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Paul AL, Haveman N, Califar B, Ferl RJ. Epigenomic Regulators Elongator Complex Subunit 2 and Methyltransferase 1 Differentially Condition the Spaceflight Response in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:691790. [PMID: 34589093 PMCID: PMC8475764 DOI: 10.3389/fpls.2021.691790] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Background: Plants subjected to the novel environment of spaceflight show transcriptomic changes that resemble aspects of several terrestrial abiotic stress responses. Under investigation here is whether epigenetic modulations, similar to those that occur in terrestrial stress responses, have a functional role in spaceflight physiological adaptation. The Advanced Plant Experiment-04 - Epigenetic Expression experiment examined the role of cytosine methylation in spaceflight adaptation. The experiment was conducted onboard the International Space Station, and evaluated the spaceflight-altered, genome-wide methylation profiles of two methylation-regulating gene mutants [methyltransferase 1 (met1-7) and elongator complex subunit 2 (elp2-5)] along with a wild-type Col-0 control. Results: The elp2-5 plants suffered in their physiological adaptation to spaceflight in that their roots failed to extend away from the seed and the overall development of the plants was greatly impaired in space. The met1-7 plants suffered less, with their morphology affected by spaceflight in a manner similar to that of the Col-0 controls. The differentially expressed genes (DEGs) in spaceflight were dramatically different in the elp2-5 and met1-7 plants compared to Col-0, indicating that the disruptions in these mutants resulted in a reprogramming of their spaceflight responses, especially in elp2-5. Many of the genes comprising the spaceflight transcriptome of each genotype were differentially methylated in spaceflight. In Col-0 the majority of the DEGs were representative of the now familiar spaceflight response, which includes genes associated with cell wall remodeling, pathogen responses and ROS signaling. However, the spaceflight transcriptomes of met1-7 and elp2-5 each presented patterns of DEGs that are almost completely different than Col-0, and to each other. Further, the DEGs of the mutant genotypes suggest a more severe spaceflight stress response in the mutants, particularly in elp2-5. Conclusion: Arabidopsis physiological adaptation to spaceflight results in differential DNA methylation in an organ-specific manner. Disruption of Met1 methyltransferase function does not dramatically affect spaceflight growth or morphology, yet met1-7 reprograms the spaceflight transcriptomic response in a unique manner. Disruption of elp2-5 results in poor development in spaceflight grown plants, together with a diminished, dramatically reprogrammed transcriptomic response.
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Affiliation(s)
- Anna-Lisa Paul
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Natasha Haveman
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Brandon Califar
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Robert J. Ferl
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- Office of Research, University of Florida, Gainesville, FL, United States
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Corbin KR, Bolt B, Rodríguez López CM. Breeding for Beneficial Microbial Communities Using Epigenomics. Front Microbiol 2020; 11:937. [PMID: 32477316 PMCID: PMC7242621 DOI: 10.3389/fmicb.2020.00937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/20/2020] [Indexed: 02/03/2023] Open
Affiliation(s)
- Kendall R Corbin
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States.,Biosystems and Agricultural Engineering, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Bridget Bolt
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Carlos M Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
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Recurrent Water Deficit and Epigenetic Memory in Medicago sativa L. Varieties. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10093110] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Global DNA methylation changes in response to recurrent drought stress were investigated in two common Greek Medicago sativa L. varieties (Lamia and Chaironia-Institute of Ιndustrial and Forage Crops). The water deficit was implemented in two phases. At the end of the first phase, which lasted for 60 days, the plants were cut at the height of 5 cm and were watered regularly for two months before being subjected to the second drought stress, which lasted for two weeks. Finally, the following groups of plants were formed: CC (controls both in phase I and phase II), CD2 (Controls in phase I, experiencing drought in phase II), and D1D2 (were subjected to drought in both phase I and phase II). At the end of phase II, samples were taken for global DNA methylation analysis with the Methylation Sensitive Amplification Polymorphism (MSAP) method, and all plants were harvested in order to measure the fresh and dry weight of roots and shoots. The variety Lamia responded better, especially the D1D2 group, compared to Chaironia in terms of root and shoot dry weight. Additionally, the shoots of Lamia had a constant water status for CD2 and D1D2 group of plants. According to DNA methylation analysis by the MSAP method, Lamia had lower total DNA methylation percentage after the second drought episode (D1D2) as compared to the plants CD2 that had experienced only one drought episode. On the other hand, the total DNA methylation percentage of Chaironia was almost the same in plants grown under recurrent drought stress conditions compared to control plants. In conclusion, the decrease of DNA methylation of Lamia stressed plants probably indicates the existence of an epigenetic mechanism that may render drought tolerance.
