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Fan Y, Sun C, Yan K, Li P, Hein I, Gilroy EM, Kear P, Bi Z, Yao P, Liu Z, Liu Y, Bai J. Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1400. [PMID: 38794470 PMCID: PMC11125032 DOI: 10.3390/plants13101400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
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Affiliation(s)
- Youfang Fan
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Pengcheng Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Ingo Hein
- The James Hutton Institute, Dundee DD2 5DA, UK; (I.H.); (E.M.G.)
| | | | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing 102199, China;
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
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Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
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Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
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Yang C, Gao Z, Wang Y, Zhang Q, Bai M, Yang H, Guo J, Zhang Y. Genome-wide DNA methylation analysis reveals layer-specific methylation patterns in deer antler tissue. Gene 2023; 884:147744. [PMID: 37640118 DOI: 10.1016/j.gene.2023.147744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/16/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
This paper explored using of deer antlers as a model for studying rapid growth and cartilage formation in mammals. The genes and regulatory mechanisms involved in antler chondrogenesis are poorly understood, however, previous research has suggested that DNA methylation played a key role in antler regeneration. By using fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP), this study measured DNA methylation levels in cartilage (CA) and reserve mesenchyme (RM) cells and tissues. Results showed that RM cells (RMCs) DNA methylation levels were significantly lower than those of CA, suggesting that DNA demethylation may be involved in antler fast cartilage differentiation. The study also identified 20 methylated fragments specific to RMCs or CA using the methylation-sensitive amplified polymorphism (MSAP) technique and confirmed these findings using southern blot analysis. The data provide the first experimental evidence of a link between epigenetic regulation and rapid cartilage differentiation in antlers.
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Affiliation(s)
- Chun Yang
- College of Basic Medicine, Beihua University, Jilin, PR China.
| | - Zizheng Gao
- College of Basic Medicine, Beihua University, Jilin, PR China
| | - Yukun Wang
- School of Stomatology, Beihua University, Jilin, PR China
| | - Qi Zhang
- School of Public Health, Beihua University, Jilin, PR China
| | - Muran Bai
- School of Stomatology, Beihua University, Jilin, PR China
| | - Huiran Yang
- School of Public Health, Beihua University, Jilin, PR China
| | - Junqi Guo
- The Third Clinical Medicine Affiliated to Changchun University of Chinese Medicine, Changchun, PR China.
| | - Yan Zhang
- School of Public Health, Beihua University, Jilin, PR China.
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Wang H, Wang L, Yang M, Zhang N, Li J, Wang Y, Wang Y, Wang X, Ruan Y, Xu S. Growth and DNA Methylation Alteration in Rice ( Oryza sativa L.) in Response to Ozone Stress. Genes (Basel) 2023; 14:1888. [PMID: 37895237 PMCID: PMC10606928 DOI: 10.3390/genes14101888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
With the development of urban industrialization, the increasing ozone concentration (O3) at ground level stresses on the survival of plants. Plants have to adapt to ozone stress. DNA methylation is crucial for a rapid response to abiotic stress in plants. Little information is known regarding the epigenetic response of DNA methylation of plants to O3 stress. This study is designed to explore the epigenetic mechanism and identify a possible core modification of DNA methylation or genes in the plant, in response to O3 stress. We investigated the agronomic traits and genome-wide DNA methylation variations of the Japonica rice cultivar Nipponbare in response to O3 stress at three high concentrations (80, 160, and 200 nmol·mol-1), simulated using open-top chambers (OTC). The flag leaf length, panicle length, and hundred-grain weight of rice showed beneficial effects at 80 nmol·mol-1 O3 and an inhibitory effect at both 160 and 200 nmol·mol-1 O3. The methylation-sensitive amplified polymorphism results showed that the O3-induced genome-wide methylation alterations account for 14.72-15.18% at three different concentrations. Our results demonstrated that methylation and demethylation alteration sites were activated throughout the O3 stress, mainly at CNG sites. By recovering and sequencing bands with methylation alteration, ten stress-related differentially amplified sequences, widely present on different chromosomes, were obtained. Our findings show that DNA methylation may be an active and rapid epigenetic response to ozone stress. These results can provide us with a theoretical basis and a reference to look for more hereditary information about the molecular mechanism of plant resistance to O3 pollution.
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Affiliation(s)
- Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Long Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang 110036, China
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
| | - Mengke Yang
- Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Ning Zhang
- Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Jiazhen Li
- Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Yuqian Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Yue Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Yanan Ruan
- Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Sheng Xu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Shenyang 110016, China
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Kumar M, Rani K. Epigenomics in stress tolerance of plants under the climate change. Mol Biol Rep 2023:10.1007/s11033-023-08539-6. [PMID: 37294468 DOI: 10.1007/s11033-023-08539-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO2, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence. EPIGENETIC MECHANISMS AND MARKS The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles. EPIGENOMICS IN CROP IMPROVEMENT To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding. CONCLUSIONS AND FUTURE PROSPECTUS A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.
