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Xavier LR, Corrêa CCG, da Paschoa RP, Vieira KDS, Pacheco DDR, Gomes LDES, Duncan BC, da Conceição LDS, Pinto VB, Santa-Catarina C, Silveira V. Time-Dependent Proteomic Signatures Associated with Embryogenic Callus Induction in Carica papaya L. PLANTS (BASEL, SWITZERLAND) 2023; 12:3891. [PMID: 38005788 PMCID: PMC10675192 DOI: 10.3390/plants12223891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
Sex segregation increases the cost of Carica papaya production through seed-based propagation. Therefore, in vitro techniques are an attractive option for clonal propagation, especially of hermaphroditic plants. Here, we performed a temporal analysis of the proteome of C. papaya calli aiming to identify the key players involved in embryogenic callus formation. Mature zygotic embryos used as explants were treated with 20 μM 2,4-dichlorophenoxyacetic acid to induce embryogenic callus. Total proteins were extracted from explants at 0 (zygotic embryo) and after 7, 14, and 21 days of induction. A total of 1407 proteins were identified using a bottom-up proteomic approach. The clustering analysis revealed four distinct patterns of protein accumulation throughout callus induction. Proteins related to seed maturation and storage are abundant in the explant before induction, decreasing as callus formation progresses. Carbohydrate and amino acid metabolisms, aerobic respiration, and protein catabolic processes were enriched throughout days of callus induction. Protein kinases associated with auxin responses, such as SKP1-like proteins 1B, accumulated in response to callus induction. Additionally, regulatory proteins, including histone deacetylase (HD2C) and argonaute 1 (AGO1), were more abundant at 7 days, suggesting their role in the acquisition of embryogenic competence. Predicted protein-protein networks revealed the regulatory role of proteins 14-3-3 accumulated during callus induction and the association of proteins involved in oxidative phosphorylation and hormone response. Our findings emphasize the modulation of the proteome during embryogenic callus initiation and identify regulatory proteins that might be involved in the activation of this process.
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Affiliation(s)
- Lucas Rodrigues Xavier
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Caio Cezar Guedes Corrêa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Roberta Pena da Paschoa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Karina da Silva Vieira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Daniel Dastan Rezabala Pacheco
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Lucas do Espirito Santo Gomes
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Bárbara Cardoso Duncan
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Laís dos Santos da Conceição
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Vitor Batista Pinto
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (V.B.P.); (C.S.-C.)
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (V.B.P.); (C.S.-C.)
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
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Li L, Sun X, Yu W, Gui M, Qiu Y, Tang M, Tian H, Liang G. Comparative transcriptome analysis of high- and low-embryogenic Hevea brasiliensis genotypes reveals involvement of phytohormones in somatic embryogenesis. BMC PLANT BIOLOGY 2023; 23:489. [PMID: 37828441 PMCID: PMC10571474 DOI: 10.1186/s12870-023-04432-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/31/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Rubber plant (Hevea brasiliensis) is one of the major sources of latex. Somatic embryogenesis (SE) is a promising alterative to its propagation by grafting and seed. Phytohormones have been shown to influence SE in different plant species. However, limited knowledge is available on the role of phytohormones in SE in Hevea. The anther cultures of two Hevea genotypes (Yunyan 73477-YT and Reken 628-RT) with contrasting SE rate were established and four stages i.e., anthers (h), anther induced callus (y), callus differentiation state (f), and somatic embryos (p) were studied. UPLC-ESI-MS/MS and transcriptome analyses were used to study phytohormone accumulation and related expression changes in biosynthesis and signaling genes. RESULTS YT showed higher callus induction rate than RT. Of the two genotypes, only YT exhibited successful SE. Auxins, cytokinins (CKs), abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), gibberellins (GAs), and ethylene (ETH) were detected in the two genotypes. Indole-3-acetic acid (IAA), CKs, ABA, and ETH had notable differences in the studied stages of the two genotypes. The differentially expressed genes identified in treatment comparisons were majorly enriched in MAPK and phytohormone signaling, biosynthesis of secondary metabolites, and metabolic pathways. The expression changes in IAA, CK, ABA, and ETH biosynthesis and signaling genes confirmed the differential accumulation of respective phytohormones in the two genotypes. CONCLUSION These results suggest potential roles of phytohormones in SE in Hevea.
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Affiliation(s)
- Ling Li
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Xiaolong Sun
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Wencai Yu
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Mingchun Gui
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Yanfen Qiu
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Min Tang
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Hai Tian
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Guoping Liang
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China.
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Zhang(张宇鹏) Y, Fan G, Toivainen T, Tengs T, Yakovlev I, Krokene P, Hytönen T, Fossdal CG, Grini PE. Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vesca ecotypes. HORTICULTURE RESEARCH 2023; 10:uhad156. [PMID: 37719273 PMCID: PMC10500154 DOI: 10.1093/hr/uhad156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/25/2023] [Indexed: 09/19/2023]
Abstract
Plants must adapt with increasing speed to global warming to maintain their fitness. One rapid adaptation mechanism is epigenetic memory, which may provide organisms sufficient time to adapt to climate change. We studied how the perennial Fragaria vesca adapted to warmer temperatures (28°C vs. 18°C) over three asexual generations. Differences in flowering time, stolon number, and petiole length were induced by warmer temperature in one or more ecotypes after three asexual generations and persisted in a common garden environment. Induced methylome changes differed between the four ecotypes from Norway, Iceland, Italy, and Spain, but shared methylome responses were also identified. Most differentially methylated regions (DMRs) occurred in the CHG context, and most CHG and CHH DMRs were hypermethylated at the warmer temperature. In eight CHG DMR peaks, a highly similar methylation pattern could be observed between ecotypes. On average, 13% of the differentially methylated genes between ecotypes also showed a temperature-induced change in gene expression. We observed ecotype-specific methylation and expression patterns for genes related to gibberellin metabolism, flowering time, and epigenetic mechanisms. Furthermore, we observed a negative correlation with gene expression when repetitive elements were found near (±2 kb) or inside genes. In conclusion, lasting phenotypic changes indicative of an epigenetic memory were induced by warmer temperature and were accompanied by changes in DNA methylation patterns. Both shared methylation patterns and transcriptome differences between F. vesca accessions were observed, indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic variation.