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Konate M, Wilkinson MJ, Taylor J, Scott ES, Berger B, Rodriguez Lopez CM. Greenhouse Spatial Effects Detected in the Barley ( Hordeum vulgare L.) Epigenome Underlie Stochasticity of DNA Methylation. FRONTIERS IN PLANT SCIENCE 2020; 11:553907. [PMID: 33013971 PMCID: PMC7511590 DOI: 10.3389/fpls.2020.553907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/24/2020] [Indexed: 05/10/2023]
Abstract
Environmental cues are known to alter the methylation profile of genomic DNA, and thereby change the expression of some genes. A proportion of such modifications may become adaptive by adjusting expression of stress response genes but others have been shown to be highly stochastic, even under controlled conditions. The influence of environmental flux on plants adds an additional layer of complexity that has potential to confound attempts to interpret interactions between environment, methylome, and plant form. We therefore adopt a positional and longitudinal approach to study progressive changes to barley DNA methylation patterns in response to salt exposure during development under greenhouse conditions. Methylation-sensitive amplified polymorphism (MSAP) and phenotypic analyses of nine diverse barley varieties were grown in a randomized plot design, under two salt treatments (0 and 75 mM NaCl). Combining environmental, phenotypic and epigenetic data analyses, we show that at least part of the epigenetic variability, previously described as stochastic, is linked to environmental micro-variations during plant growth. Additionally, we show that differences in methylation increase with time of exposure to micro-variations in environment. We propose that subsequent epigenetic studies take into account microclimate-induced epigenetic variability.
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Affiliation(s)
- Moumouni Konate
- Institut de l'Environnement et de Recherche Agricole (INERA), DRREA-Ouest, Bobo Dioulasso, Burkina Faso
| | - Michael J. Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth, United Kingdom
- *Correspondence: Carlos Marcelino Rodriguez Lopez, ; Michael J. Wilkinson,
| | - Julian Taylor
- Biometry Hub, School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Eileen S. Scott
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Bettina Berger
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Carlos Marcelino Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
- *Correspondence: Carlos Marcelino Rodriguez Lopez, ; Michael J. Wilkinson,
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Zhou M, Sng NJ, LeFrois CE, Paul AL, Ferl RJ. Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana. BMC Genomics 2019; 20:205. [PMID: 30866818 PMCID: PMC6416986 DOI: 10.1186/s12864-019-5554-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/21/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Plants adapted to diverse environments on Earth throughout their evolutionary history, and developed mechanisms to thrive in a variety of terrestrial habitats. When plants are grown in the novel environment of spaceflight aboard the International Space Station (ISS), an environment completely outside their evolutionary history, they respond with unique alterations to their gene expression profile. Identifying the genes important for physiological adaptation to spaceflight and dissecting the biological processes and pathways engaged by plants during spaceflight has helped reveal spaceflight adaptation, and has furthered understanding of terrestrial growth processes. However, the underlying regulatory mechanisms responsible for these changes in gene expression patterns are just beginning to be explored. Epigenetic modifications, such as DNA methylation at position five in cytosine, has been shown to play a role in the physiological adaptation to adverse terrestrial environments, and may play a role in spaceflight as well. RESULTS Whole Genome Bisulfite Sequencing of DNA of Arabidopsis grown on the ISS from seed revealed organ-specific patterns of differential methylation compared to ground controls. The overall levels of methylation in CG, CHG, and CHH contexts were similar between flight and ground DNA, however, thousands of specifically differentially methylated cytosines were discovered, and there were clear organ-specific differences in methylation patterns. Spaceflight leaves had higher methylation levels in CHG and CHH contexts within protein-coding genes in spaceflight; about a fifth of the leaf genes were also differentially regulated in spaceflight, almost half of which were associated with reactive oxygen signaling. CONCLUSIONS The physiological adaptation of plants to spaceflight is likely nuanced by epigenomic modification. This is the first examination of differential genomic methylation from plants grown completely in the spaceflight environment of the ISS in plant growth hardware developed for informing exploration life support strategies. Yet even in this optimized plant habitat, plants respond as if stressed. These data suggest that gene expression associated with physiological adaptation to spaceflight is regulated in part by methylation strategies similar to those engaged with familiar terrestrial stress responses. The differential methylation maps generated here provide a useful reference for elucidating the layers of regulation of spaceflight responses.