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Affiliation(s)
- Mithlesh Kumar
- AICRN On Potential Crops, ARS Mandor, Agriculture University, Jodhpur, 342 304, Rajasthan, India.
| | - Kirti Rani
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Jodhpur, 342 003, Rajasthan, India
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Wang X, Du L, Wang W, Zhang Z, Wu Y, Wang Y. Functional identification of ZDS gene in apple ( Malus halliana) and demonstration of it's role in improving saline-alkali stress tolerance. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:799-813. [PMID: 37520810 PMCID: PMC10382441 DOI: 10.1007/s12298-023-01333-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Carotenoids are powerful antioxidants that mediate transfer of electrons, directly affect abiotic stress responses in plants through regulating activity of antioxidant enzymes. ζ-Carotene desaturase (ZDS) is a key enzyme in carotenoid biosynthesis pathway, which can catalyze ζ-carotene to form lycopene to regulate carotenoid biosynthesis and accumulation. However, the mechanism of its regulation of saline-alkali stress remains unclear. In this research, based on transcriptomic analysis of Malus halliana with a apple rootstock, we screened out ZDS gene (LOC103451012), with significantly high expression by saline-alkali stress, whose expression in the leaves was 10.8-fold than that of the control (0 h) under 48 h of stress. Subsequently, the MhZDS gene was isolated from M. halliana, and transgenic Arabidopsis thaliana, tobacco, and apple calli were successfully obtained through agrobacterium-mediated genetic transformation. We found that overexpression of MhZDS enhanced the tolerance of A. thaliana, tobacco and apple calli under saline-alkali stress and caused a variety of physiological and biochemical changes: compared with wild-type, transgenic plants grew better under saline stress and MhZDS-OE lines showed higher chlorophyll content, POD, SOD, CAT activities and proline content, lower electrical conductivity and MDA content. These results indicate that MhZDS plays an important role in plant resistance to saline-alkali stress, providing excellent resistance genes for the regulatory network of salinity stress response in apples and provide a theoretical basis for the breeding of apple varieties with strong saline-alkali resistance. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01333-5.
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Affiliation(s)
- Xiu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Lei Du
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Wanxia Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Zhongxing Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Yuxia Wu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Yanxiu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
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Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. FRONTIERS IN PLANT SCIENCE 2023; 14:1181039. [PMID: 37389288 PMCID: PMC10306282 DOI: 10.3389/fpls.2023.1181039] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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Affiliation(s)
- Dolores Rita Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Biology Department, Ġ.F.Abela Junior College, Msida, Malta
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Evangelia Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Miroslav Baranek
- Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Elena Carneros
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Aleksandra Radanovic
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jean-Paul Ebejer
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Francesco Guarino
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vera Inácio
- BioISI – BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Michal Lieberman-Lazarovich
- Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel
| | | | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d’Orléans, Orléans, France
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Pilar S. Testillano
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Dimitar Todorov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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8
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Liu J, Wu Y, Dong G, Zhu G, Zhou G. Progress of Research on the Physiology and Molecular Regulation of Sorghum Growth under Salt Stress by Gibberellin. Int J Mol Sci 2023; 24:ijms24076777. [PMID: 37047750 PMCID: PMC10094886 DOI: 10.3390/ijms24076777] [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: 03/20/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023] Open
Abstract
Plant growth often encounters diverse abiotic stresses. As a global resource-based ecological problem, salinity is widely distributed and one of the major abiotic stresses affecting crop yields worldwide. Sorghum, a cereal crop with medium salt tolerance and great value for the development and utilization of salted soils, is an important source of food, brewing, energy, and forage production. However, in soils with high salt concentrations, sorghum experiences low emergence and suppressed metabolism. It has been demonstrated that the effects of salt stress on germination and seedling growth can be effectively mitigated to a certain extent by the exogenous amendment of hormonal gibberellin (GA). At present, most of the studies on sorghum salt tolerance at home and abroad focus on morphological and physiological levels, including the transcriptome analysis of the exogenous hormone on sorghum salt stress tolerance, the salt tolerance metabolism pathway, and the mining of key salt tolerance regulation genes. The high-throughput sequencing technology is increasingly widely used in the study of crop resistance, which is of great significance to the study of plant resistance gene excavation and mechanism. In this study, we aimed to review the effects of the exogenous hormone GA on leaf morphological traits of sorghum seedlings and further analyze the physiological response of sorghum seedling leaves and the regulation of sorghum growth and development. This review not only focuses on the role of GA but also explores the signal transduction pathways of GA and the performance of their responsive genes under salt stress, thus helping to further clarify the mechanism of regulating growth and production under salt stress. This will serve as a reference for the molecular discovery of key genes related to salt stress and the development of new sorghum varieties.