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Affiliation(s)
- YuPeng Zhang(张宇鹏)
- EVOGENE, Department of Biosciences, University of Oslo, 0313 Oslo, Norway
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Guangxun Fan
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Tuomas Toivainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Torstein Tengs
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Igor Yakovlev
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Paal Krokene
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Carl Gunnar Fossdal
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Paul E. Grini
- EVOGENE, Department of Biosciences, University of Oslo, 0313 Oslo, Norway
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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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Pérez-Oliver MA, González-Mas MDC, Renau-Morata B, Arrillaga I, Sales E. Heat-Priming during Somatic Embryogenesis Increased Resilience to Drought Stress in the Generated Maritime Pine ( Pinus pinaster) Plants. Int J Mol Sci 2023; 24:ijms24119299. [PMID: 37298255 DOI: 10.3390/ijms24119299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Drought stress is becoming the most important factor of global warming in forests, hampering the production of reproductive material with improved resilience. Previously, we reported that heat-priming maritime pine (Pinus pinaster) megagametophytes during SE produced epigenetic changes that generated plants better adapted to subsequent heat stress. In this work, we tested, in an experiment performed under greenhouse conditions, whether heat-priming will produce cross-tolerance to mild drought stress (30 days) in 3-year-old priming-derived plants. We found that they maintain constitutive physiological differences as compared to controls, such as higher proline, abscisic acid, starch, and reduced glutathione and total protein contents, as well as higher ΦPSII yield. Primed plants also displayed a constitutive upregulation of the WRKY transcription factor and the Responsive to Dehydration 22 (RD22) genes, as well as of those coding for antioxidant enzymes (APX, SOD, and GST) and for proteins that avoid cell damage (HSP70 and DHNs). Furthermore, osmoprotectants as total soluble sugars and proteins were early accumulated in primed plants during the stress. Prolongated water withdrawal increased ABA accumulation and negatively affected photosynthesis in all plants but primed-derived plants recovered faster than controls. We concluded that high temperature pulses during somatic embryogenesis resulted in transcriptomic and physiological changes in maritime pine plants that can increase their resilience to drought stress, since heat-primed plants exhibit permanent activation of mechanisms for cell protection and overexpression of stress pathways that pre-adapt them to respond more efficiently to soil water deficit.
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Affiliation(s)
- María Amparo Pérez-Oliver
- Biotechnology and Biomedicine (BiotecMed) Institute and Plant Biology Department, Faculty of Pharmacy, Universitat de València, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain
| | - María Del Carmen González-Mas
- Biotechnology and Biomedicine (BiotecMed) Institute and Plant Biology Department, Faculty of Pharmacy, Universitat de València, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain
| | - Begoña Renau-Morata
- Biotechnology and Biomedicine (BiotecMed) Institute and Plant Biology Department, Faculty of Pharmacy, Universitat de València, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain
| | - Isabel Arrillaga
- Biotechnology and Biomedicine (BiotecMed) Institute and Plant Biology Department, Faculty of Pharmacy, Universitat de València, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain
| | - Ester Sales
- Agrarian and Environmental Sciences Department, Institute of Environmental Sciences (IUCA), University of Zaragoza, High Polytechnic School, Ctra. Cuarte s/n, 22197 Huesca, Spain
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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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Fischerová L, Gemperlová L, Cvikrová M, Matušíková I, Moravčíková J, Gerši Z, Malbeck J, Kuderna J, Pavlíčková J, Motyka V, Eliášová K, Vondráková Z. The humidity level matters during the desiccation of Norway spruce somatic embryos. FRONTIERS IN PLANT SCIENCE 2022; 13:968982. [PMID: 35968100 PMCID: PMC9372446 DOI: 10.3389/fpls.2022.968982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In Norway spruce, as in many other conifers, the germination capacity of somatic embryos is strongly influenced by the desiccation phase inserted after maturation. The intensity of drying during desiccation eminently affected the formation of emblings (i.e., seedlings developed from somatic embryos). Compared to non-desiccated embryos, the germination capacity of embryos desiccated at 100% relative humidity was about three times higher, but the reduction of relative humidity to 95 and 90% had a negative effect on the subsequent embryo development. The water loss observed in these embryos did not lead to an increase in lipid peroxidation, as shown by malondialdehyde levels. Another metabolic pathway in plants that mediates a response to abiotic stresses is directed toward the biosynthesis of polyamines (PAs). The activities of PA biosynthetic enzymes increased steadily in embryos during desiccation at 100% relative humidity, whereas they decreased at lower humidity. The total content of free PAs in the embryos gradually decreased throughout desiccation. The increase in free putrescine (Put) and perchloric acid-insoluble Put conjugates was observed in embryos desiccated at lower humidity. These changes were accompanied to some extent by the transcription of the genes for the PA biosynthesis enzymes. Desiccation at 100% relative humidity increased the activity of the cell wall-modifying enzymes β-1,3-glucanases and chitinases; the activities of these enzymes were also significantly suppressed at reduced humidity. The same pattern was observed in the transcription of some β-1,3-glucanase and chitinase genes. Desiccation treatments triggered metabolic processes that responded to water availability, suggesting an active response of the embryo to the reduction in humidity. A positive effect was demonstrated only for desiccation at high relative humidity. Some of the physiological characteristics described can be used as markers of inappropriate relative humidity during somatic embryo desiccation.
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Affiliation(s)
- Lucie Fischerová
- Laboratory of Biologically Active Compounds, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Lenka Gemperlová
- Laboratory of Biologically Active Compounds, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Milena Cvikrová
- Laboratory of Biologically Active Compounds, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Ildiko Matušíková
- Department of Ecochemistry and Radioecology, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Jana Moravčíková
- Department of Biotechnologies, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Zuzana Gerši
- Department of Biology, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Jiří Malbeck
- Laboratory of Mass Spectroscopy, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Jan Kuderna
- Laboratory of Biologically Active Compounds, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Pavlíčková
- Laboratory of Biologically Active Compounds, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Václav Motyka
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Kateřina Eliášová
- Laboratory of Biologically Active Compounds, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Zuzana Vondráková
- Laboratory of Biologically Active Compounds, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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8
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miR172 Regulates WUS during Somatic Embryogenesis in Arabidopsis via AP2. Cells 2022; 11:cells11040718. [PMID: 35203367 PMCID: PMC8869827 DOI: 10.3390/cells11040718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
In plants, the embryogenic transition of somatic cells requires the reprogramming of the cell transcriptome, which is under the control of genetic and epigenetic factors. Correspondingly, the extensive modulation of genes encoding transcription factors and miRNAs has been indicated as controlling the induction of somatic embryogenesis in Arabidopsis and other plants. Among the MIRNAs that have a differential expression during somatic embryogenesis, members of the MIRNA172 gene family have been identified, which implies a role of miR172 in controlling the embryogenic transition in Arabidopsis. In the present study, we found a disturbed expression of both MIRNA172 and candidate miR172-target genes, including AP2, TOE1, TOE2, TOE3, SMZ and SNZ, that negatively affected the embryogenic response of transgenic explants. Next, we examined the role of AP2 in the miR172-mediated mechanism that controls the embryogenic response. We found some evidence that by controlling AP2, miR172 might repress the WUS that has an important function in embryogenic induction. We showed that the mechanism of the miR172-AP2-controlled repression of WUS involves histone acetylation. We observed the upregulation of the WUS transcripts in an embryogenic culture that was overexpressing AP2 and treated with trichostatin A (TSA), which is an inhibitor of HDAC histone deacetylases. The increased expression of the WUS gene in the embryogenic culture of the hdac mutants further confirmed the role of histone acetylation in WUS control during somatic embryogenesis. A chromatin-immunoprecipitation analysis provided evidence about the contribution of HDA6/19-mediated histone deacetylation to AP2-controlled WUS repression during embryogenic induction. The upstream regulatory elements of the miR172-AP2-WUS pathway might involve the miR156-controlled SPL9/SPL10, which control the level of mature miR172 in an embryogenic culture.