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Affiliation(s)
- Mingqi Zhou
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Natasha J. Sng
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Collin E. LeFrois
- 0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Anna-Lisa Paul
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Robert J. Ferl
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Interdisciplinary Center for Biotechnology, University of Florida, Gainesville, FL USA
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Bräutigam K, Cronk Q. DNA Methylation and the Evolution of Developmental Complexity in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1447. [PMID: 30349550 PMCID: PMC6186995 DOI: 10.3389/fpls.2018.01447] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/12/2018] [Indexed: 05/20/2023]
Abstract
All land plants so far examined use DNA methylation to silence transposons (TEs). DNA methylation therefore appears to have been co-opted in evolution from an original function in TE management to a developmental function (gene regulation) in both phenotypic plasticity and in normal development. The significance of DNA methylation to the evolution of developmental complexity in plants lies in its role in the management of developmental pathways. As such it is more important in fine tuning the presence, absence, and placement of organs rather than having a central role in the evolution of new organs. Nevertheless, its importance should not be underestimated as it contributes considerably to the range of phenotypic expression and complexity available to plants: the subject of the emerging field of epi-evodevo. Furthermore, changes in DNA methylation can function as a "soft" mutation that may be important in the early stages of major evolutionary novelty.
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Affiliation(s)
- Katharina Bräutigam
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Quentin Cronk
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Quentin Cronk,
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Singh P, Dave A, Vaistij FE, Worrall D, Holroyd GH, Wells JG, Kaminski F, Graham IA, Roberts MR. Jasmonic acid-dependent regulation of seed dormancy following maternal herbivory in Arabidopsis. THE NEW PHYTOLOGIST 2017; 214:1702-1711. [PMID: 28332706 DOI: 10.1111/nph.14525] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/14/2017] [Indexed: 05/11/2023]
Abstract
Maternal experience of abiotic environmental factors such as temperature and light are well known to control seed dormancy in many plant species. Maternal biotic stress alters offspring defence phenotypes, but whether it also affects seed dormancy remains unexplored. We exposed Arabidopsis thaliana plants to herbivory and investigated plasticity in germination and defence phenotypes in their offspring, along with the roles of phytohormone signalling in regulating maternal effects. Maternal herbivory resulted in the accumulation of jasmonic acid-isoleucine and loss of dormancy in seeds of stressed plants. Dormancy was also reduced by engineering seed-specific accumulation of jasmonic acid in transgenic plants. Loss of dormancy was dependent on an intact jasmonate signalling pathway and was associated with increased gibberellin content and reduced abscisic acid sensitivity during germination. Altered dormancy was only observed in the first generation following herbivory, whereas defence priming was maintained for at least two generations. Herbivory generates a jasmonic acid-dependent reduction in seed dormancy, mediated by alteration of gibberellin and abscisic acid signalling. This is a direct maternal effect, operating independently from transgenerational herbivore resistance priming.
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Affiliation(s)
- Prashant Singh
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Anuja Dave
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Fabian E Vaistij
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Dawn Worrall
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Geoff H Holroyd
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Jonathan G Wells
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Filip Kaminski
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Ian A Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Michael R Roberts
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
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Xie H, Konate M, Sai N, Tesfamicael KG, Cavagnaro T, Gilliham M, Breen J, Metcalfe A, Stephen JR, De Bei R, Collins C, Lopez CMR. Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine ( Vitis vinifera cv. Shiraz). FRONTIERS IN PLANT SCIENCE 2017; 8:1860. [PMID: 29163587 PMCID: PMC5670326 DOI: 10.3389/fpls.2017.01860] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/11/2017] [Indexed: 05/21/2023]
Abstract
Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant's phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia. Methylation sensitive amplified polymorphisms (MSAPs) were used to obtain global patterns of DNA methylation. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Pairwise epigenetic distances between vineyards indicate that the main contributor (23-24%) to the detected variability is associated to the distribution of the vineyards on the N-S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive genotyping by sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique gene ontology terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.
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Affiliation(s)
- Huahan Xie
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Moumouni Konate
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Na Sai
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - Kiflu G. Tesfamicael
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Timothy Cavagnaro
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Gilliham
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - James Breen
- Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Andrew Metcalfe
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - John R. Stephen
- Plant Genomics Centre, Australian Genome Research Facility Ltd., Adelaide, SA, Australia
| | - Roberta De Bei
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Cassandra Collins
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Carlos M. R. Lopez
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Carlos M. R. Lopez,
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Consuegra S, Rodríguez López CM. Epigenetic-induced alterations in sex-ratios in response to climate change: An epigenetic trap? Bioessays 2016; 38:950-8. [PMID: 27548838 DOI: 10.1002/bies.201600058] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We hypothesize that under the predicted scenario of climate change epigenetically mediated environmental sex determination could become an epigenetic trap. Epigenetically regulated environmental sex determination is a mechanism by which species can modulate their breeding strategies to accommodate environmental change. Growing evidence suggests that epigenetic mechanisms may play a key role in phenotypic plasticity and in the rapid adaptation of species to environmental change, through the capacity of organisms to maintain a non-genetic plastic memory of the environmental and ecological conditions experienced by their parents. However, inherited epigenetic variation could also be maladaptive, becoming an epigenetic trap. This is because environmental sex determination can alter sex ratios by increasing the survival of one of the sexes at the expense of negative fitness consequences for the other, which could lead not only to the collapse of natural populations, but also have an impact in farmed animal and plant species.
