of reproductive-stage stress on germination and seedling establishment in durum wheat. New insights gained on the epigenetic level indicate that durum miRNAs could be key factors in optimising seed vigour for breeding superior germplasm and/or varieties.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae SA5064, Australia; (A.J.A.); (J.A.A.)
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24
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Rodrigues AS, Chaves I, Costa BV, Lin YC, Lopes S, Milhinhos A, Van de Peer Y, Miguel CM. Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos. Sci Rep 2019; 9:11327. [PMID: 31383905 PMCID: PMC6683148 DOI: 10.1038/s41598-019-47789-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 07/24/2019] [Indexed: 02/07/2023] Open
Abstract
Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) and from somatic embryos of Pinus pinaster were analysed to identify putative regulators of seed/embryo development in conifers. In total, sixteen sRNA libraries covering several developmental stages were sequenced. We show that embryos and megagametophytes express a large population of 21-nt sRNAs and that substantial amounts of 24-nt sRNAs were also detected, especially in somatic embryos. A total of 215 conserved miRNAs, one third of which are conifer-specific, and 212 high-confidence novel miRNAs were annotated. MIR159, MIR171 and MIR394 families were found in embryos, but were greatly reduced in megagametophytes. Other families, like MIR397 and MIR408, predominated in somatic embryos and megagametophytes, suggesting their expression in somatic embryos is associated with in vitro conditions. Analysis of the predicted miRNA targets suggests that miRNA functions are relevant in several processes including transporter activity at the cotyledon-forming stage, and sulfur metabolism across several developmental stages. An important resource for studying conifer embryogenesis is made available here, which may also provide insightful clues for improving clonal propagation via somatic embryogenesis.
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Affiliation(s)
- Andreia S Rodrigues
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Inês Chaves
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Bruno Vasques Costa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, Lisboa, 1000-029, Portugal
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan and Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Susana Lopes
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Ana Milhinhos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Célia M Miguel
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal.
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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25
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Huang Y, Xiong J, Brown PB, Sun X. Discovery of MicroRNAs from Batrachuperus yenyuanensis Using Deep Sequencing and Prediction of Their Targets. BIOCHEMISTRY (MOSCOW) 2019; 84:380-389. [PMID: 31228929 DOI: 10.1134/s0006297919040059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs), a family of ∼22-nucleotide non-coding single-stranded RNA molecules, are considered as key post-transcriptional regulators of gene expression that regulate various biological processes in living organism. Many miRNAs have been identified in animals; however, few have been reported in Hynobiidae species. The present study is aimed to identify a full repertoire of miRNAs in Batrachuperus yenyuanensis (Yenyuan stream salamander), which would significantly increase our knowledge of miRNAs in amphibians. A small RNA library was constructed from B. yenyuanensis and sequenced using deep sequencing. As a result, 1,717,751 clean reads were obtained, representing 356 known and 80 novel miRNAs. Additionally, expression levels of eight randomly selected miRNAs in B. yenyuanensis were confirmed using the stem-loop quantitative real-time reverse transcription PCR. In addition, 13,972 targets were predicted for these identified miRNAs, although the physiological functions of many of these targets remain unknown. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the predicted targets are involved in a variety of physiological regulatory functions in B. yenyuanensis. These results provide useful information for further research on the miRNAs involved in the growth and development of B. yenyuanensis, as well as adaptation of this species to its high-altitude habitats.
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Affiliation(s)
- Y Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China.
| | - J Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China.
| | - P B Brown
- Purdue University, Department of Forestry and Natural Resources, West Lafayette, IN 47907, USA
| | - X Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China
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26
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Le Gac AL, Lafon-Placette C, Chauveau D, Segura V, Delaunay A, Fichot R, Marron N, Le Jan I, Berthelot A, Bodineau G, Bastien JC, Brignolas F, Maury S. Winter-dormant shoot apical meristem in poplar trees shows environmental epigenetic memory. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4821-4837. [PMID: 30107545 PMCID: PMC6137975 DOI: 10.1093/jxb/ery271] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/02/2018] [Indexed: 05/04/2023]
Abstract
Trees have a long lifespan and must continually adapt to environmental pressures, notably in the context of climate change. Epigenetic mechanisms are doubtless involved in phenotypic plasticity and in stress memory; however, little evidence of the role of epigenetic processes is available for trees growing in fields. Here, we analyzed the possible involvement of epigenetic mechanisms in the winter-dormant shoot apical meristem of Populus × euramericana clones in memory of the growing conditions faced during the vegetative period. We aimed to estimate the range of genetic and environmentally induced variations in global DNA methylation and to evaluate their correlation with changes in biomass production, identify differentially methylated regions (DMRs), and characterize common DMRs between experiments. We showed that the variations in global DNA methylation between conditions were genotype dependent and correlated with biomass production capacity. Microarray chip analysis allowed detection of DMRs 6 months after the stressful summer period. The 161 DMRs identified as common to three independent experiments most notably targeted abiotic stress and developmental response genes. Results are consistent with a winter-dormant shoot apical meristem epigenetic memory of stressful environmental conditions that occurred during the preceding summer period. This memory may facilitate tree acclimation.
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Affiliation(s)
| | | | | | | | | | - Régis Fichot
- LBLGC, INRA, Université d’Orléans, Orléans, France
| | - Nicolas Marron
- Silva, INRA Grand Est, Nancy, AgroParisTech, Université de Lorraine, UMR, Nancy, France
| | | | - Alain Berthelot
- FCBA Délégation Territoriale Nord-Est, Charrey-Sur-Saône, France
| | | | | | | | - Stéphane Maury
- LBLGC, INRA, Université d’Orléans, Orléans, France
- Correspondence:
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