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Zhou L, Yarra R, Jin L, Yang Y, Cao H, Zhao Z. Identification and expression analysis of histone modification gene (HM) family during somatic embryogenesis of oil palm. BMC Genomics 2022; 23:11. [PMID: 34983381 PMCID: PMC8729141 DOI: 10.1186/s12864-021-08245-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/07/2021] [Indexed: 11/23/2022] Open
Abstract
Background Oil palm (Elaeis guineensis, Jacq.) is an important vegetable oil-yielding plant. Somatic embryogenesis is a promising method to produce large-scale elite clones to meet the demand for palm oil. The epigenetic mechanisms such as histone modifications have emerged as critical factors during somatic embryogenesis. These histone modifications are associated with the regulation of various genes controlling somatic embryogenesis. To date, none of the information is available on the histone modification gene (HM) family in oil palm. Results We reported the identification of 109 HM gene family members including 48 HMTs, 27 HDMs, 13 HATs, and 21 HDACs in the oil palm genome. Gene structural and motif analysis of EgHMs showed varied exon–intron organization and with conserved motifs among them. The identified 109 EgHMs were distributed unevenly across 16 chromosomes and displayed tandem duplication in oil palm genome. Furthermore, relative expression analysis showed the differential expressional pattern of 99 candidate EgHM genes at different stages (non-embryogenic, embryogenic, somatic embryo) of somatic embryogenesis process in oil palm, suggesting the EgHMs play vital roles in somatic embryogenesis. Our study laid a foundation to understand the regulatory roles of several EgHM genes during somatic embryogenesis. Conclusions A total of 109 histone modification gene family members were identified in the oil palm genome via genome-wide analysis. The present study provides insightful information regarding HM gene’s structure, their distribution, duplication in oil palm genome, and also their evolutionary relationship with other HM gene family members in Arabidopsis and rice. Finally, our study provided an essential role of oil palm HM genes during somatic embryogenesis process. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08245-2.
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Affiliation(s)
- Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China.
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Longfei Jin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Yaodong Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Zhihao Zhao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
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10
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Can Forest Trees Cope with Climate Change?-Effects of DNA Methylation on Gene Expression and Adaptation to Environmental Change. Int J Mol Sci 2021; 22:ijms222413524. [PMID: 34948318 PMCID: PMC8703565 DOI: 10.3390/ijms222413524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications, including chromatin modifications and DNA methylation, play key roles in regulating gene expression in both plants and animals. Transmission of epigenetic markers is important for some genes to maintain specific expression patterns and preserve the status quo of the cell. This article provides a review of existing research and the current state of knowledge about DNA methylation in trees in the context of global climate change, along with references to the potential of epigenome editing tools and the possibility of their use for forest tree research. Epigenetic modifications, including DNA methylation, are involved in evolutionary processes, developmental processes, and environmental interactions. Thus, the implications of epigenetics are important for adaptation and phenotypic plasticity because they provide the potential for tree conservation in forest ecosystems exposed to adverse conditions resulting from global warming and regional climate fluctuations.
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11
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Pereira C, Castander-Olarieta A, Sales E, Montalbán IA, Canhoto J, Moncaleán P. Heat Stress in Pinus halepensis Somatic Embryogenesis Induction: Effect in DNA Methylation and Differential Expression of Stress-Related Genes. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112333. [PMID: 34834696 PMCID: PMC8622292 DOI: 10.3390/plants10112333] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 05/13/2023]
Abstract
In the current context of climate change, plants need to develop different mechanisms of stress tolerance and adaptation to cope with changing environmental conditions. Temperature is one of the most important abiotic stresses that forest trees have to overcome. Recent research developed in our laboratory demonstrated that high temperatures during different stages of conifer somatic embryogenesis (SE) modify subsequent phases of the process and the behavior of the resulting ex vitro somatic plants. For this reason, Aleppo pine SE was induced under different heat stress treatments (40 °C for 4 h, 50 °C for 30 min, and 60 °C for 5 min) in order to analyze its effect on the global DNA methylation rates and the differential expression of four stress-related genes at different stages of the SE process. Results showed that a slight decrease of DNA methylation at proliferating embryonal masses (EMs) can correlate with the final efficiency of the process. Additionally, different expression patterns for stress-related genes were found in EMs and needles from the in vitro somatic plants obtained; the DEHYDRATION INDUCED PROTEIN 19 gene was up-regulated in response to heat at proliferating EMs, whereas HSP20 FAMILY PROTEIN and SUPEROXIDE DISMUTASE [Cu-Zn] were down-regulated in needles.
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Affiliation(s)
- Cátia Pereira
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- Department of Forestry Science, NEIKER-BRTA, 01080 Arkaute, Spain; (A.C.-O.); (I.A.M.)
| | | | - Ester Sales
- Departament of Ciencias Agrarias y del Medio Natural, Instituto Universitario de Ciencias Ambientales, Universidad de Zaragoza, Escuela Politécnica Superior, 22071 Huesca, Spain;
| | - Itziar A. Montalbán
- Department of Forestry Science, NEIKER-BRTA, 01080 Arkaute, Spain; (A.C.-O.); (I.A.M.)
| | - Jorge Canhoto
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- Correspondence: (J.C.); (P.M.)
| | - Paloma Moncaleán
- Department of Forestry Science, NEIKER-BRTA, 01080 Arkaute, Spain; (A.C.-O.); (I.A.M.)
- Correspondence: (J.C.); (P.M.)
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12
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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: 18] [Impact Index Per Article: 6.0] [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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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro 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;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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14
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Garai S, Citu, Singla-Pareek SL, Sopory SK, Kaur C, Yadav G. Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:707286. [PMID: 34381483 PMCID: PMC8350573 DOI: 10.3389/fpls.2021.707286] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/29/2021] [Indexed: 08/01/2023]
Abstract
Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its "prionome." In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.
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Affiliation(s)
- Sampurna Garai
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Citu
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sudhir K. Sopory
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Charanpreet Kaur
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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15
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The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts. Nat Commun 2021; 12:4247. [PMID: 34253727 PMCID: PMC8275611 DOI: 10.1038/s41467-021-24528-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant's longevity and tolerance to temperature, nutrient and water stress.
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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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Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis. FORESTS 2021. [DOI: 10.3390/f12030364] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed.
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Wang Y, Li HL, Zhou YK, Guo D, Zhu JH, Peng SQ. Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis. BMC Genomics 2021; 22:183. [PMID: 33711923 PMCID: PMC7953812 DOI: 10.1186/s12864-021-07501-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood. RESULTS In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. CONCLUSIONS This study provides important information to elucidate the molecular regulation during rubber tree late SE.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Hui-Liang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Yong-Kai Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Dong Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Jia-Hong Zhu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Shi-Qing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China.
- Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, 571101, China.