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Affiliation(s)
- Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Swansea, UK.
| | - Carlos M Rodríguez López
- Environmental Epigenetics and Genetics Group, School of Agriculture, University of Adelaide, Glen Osmond, South Australia, Australia.
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Rodríguez López CM, Wilkinson MJ. Epi-fingerprinting and epi-interventions for improved crop production and food quality. FRONTIERS IN PLANT SCIENCE 2015; 6:397. [PMID: 26097484 PMCID: PMC4456566 DOI: 10.3389/fpls.2015.00397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/18/2015] [Indexed: 05/05/2023]
Abstract
Increasing crop production at a time of rapid climate change represents the greatest challenge facing contemporary agricultural research. Our understanding of the genetic control of yield derives from controlled field experiments designed to minimize environmental variance. In spite of these efforts there is substantial residual variability among plants attributable to Genotype × Environment interactions. Recent advances in the field of epigenetics have revealed a plethora of gene control mechanisms that could account for much of this unassigned variation. These systems act as a regulatory interface between the perception of the environment and associated alterations in gene expression. Direct intervention of epigenetic control systems hold the enticing promise of creating new sources of variability that could enhance crop performance. Equally, understanding the relationship between various epigenetic states and responses of the crop to specific aspects of the growing environment (epigenetic fingerprinting) could allow for a more tailored approach to plant agronomy. In this review, we explore the many ways in which epigenetic interventions and epigenetic fingerprinting can be deployed for the improvement of crop production and quality.
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Affiliation(s)
- Carlos M. Rodríguez López
- *Correspondence: Carlos M. Rodríguez López, Plant Research Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, Adelaide, SA 5064, Australia
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Tricker PJ. Transgenerational inheritance or resetting of stress-induced epigenetic modifications: two sides of the same coin. FRONTIERS IN PLANT SCIENCE 2015; 6:699. [PMID: 26442015 PMCID: PMC4561384 DOI: 10.3389/fpls.2015.00699] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/21/2015] [Indexed: 05/06/2023]
Abstract
The transgenerational inheritance of stress-induced epigenetic modifications is still controversial. Despite several examples of defense "priming" and induced genetic rearrangements, the involvement and persistence of transgenerational epigenetic modifications is not known to be general. Here I argue that non-transmission of epigenetic marks through meiosis may be regarded as an epigenetic modification in itself, and that we should understand the implications for plant evolution in the context of both selection for and selection against transgenerational epigenetic memory. Recent data suggest that both epigenetic inheritance and resetting are mechanistically directed and targeted. Stress-induced epigenetic modifications may buffer against DNA sequence-based evolution to maintain plasticity, or may form part of plasticity's adaptive potential. To date we have tended to concentrate on the question of whether and for how long epigenetic memory persists. I argue that we should now re-direct our question to investigate the differences between where it persists and where it does not, to understand the higher order evolutionary methods in play and their contribution.
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Affiliation(s)
- Penny J. Tricker
- *Correspondence: Penny J. Tricker, Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Hartley Grove, Urrbrae, SA 5064, Australia,
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Kinoshita T, Seki M. Epigenetic memory for stress response and adaptation in plants. PLANT & CELL PHYSIOLOGY 2014; 55:1859-63. [PMID: 25298421 DOI: 10.1093/pcp/pcu125] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In contrast to the majority of animal species, plants are sessile organisms and are, therefore, constantly challenged by environmental perturbations. Over the past few decades, our knowledge of how plants perceive environmental stimuli has increased considerably, e.g. the mechanisms for transducing environmental stress stimuli into cellular signaling cascades and gene transcription networks. In addition, it has recently been shown that plants can remember past environmental events and can use these memories to aid responses when these events recur. In this mini review, we focus on recent progress in determination of the epigenetic mechanisms used by plants under various environmental stresses. Epigenetic mechanisms are now known to play a vital role in the control of gene expression through small RNAs, histone modifications and DNA methylation. These are inherited through mitotic cell divisions and, in some cases, can be transmitted to the next generation. They therefore offer a possible mechanism for stress memories in plants. Recent studies have yielded evidence indicating that epigenetic mechanisms are indeed essential for stress memories and adaptation in plants.
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Affiliation(s)
- Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa, 244-0813 Japan
| | - Motoaki Seki
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa, 244-0813 Japan Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012 Japan
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