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Pérez-Oliver MA, Haro JG, Pavlović I, Novák O, Segura J, Sales E, Arrillaga I. Priming Maritime Pine Megagametophytes during Somatic Embryogenesis Improved Plant Adaptation to Heat Stress. PLANTS 2021; 10:plants10030446. [PMID: 33652929 PMCID: PMC7996847 DOI: 10.3390/plants10030446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022]
Abstract
In the context of global climate change, forest tree research should be addressed to provide genotypes with increased resilience to high temperature events. These improved plants can be obtained by heat priming during somatic embryogenesis (SE), which would produce an epigenetic-mediated transgenerational memory. Thereby, we applied 37 °C or 50 °C to maritime pine (Pinus pinaster) megagametophytes and the obtained embryogenic masses went through the subsequent SE phases to produce plants that were further subjected to heat stress conditions. A putative transcription factor WRKY11 was upregulated in priming-derived embryonal masses, and also in the regenerated P37 and P50 plants, suggesting its role in establishing an epigenetic memory in this plant species. In vitro-grown P50 plants also showed higher cytokinin content and SOD upregulation, which points to a better responsiveness to heat stress. Heat exposure of two-year-old maritime pine plants induced upregulation of HSP70 in those derived from primed embryogenic masses, that also showed better osmotic adjustment and higher increases in chlorophyll, soluble sugars and starch contents. Moreover, ϕPSII of P50 plants was less affected by heat exposure. Thus, our results suggest that priming at 50 °C at the SE induction phase is a promising strategy to improve heat resilience in maritime pine.
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Affiliation(s)
- María Amparo Pérez-Oliver
- Plant Biology Department, Faculty of Pharmacy, Biotechnology and Biomedicine (BiotecMed) Institute, Universidad de Valencia, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain; (M.A.P.-O.); (J.G.H.); (J.S.)
| | - Juan Gregorio Haro
- Plant Biology Department, Faculty of Pharmacy, Biotechnology and Biomedicine (BiotecMed) Institute, Universidad de Valencia, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain; (M.A.P.-O.); (J.G.H.); (J.S.)
| | - Iva Pavlović
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (I.P.); (O.N.)
- Laboratory for Chemical Biology, Division of MoLecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (I.P.); (O.N.)
| | - Juan Segura
- Plant Biology Department, Faculty of Pharmacy, Biotechnology and Biomedicine (BiotecMed) Institute, Universidad de Valencia, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain; (M.A.P.-O.); (J.G.H.); (J.S.)
| | - Ester Sales
- Agrarian and Environmental Sciences Department, Institute of Environmental Sciences (IUCA), University of Zaragoza, High Polytechnic School, Ctra. Cuarte s/n, 22071 Huesca, Spain;
| | - Isabel Arrillaga
- Plant Biology Department, Faculty of Pharmacy, Biotechnology and Biomedicine (BiotecMed) Institute, Universidad de Valencia, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain; (M.A.P.-O.); (J.G.H.); (J.S.)
- Correspondence:
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20
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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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21
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García-García I, Méndez-Cea B, Martín-Gálvez D, Seco JI, Gallego FJ, Linares JC. Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline. FRONTIERS IN PLANT SCIENCE 2021; 12:797958. [PMID: 35058957 PMCID: PMC8764141 DOI: 10.3389/fpls.2021.797958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/13/2021] [Indexed: 05/14/2023]
Abstract
Forest tree species are highly vulnerable to the effects of climate change. As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough. However, the current lack of knowledge on this field is remarkable, due to many challenges that researchers face when studying this issue. Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change drives tree species epigenetic modifications. In spite of this challenging framework, some insights on the relationships among climate change-induced stress and epigenomics are coming. Advances in DNA sequencing technologies and an increasing number of studies dealing with this topic must boost our knowledge on tree adaptive capacity to changing environmental conditions. Here, we discuss challenges and perspectives in the epigenetics of climate change-induced forests decline, aiming to provide a general overview of the state of the art.
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Affiliation(s)
- Isabel García-García
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Isabel García-García,
| | - Belén Méndez-Cea
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- Belén Méndez-Cea,
| | - David Martín-Gálvez
- Departamento de Biodiversidad, Ecología y Evolución, UD Zoología, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - José Ignacio Seco
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
| | - Francisco Javier Gallego
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Carlos Linares
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
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22
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Vigneaud J, Maury S. [Developmental plasticity in plants: an interaction between hormones and epigenetics at the meristem level]. Biol Aujourdhui 2020; 214:125-135. [PMID: 33357371 DOI: 10.1051/jbio/2020011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 12/25/2022]
Abstract
Plants are fixed organisms with continuous development throughout their life and great sensitivity to environmental variations. They react in this way by exhibiting large developmental phenotypic plasticity. This plasticity is partly controlled by (phyto)hormones, but recent studies also suggest the involvement of epigenetic mechanisms. It seems that these two factors may interact in a complex way and especially in the stem cells grouped together in meristems. The objective of this review is to present the current arguments about this interaction which would promote developmental plasticity. Three major points are thus addressed to justify this interaction between hormonal control and epigenetics (control at the chromatin level) for the developmental plasticity of plants: the arguments in favor of an effect of hormones on chromatin and vice versa, the arguments in favor of their roles on developmental plasticity and finally the arguments in favor of the central place of these interactions, the meristems. Various perspectives and applications are discussed.
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Affiliation(s)
- Julien Vigneaud
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAe, Université d'Orléans, EA1207 USC1328, 45067 Orléans, France
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAe, Université d'Orléans, EA1207 USC1328, 45067 Orléans, France
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23
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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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24
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Pinus spp. Somatic Embryo Conversion under High Temperature: Effect on the Morphological and Physiological Characteristics of Plantlets. FORESTS 2020. [DOI: 10.3390/f11111181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Climatic variations in the current environmental scenario require plants with tolerance to sudden changes in temperature and a decrease in water availability. Accordingly, this tolerance will enable successful plantations and the maintenance of natural and planted forests. Consequently, in the last two decades, drought tolerance and high temperatures in conifers have been an important target for morphological, physiological, and epigenetic studies. Based on this, our research team has optimized different stages of somatic embryogenesis (SE) in Pinus spp. improving the success of the process. Through this method, we can obtain a large amount of clonal material and then analyze the somatic plants under different conditions ex vitro. The analysis of the morphological and physiological parameters in somatic embryos (ses) and plants with different tolerances to abiotic stress can provide us with valuable information about the mechanisms used by plants to survive under adverse environmental conditions. Thus, the objective of this work was to evaluate the influence of high temperatures (23, 40, 50, and 60 °C, after 12 weeks, 90, 30, 5 min, respectively) on the morphology of somatic embryos obtained from Pinus radiata D.Don (Radiata pine) and Pinus halepensis Mill. (Aleppo pine). In addition, we carried out a physiological evaluation of the somatic plants of P. radiata submitted to heat and water stress in a greenhouse. We observed that the number of somatic embryos was not affected by maturation temperatures in both species. Likewise, P. radiata plants obtained from these somatic embryos survived drought and heat stress in the greenhouse. In addition, plants originating from embryonal masses (EMs) subjected to high maturation temperature (40 and 60 °C) had a significant increase in gs and E. Therefore, it is possible to modulate the characteristics of somatic plants produced by the manipulation of environmental conditions during the process of SE.
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25
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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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26
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Mageroy MH, Wilkinson SW, Tengs T, Cross H, Almvik M, Pétriacq P, Vivian-Smith A, Zhao T, Fossdal CG, Krokene P. Molecular underpinnings of methyl jasmonate-induced resistance in Norway spruce. PLANT, CELL & ENVIRONMENT 2020; 43:1827-1843. [PMID: 32323322 DOI: 10.1111/pce.13774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/15/2020] [Indexed: 05/13/2023]
Abstract
In response to various stimuli, plants acquire resistance against pests and/or pathogens. Such acquired or induced resistance allows plants to rapidly adapt to their environment. Spraying the bark of mature Norway spruce (Picea abies) trees with the phytohormone methyl jasmonate (MeJA) enhances resistance to tree-killing bark beetles and their associated phytopathogenic fungi. Analysis of spruce chemical defenses and beetle colonization success suggests that MeJA treatment both directly induces immune responses and primes inducible defenses for a faster and stronger response to subsequent beetle attack. We used metabolite and transcriptome profiling to explore the mechanisms underlying MeJA-induced resistance in Norway spruce. We demonstrated that MeJA treatment caused substantial changes in the bark transcriptional response to a triggering stress (mechanical wounding). Profiling of mRNA expression showed a suite of spruce inducible defenses are primed following MeJA treatment. Although monoterpenes and diterpene resin acids increased more rapidly after wounding in MeJA-treated than control bark, expression of their biosynthesis genes did not. We suggest that priming of inducible defenses is part of a complex mixture of defense responses that underpins the increased resistance against bark beetle colonization observed in Norway spruce. This study provides the most detailed insights yet into the mechanisms underlying induced resistance in a long-lived gymnosperm.
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Affiliation(s)
- Melissa H Mageroy
- Molecular plant biology and Forest Genetics and biodiversity, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Samuel W Wilkinson
- P3 Centre for Translational Plant and Soil Biology, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Torstein Tengs
- Molecular plant biology and Forest Genetics and biodiversity, Norwegian Institute of Bioeconomy Research, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Hugh Cross
- Molecular plant biology and Forest Genetics and biodiversity, Norwegian Institute of Bioeconomy Research, Ås, Norway
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Marit Almvik
- Molecular plant biology and Forest Genetics and biodiversity, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Pierre Pétriacq
- P3 Centre for Translational Plant and Soil Biology, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- UMR 1332 BFP, INRA, University of Bordeaux, MetaboHUB-Bordeaux, MetaboHUB, PHENOME-EMPHASIS, Villenave d'Ornon, France
| | - Adam Vivian-Smith
- Molecular plant biology and Forest Genetics and biodiversity, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Tao Zhao
- School of Science and Technology, Örebro University, Örebro, Sweden
| | - Carl Gunnar Fossdal
- Molecular plant biology and Forest Genetics and biodiversity, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Paal Krokene
- Molecular plant biology and Forest Genetics and biodiversity, Norwegian Institute of Bioeconomy Research, Ås, Norway
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27
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Wójcikowska B, Wójcik AM, Gaj MD. Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants. Int J Mol Sci 2020; 21:ijms21072307. [PMID: 32225116 PMCID: PMC7177879 DOI: 10.3390/ijms21072307] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 12/22/2022] Open
Abstract
Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.
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28
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Chen Y, Xu X, Liu Z, Zhang Z, XuHan X, Lin Y, Lai Z. Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour. BMC Genomics 2020; 21:4. [PMID: 31898486 PMCID: PMC6941269 DOI: 10.1186/s12864-019-6393-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE). RESULTS RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22,743, 19,745, 21,144, 21,102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4180, 5846 and 1785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM value of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data. CONCLUSION This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.
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Affiliation(s)
- Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhuanxia Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhongxion Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome. Sci Rep 2019; 9:19314. [PMID: 31848418 PMCID: PMC6917789 DOI: 10.1038/s41598-019-55826-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 11/29/2019] [Indexed: 01/02/2023] Open
Abstract
5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene expression in metazoans and plants. Iron-(II)/α-ketoglutarate-dependent dioxygenases can oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Although these oxidized forms of 5mC may serve as demethylation intermediates or contribute to transcriptional regulation in animals and fungi, experimental evidence for their presence in plant genomes is ambiguous. Here, employing reversed-phase HPLC coupled with sensitive mass spectrometry, we demonstrated that, unlike 5caC, both 5hmC and 5fC are detectable in non-negligible quantities in the DNA of a conifer, Norway spruce. Remarkably, whereas 5hmC content of spruce DNA is approximately 100-fold lower relative to human colorectal carcinoma cells, the levels of both - 5fC and a thymine base modification, 5-hydroxymethyluracil, are comparable in these systems. We confirmed the presence of modified DNA bases by immunohistochemistry in Norway spruce buds based on peroxidase-conjugated antibodies and tyramide signal amplification. Our results reveal the presence of specific range of noncanonical DNA bases in conifer genomes implying potential roles for these modifications in plant development and homeostasis.
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31
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Quintana-Escobar AO, Nic-Can GI, Galaz Avalos RM, Loyola-Vargas VM, Gongora-Castillo E. Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes. PeerJ 2019; 7:e7752. [PMID: 31637116 PMCID: PMC6800528 DOI: 10.7717/peerj.7752] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/25/2019] [Indexed: 01/24/2023] Open
Abstract
Background Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Methods Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. Results A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. Discussion The results of this study allow a better understanding of the genes involved in the auxin signaling pathway as well as their expression profiles during the SE process.
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Affiliation(s)
- Ana O Quintana-Escobar
- Unidad de Bioquímica y Biologia Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Geovanny I Nic-Can
- CONACYT Research Fellow-Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Rosa María Galaz Avalos
- Unidad de Bioquímica y Biologia Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biologia Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Elsa Gongora-Castillo
- CONACYT Research Fellow-Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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Li HL, Guo D, Zhu JH, Wang Y, Peng SQ. Identification of histone methylation modifiers and their expression patterns during somatic embryogenesis in Hevea brasiliensis. Genet Mol Biol 2019; 43:e20180141. [PMID: 31441928 PMCID: PMC7229888 DOI: 10.1590/1678-4685-gmb-2018-0141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 03/10/2019] [Indexed: 12/17/2022] Open
Abstract
Histone methylation plays a crucial role in various biological processes, from heterochromatin formation to transcriptional regulation. Currently, no information is available regarding histone methylation modifiers in the important rubber-producing plant Hevea brasiliensis. Here, we identified 47 histone methyltransferase (HMT) genes and 25 histone demethylase (HDM) genes as possible members of the histone methylation modifiers in the rubber tree genome. According to the structural features of HMT and HDM, the HbHMTs were classified into two groups (HbPRMs and HbSDGs), the HbHDMs have two groups (HbLSDs and HbJMJs). Expression patterns were analyzed in five different tissues and at different phases of somatic embryogenesis. HbSDG10, 21, 25, 33, HbJMJ2, 18, 20 were with high expression at different phases of somatic embryogenesis. HbSDG10,14, 20, 21, 33 and HbPRMT4 were expressed highly in anther, HbSDG14, 20, 21, 22, 23, 33, 35 and HbPRMT1 HbJMJ7 and HbLSD1, 2, 3, 4 showed high expression levels in callus. HbSDG1, 7, 10, 13, 14, 18, 19, 21, 22, 23, 35, HbPRMT1, 8, HbJMJ5, 7, 11, 16, 20 and HbLSD2, 3, 4 were expressed highly in somatic embryo. HbSDG10, 21, 25, 33, HbLSD2, 3 were expressed highly in bud of regenerated plant. The analyses reveal that HbHMTs and HbHDMs exhibit different expression patterns at different phases during somatic embryogenesis, implying that some HbHMTs and HbHDMs play important roles during somatic embryogenesis. This study provide fundamental information for further studies on histone methylation in Hevea brasiliensis.
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Affiliation(s)
- Hui-Liang Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dong Guo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jia-Hong Zhu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ying Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shi-Qing Peng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Johnson JS, Cantrell RS, Cosner C, Hartig F, Hastings A, Rogers HS, Schupp EW, Shea K, Teller BJ, Yu X, Zurell D, Pufal G. Rapid changes in seed dispersal traits may modify plant responses to global change. AOB PLANTS 2019; 11:plz020. [PMID: 31198528 PMCID: PMC6548345 DOI: 10.1093/aobpla/plz020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/26/2019] [Indexed: 05/22/2023]
Abstract
When climatic or environmental conditions change, plant populations must either adapt to these new conditions, or track their niche via seed dispersal. Adaptation of plants to different abiotic environments has mostly been discussed with respect to physiological and demographic parameters that allow local persistence. However, rapid modifications in response to changing environmental conditions can also affect seed dispersal, both via plant traits and via their dispersal agents. Studying such changes empirically is challenging, due to the high variability in dispersal success, resulting from environmental heterogeneity, and substantial phenotypic variability of dispersal-related traits of seeds and their dispersers. The exact mechanisms that drive rapid changes are often not well understood, but the ecological implications of these processes are essential determinants of dispersal success, and deserve more attention from ecologists, especially in the context of adaptation to global change. We outline the evidence for rapid changes in seed dispersal traits by discussing variability due to plasticity or genetics broadly, and describe the specific traits and biological systems in which variability in dispersal is being studied, before discussing some of the potential underlying mechanisms. We then address future research needs and propose a simulation model that incorporates phenotypic plasticity in seed dispersal. We close with a call to action and encourage ecologists and biologist to embrace the challenge of better understanding rapid changes in seed dispersal and their consequences for the reaction of plant populations to global change.
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Affiliation(s)
- Jeremy S Johnson
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
- Dorena Genetic Resource Center, USDA Forest Service, Cottage Grove, OR, USA
| | | | - Chris Cosner
- Department of Mathematics, The University of Miami, Coral Gables, FL, USA
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany
| | - Alan Hastings
- Department of Environmental Science and Policy, University of California, Davis, CA, USA
| | - Haldre S Rogers
- Department of Ecology, Evolution, and Behavior, Iowa State University, Ames, IA, USA
| | - Eugene W Schupp
- Department of Wildland Resources & Ecology Center, Utah State University, Logan, UT, USA
| | - Katriona Shea
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Brittany J Teller
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Xiao Yu
- Department of Mathematics, The University of Miami, Coral Gables, FL, USA
| | - Damaris Zurell
- Department of Geography, Humboldt-University Berlin, Berlin, Germany
- Department of Land Change and Science, Swiss Federal Institute WSL, Birmensdorf, Switzerland
| | - Gesine Pufal
- Nature Conservation and Landscape Ecology, University of Freiburg, Freiburg, Germany
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Maury S, Sow MD, Le Gac AL, Genitoni J, Lafon-Placette C, Mozgova I. Phytohormone and Chromatin Crosstalk: The Missing Link For Developmental Plasticity? FRONTIERS IN PLANT SCIENCE 2019; 10:395. [PMID: 31024580 PMCID: PMC6459951 DOI: 10.3389/fpls.2019.00395] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/14/2019] [Indexed: 05/29/2023]
Affiliation(s)
- Stéphane Maury
- LBLGC, INRA, Université d'Orléans, EA1207 USC 1328, Orléans, France
| | - Mamadou Dia Sow
- LBLGC, INRA, Université d'Orléans, EA1207 USC 1328, Orléans, France
| | - Anne-Laure Le Gac
- BIOSS Centre for Biological Signaling Studies, Institute for Biology III, University of Freiburg, Freiburg, Germany
| | - Julien Genitoni
- LBLGC, INRA, Université d'Orléans, EA1207 USC 1328, Orléans, France
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest, INRA, Rennes, France
| | | | - Iva Mozgova
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Trebon, Czechia
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Ceske Budejovice, Czechia
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Méndez-Hernández HA, Ledezma-Rodríguez M, Avilez-Montalvo RN, Juárez-Gómez YL, Skeete A, Avilez-Montalvo J, De-la-Peña C, Loyola-Vargas VM. Signaling Overview of Plant Somatic Embryogenesis. FRONTIERS IN PLANT SCIENCE 2019; 10:77. [PMID: 30792725 PMCID: PMC6375091 DOI: 10.3389/fpls.2019.00077] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/17/2019] [Indexed: 05/17/2023]
Abstract
Somatic embryogenesis (SE) is a means by which plants can regenerate bipolar structures from a somatic cell. During the process of cell differentiation, the explant responds to endogenous stimuli, which trigger the induction of a signaling response and, consequently, modify the gene program of the cell. SE is probably the most studied plant regeneration model, but to date it is the least understood due to the unclear mechanisms that occur at a cellular level. In this review, the authors seek to emphasize the importance of signaling on plant SE, highlighting the interactions between the different plant growth regulators (PGR), mainly auxins, cytokinins (CKs), ethylene and abscisic acid (ABA), during the induction of SE. The role of signaling is examined from the start of cell differentiation through the early steps on the embryogenic pathway, as well as its relation to a plant's tolerance of different types of stress. Furthermore, the role of genes encoded to transcription factors (TFs) during the embryogenic process such as the LEAFY COTYLEDON (LEC), WUSCHEL (WUS), BABY BOOM (BBM) and CLAVATA (CLV) genes, Arabinogalactan-proteins (AGPs), APETALA 2 (AP2) and epigenetic factors is discussed.
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Affiliation(s)
- Hugo A. Méndez-Hernández
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Maharshi Ledezma-Rodríguez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Randy N. Avilez-Montalvo
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Yary L. Juárez-Gómez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Analesa Skeete
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Johny Avilez-Montalvo
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
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Castander-Olarieta A, Montalbán IA, De Medeiros Oliveira E, Dell’Aversana E, D’Amelia L, Carillo P, Steiner N, Fraga HPDF, Guerra MP, Goicoa T, Ugarte MD, Pereira C, Moncaleán P. Effect of Thermal Stress on Tissue Ultrastructure and Metabolite Profiles During Initiation of Radiata Pine Somatic Embryogenesis. FRONTIERS IN PLANT SCIENCE 2019; 9:2004. [PMID: 30705684 PMCID: PMC6344425 DOI: 10.3389/fpls.2018.02004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/27/2018] [Indexed: 05/22/2023]
Abstract
Climate change will inevitably lead to environmental variations, thus plant drought tolerance will be a determinant factor in the success of plantations and natural forestry recovery. Some metabolites, such as soluble carbohydrates and amino acids, have been described as being the key to both embryogenesis efficiency and abiotic stress response, contributing to phenotypic plasticity and the adaptive capacity of plants. For this reason, our main objectives were to evaluate if the temperature during embryonal mass initiation in radiata pine was critical to the success of somatic embryogenesis, to alter the morphological and ultrastructural organization of embryonal masses at cellular level and to modify the carbohydrate, protein, or amino acid contents. The first SE initiation experiments were carried out at moderate and high temperatures for periods of different durations prior to transfer to the control temperature of 23°C. Cultures initiated at moderate temperatures (30°C, 4 weeks and 40°C, 4 days) showed significantly lower initiation and proliferation rates than those at the control temperature or pulse treatment at high temperatures (50°C, 5 min). No significant differences were observed either for the percentage of embryogenic cell lines that produced somatic embryos, or for the number of somatic embryos per gram of embryonal mass. Based on the results from the first experiments, initiation was carried out at 40°C 4 h; 50°C, 30 min; and a pulse treatment of 60°C, 5 min. No significant differences were found for the initiation or number of established lines or for the maturation of somatic embryos. However, large morphological differences were observed in the mature somatic embryos. At the same time, changes observed at cellular level suggested that strong heat shock treatments may trigger the programmed cell death of embryogenic cells, leading to an early loss of embryogenic potential, and the formation of supernumerary suspensor cells. Finally, among all the differences observed in the metabolic profile, it is worth highlighting the accumulation of tyrosine and isoleucine, both amino acids involved in the synthesis of abiotic stress response-related secondary metabolites.
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Affiliation(s)
| | | | | | - Emilia Dell’Aversana
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | - Luisa D’Amelia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | - Petronia Carillo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | - Neusa Steiner
- Department of Botany, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | | | - Miguel Pedro Guerra
- Laboratório de Fisiología do Desenvolvimento e Genética Vegetal, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Tomás Goicoa
- Department of Statistics, Computer Science and Mathematics, Universidad Pública de Navarra, Pamplona, Spain
| | - María Dolores Ugarte
- Department of Statistics, Computer Science and Mathematics, Universidad Pública de Navarra, Pamplona, Spain
| | - Catia Pereira
- Department of Life Sciences, Universidade de Coimbra, Coimbra, Portugal
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Alakärppä E, Salo HM, Valledor L, Cañal MJ, Häggman H, Vuosku J. Natural variation of DNA methylation and gene expression may determine local adaptations of Scots pine populations. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5293-5305. [PMID: 30113688 DOI: 10.1093/jxb/ery292] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/01/2018] [Indexed: 05/27/2023]
Abstract
Long-lived conifers are vulnerable to climate change because classical evolutionary processes are slow in developing adaptive responses. Therefore, the capacity of a genotype to adopt different phenotypes is important. Gene expression is the primary mechanism that converts genome-encoded information into phenotypes, and DNA methylation is employed in the epigenetic regulation of gene expression. We investigated variations in global DNA methylation and gene expression between three Scots pine (Pinus sylvestris L.) populations located in northern and southern Finland using mature seeds. Gene expression levels were studied in six DNA methyltransferase (DNMT) genes, which were characterized in this study, and in 19 circadian clock genes regulating adaptive traits. In embryos, expression diversity was found for three DNMT genes, which maintain DNA methylation. The expression of two DNMT genes was strongly correlated with climate variables, which suggests a role for DNA methylation in local adaptation. For adaptation-related genes, expression levels showed between-population variation in 11 genes in megagametophytes and in eight genes in embryos, and many of these genes were linked to climate factors. Altogether, our results suggest that differential DNA methylation and gene expression contribute to local adaptation in Scots pine populations and may enhance the fitness of trees under rapidly changing climatic conditions.
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Affiliation(s)
- Emmi Alakärppä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Heikki M Salo
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Luis Valledor
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Maria Jesús Cañal
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Hely Häggman
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jaana Vuosku
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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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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Plitta-Michalak BP, Naskret-Barciszewska MZ, Kotlarski S, Tomaszewski D, Tylkowski T, Barciszewski J, Chmielarz P, Michalak M. Changes in genomic 5-methylcytosine level mirror the response of orthodox (Acer platanoides L.) and recalcitrant (Acer pseudoplatanus L.) seeds to severe desiccation. TREE PHYSIOLOGY 2018; 38:617-629. [PMID: 29121348 DOI: 10.1093/treephys/tpx134] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Poor storability of recalcitrant seeds is due to their inability to tolerate low moisture content. Understanding the processes underlying their recalcitrance is a prerequisite to developing a maintenance strategy and prolonging their lifespan. Multiple studies have investigated the differences between orthodox (desiccation-tolerant) and recalcitrant (desiccation-sensitive) seeds. Information on epigenetic regulation, however, is lacking and thus limits our understanding of the processes defining the physiology of seeds. In the present comparative study, changes in the global levels of 5-methylcytosine (m5C) in orthodox and recalcitrant seeds of Acer platanoides L. and Acer pseudoplatanus L. were characterized during progressive stages of severe drying. Concomitant with their differential sensitivity to desiccation stress, we demonstrate variation in the response of embryonic axes and cotyledons to water deficit at the level of DNA methylation. Results indicate that desiccation-induced changes in m5C are both tissue- and seed category-specific and are highly correlated with recalcitrant seed viability. Moreover, we demonstrate that m5C global changes in response to desiccation are not retained in DNA isolated from seedlings, except in seedlings that are derived from strongly desiccated orthodox seeds (moisture content of 3.5%). Finally, the potential utilization of m5C status as a universal seed viability marker is discussed.
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Affiliation(s)
| | | | - Szymon Kotlarski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Dominik Tomaszewski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Tadeusz Tylkowski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Pawel Chmielarz
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Marcin Michalak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
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Yakovlev IA, Fossdal CG. In Silico Analysis of Small RNAs Suggest Roles for Novel and Conserved miRNAs in the Formation of Epigenetic Memory in Somatic Embryos of Norway Spruce. Front Physiol 2017; 8:674. [PMID: 28943851 PMCID: PMC5596105 DOI: 10.3389/fphys.2017.00674] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/23/2017] [Indexed: 12/27/2022] Open
Abstract
Epigenetic memory in Norway spruce affects the timing of bud burst and bud set, vitally important adaptive traits for this long-lived forest species. Epigenetic memory is established in response to the temperature conditions during embryogenesis. Somatic embryogenesis at different epitype inducing (EpI) temperatures closely mimics the natural processes of epigenetic memory formation in seeds, giving rise to epigenetically different clonal plants in a reproducible and predictable manner, with respect to altered bud phenology. MicroRNAs (miRNAs) and other small non-coding RNAs (sRNAs) play an essential role in the regulation of plant gene expression and may affect this epigenetic mechanism. We used NGS sequencing and computational in silico methods to identify and profile conserved and novel miRNAs among small RNAs in embryogenic tissues of Norway spruce at three EpI temperatures (18, 23 and 28°C). We detected three predominant classes of sRNAs related to a length of 24 nt, followed by a 21–22 nt class and a third 31 nt class of sRNAs. More than 2100 different miRNAs within the prevailing length 21–22 nt were identified. Profiling these putative miRNAs allowed identification of 1053 highly expressed miRNAs, including 523 conserved and 530 novels. 654 of these miRNAs were found to be differentially expressed (DEM) depending on EpI temperature. For most DEMs, we defined their putative mRNA targets. The targets represented mostly by transcripts of multiple-repeats proteins, like TIR, NBS-LRR, PPR and TPR repeat, Clathrin/VPS proteins, Myb-like, AP2, etc. Notably, 124 DE miRNAs targeted 203 differentially expressed epigenetic regulators. Developing Norway spruce embryos possess a more complex sRNA structure than that reported for somatic tissues. A variety of the predicted miRNAs showed distinct EpI temperature dependent expression patterns. These putative EpI miRNAs target spruce genes with a wide range of functions, including genes known to be involved in epigenetic regulation, which in turn could provide a feedback process leading to the formation of epigenetic marks. We suggest that TIR, NBS and LRR domain containing proteins could fulfill more general functions for signal transduction from external environmental stimuli and conversion them into molecular response. Fine-tuning of the miRNA production likely participates in both developmental regulation and epigenetic memory formation in Norway spruce.
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Carneros E, Yakovlev I, Viejo M, Olsen JE, Fossdal CG. The epigenetic memory of temperature during embryogenesis modifies the expression of bud burst-related genes in Norway spruce epitypes. PLANTA 2017; 246:553-566. [PMID: 28577177 PMCID: PMC5561168 DOI: 10.1007/s00425-017-2713-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/23/2017] [Indexed: 05/05/2023]
Abstract
Epigenetic memory affects the timing of bud burst phenology and the expression of bud burst-related genes in genetically identical Norway spruce epitypes in a manner usually associated with ecotypes. In Norway spruce, a temperature-dependent epigenetic memory established during embryogenesis affects the timing of bud burst and bud set in a reproducible and predictable manner. We hypothesize that the clinal variation in these phenological traits, which is associated with adaptation to growth under frost-free conditions, has an epigenetic component. In Norway spruce, dehydrins (DHNs) have been associated with extreme frost tolerance. DHN transcript levels decrease gradually prior to flushing, a time when trees are highly sensitive to frost. Furthermore, EARLY BUD BREAK 1 genes (EBB1) and the FT-TFL1-LIKE 2-gene (PaFTL2) were previously suggested to be implied in control of bud phenology. Here we report an analysis of transcript levels of 12 DHNs, 3 EBB1 genes and FTL2 in epitypes of the same genotype generated at different epitype-inducing temperatures, before and during spring bud burst. Earlier flushing of epitypes originating from embryos developed at 18 °C as compared to 28 °C, was associated with differential expression of these genes between epitypes and between buds and last year's needles. The majority of these genes showed significantly different expressions between epitypes in at least one time point. The general trend in DHN expression pattern in buds showed the expected reduction in transcript levels when approaching flushing, whereas, surprisingly, transcript levels peaked later in needles, mainly at the moment of bud burst. Collectively, our results demonstrate that the epigenetic memory of temperature during embryogenesis affects bud burst phenology and expression of the bud burst-related DHN, EBB1 and FTL2 genes in genetically identical Norway spruce epitypes.
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Affiliation(s)
- Elena Carneros
- Norwegian Institute of Bioeconomy Research, 1431, Ås, Norway
- Department of Life Sciences, University of Alcalá, Ctra. de Barcelona km 33.600, 28805, Alcalá De Henares, Madrid, Spain
| | - Igor Yakovlev
- Norwegian Institute of Bioeconomy Research, 1431, Ås, Norway
| | - Marcos Viejo
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jorunn E Olsen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432, Ås, Norway
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Tikhenko N, Rutten T, Senula A, Rubtsova M, Keller ERJ, Börner A. The changes in the reproductive barrier between hexaploid wheat (Triticum aestivum L.) and rye (Secale cereale L.): different states lead to different fates. PLANTA 2017; 246:377-388. [PMID: 28424873 DOI: 10.1007/s00425-017-2694-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
The changes in the reproductive barrier between hexaploid wheat ( Triticum aestivum L.) and rye ( Secale cereale L.) can be induced using in situ embryo rescue of abnormal embryos, yielding stable fertile amphidiploid plants. In intergeneric crosses between hexaploid wheat (Triticum aestivum L.) and rye (Secale cereale L.), postzygotic barriers may occur at different stages of hybrid development. One such mechanism is embryo lethality, which is genetically determined by the interaction and expression of two incompatible genes in wheat (Eml-A1) and rye (Eml-R1). Using in vitro culture methods as stressors, we overcame this hybrid lethality. Normal and abnormal embryos were observed to build embryogenic calli and produce regenerated plantlets in a similar manner. The high regenerative capacity of the abnormal embryos led us to conclude that the reproductive barrier in these intergeneric hybrids may have an epigenetic origin that can be easily overcome by culturing immature embryos via callus induction. After colchicine treatment during callus culture, amphidiploid plants were obtained. However, most of these plants did not produce seeds, due mainly to sterility of the pollen but also of the embryo sacs. These findings demonstrate that hybrid sterility affects both male and female gametophytes in plants obtained from abnormal embryos. The key roles of double fertilization and stress factors in the implementation of the apical meristem formation program in embryos from incompatible intergeneric crosses between hexaploid wheat and rye during in vitro culture are discussed. We also propose a hypothetical model for a wheat-rye lethality system involving differential expression of incompatible wheat Eml-A1 and rye Eml-R1b alleles in an identical genetic background.
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Affiliation(s)
- Natalia Tikhenko
- SPb Branch Vavilov Institute of General Genetics, RAS, 199034, St. Petersburg, Russia
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Angelika Senula
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Myroslava Rubtsova
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - E R Joachim Keller
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany.
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Xia Y, Jing D, Kong L, Zhang J, OuYang F, Zhang H, Wang J, Zhang S. Global Lysine Acetylome Analysis of Desiccated Somatic Embryos of Picea asperata. FRONTIERS IN PLANT SCIENCE 2016; 7:1927. [PMID: 28066480 PMCID: PMC5179564 DOI: 10.3389/fpls.2016.01927] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/05/2016] [Indexed: 05/22/2023]
Abstract
Partial desiccation treatment (PDT) promotes the germination capacity of conifer somatic embryos. Lysine acetylation (LysAc) is a dynamic and reversible post-translational modification that plays a key role in many biological processes including metabolic pathways and stress response. To investigate the functional impact of LysAc in the response of Picea asperata somatic embryos to PDT, we performed a global lysine acetylome analysis. Here, combining antibody-based affinity enrichment and high-resolution mass spectrometry, we identified and validated 1079 acetylation sites in 556 acetylated proteins from P. asperata somatic embryos during PDT. These data represent a novel large-scale dataset of lysine-acetylated proteins from the conifer family. Intensive bioinformatics analysis of the Gene Ontology of molecular functions demonstrated that lysine-acetylated proteins were mainly associated with binding, catalytic activities, and structural molecular activities. Functional characterization of the acetylated proteins revealed that in the desiccated somatic embryos, LysAc is mainly involved in the response to stress and central metabolism. Accordingly, the majority of these interacting proteins were also highly enriched in ribosome, proteasome, spliceosome, and carbon metabolism clusters. This work provides the most comprehensive profile of LysAc for a coniferous species obtained to date and facilitates the systematic study of the physiological role of LysAc in desiccated somatic embryos of P. asperata.
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Affiliation(s)
- Yan Xia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Danlong Jing
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Lisheng Kong
- Centre for Forest Biology, Department of Biology, University of VictoriaVictoria, BC, Canada
| | - Jianwei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Fangqun OuYang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
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Abstract
DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.
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