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Affiliation(s)
- Jiao Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yanqing Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guichun Dong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guanglong Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guisheng Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
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9
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Tobiasz-Salach R, Mazurek M, Jacek B. Physiological, Biochemical, and Epigenetic Reaction of Maize ( Zea mays L.) to Cultivation in Conditions of Varying Soil Salinity and Foliar Application of Silicon. Int J Mol Sci 2023; 24:ijms24021141. [PMID: 36674673 PMCID: PMC9861071 DOI: 10.3390/ijms24021141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Soil salinity is one of the basic factors causing physiological, biochemical and epigenetic changes in plants. The negative effects of salt in the soil environment can be reduced by foliar application of silicon (Si). The study showed some positive effects of Si on maize plants (Zea mays L.) grown in various salinity conditions. At high soil salinity (300 and 400 mM NaCl), higher CCI content was demonstrated following the application of 0.2 and 0.3% Si. Chlorophyll fluorescence parameters (PI, FV/F0, Fv/Fm and RC/ABS) were higher after spraying at 0.3 and 0.4% Si, and plant gas exchange (Ci, PN, gs, E) was higher after spraying from 0.1 to 0.4% Si. Soil salinity determined by the level of chlorophyll a and b, and carotenoid pigments caused the accumulation of free proline in plant leaves. To detect changes in DNA methylation under salt stress and in combination with Si treatment of maize plants, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation level within the 3'CCGG 5' sequence varied among groups of plants differentially treated. Results obtained indicated alterations of DNA methylation in plants as a response to salt stress, and the effects of NaCl + Si were dose-dependent. These changes may suggest mechanisms for plant adaptation under salt stress.
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Affiliation(s)
- Renata Tobiasz-Salach
- Department of Crop Production, University of Rzeszow, Zelwerowicza 4, 35-601 Rzeszow, Poland
- Correspondence:
| | - Marzena Mazurek
- Department of Physiology and Plant Biotechnology, University of Rzeszow, Ćwiklińskiej 2, 35-601 Rzeszow, Poland
| | - Beata Jacek
- Department of Physiology and Plant Biotechnology, University of Rzeszow, Ćwiklińskiej 2, 35-601 Rzeszow, Poland
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10
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Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution. Int J Mol Sci 2022; 23:ijms23158299. [PMID: 35955429 PMCID: PMC9368846 DOI: 10.3390/ijms23158299] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 01/06/2023] Open
Abstract
DNA methylation is an epigenetic modification of the genome involved in the regulation of gene expression and modulation of chromatin structure. Plant genomes are widely methylated, and the methylation generally occurs on the cytosine bases through the activity of specific enzymes called DNA methyltransferases. On the other hand, methylated DNA can also undergo demethylation through the action of demethylases. The methylation landscape is finely tuned and assumes a pivotal role in plant development and evolution. This review illustrates different molecular aspects of DNA methylation and some plant physiological processes influenced by this epigenetic modification in model species, crops, and ornamental plants such as orchids. In addition, this review aims to describe the relationship between the changes in plant DNA methylation levels and the response to biotic and abiotic stress. Finally, we discuss the possible evolutionary implications and biotechnological applications of DNA methylation.
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11
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Miao Y, Cong W, Mu J, Fu T, Zhuang T, Yan Y, Kang Y, Yu L, Zhao W, Li H, Lv Y, Zhang J, Rustgi S, Liu B, Ou X. Various potentially toxic element tolerances in different rice genotypes correlate with distinct physiological responses and alterations in DNA methylation. CHEMOSPHERE 2022; 292:133462. [PMID: 34973255 DOI: 10.1016/j.chemosphere.2021.133462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/12/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Potentially toxic elements (PTEs) are harmful to plant growth and reduce crop productivity. In this work, we studied three rice genotypes (T-35, RZ-1, and RZ-2) to quantify the diverse PTE effects and tolerances by examining morphology, physiology, and DNA methylation patterns. Morphological results showed that T-35 exhibits the highest tolerance to all studied PTE stressors (Cu, Cd, Cr). Physiological responses under PTE stresses confirmed earlier findings, where T-35 showed a higher potassium (K+) content and more peroxidase (POD) accumulation in the roots than the other two rice genotypes. The differences in PTE tolerance levels observed among the three rice genotypes were also associated with variations in the heavy metal transportation (HMT) gene expression level. Moreover, methylation-sensitive blotting analysis of the selected genes showed that the DNA methylation changes occurring due to PTE treatments are mainly CHG hypomethylation in T-35 but hypermethylation in RZ-1 and RZ-2. Our results demonstrate a tight relationship among physiological response, expression levels of the HMT genes, and DNA methylation pattern under PTEs stresses. It is also indicated that plants use generic mechanisms to tolerate stresses; however, different genotypes employ different combinations of such tactics to confer tolerance, which results in diverse PTE stress tolerances. These findings shed light on the PTE stresses tolerance mechanism and help direct future breeding activities in rice.
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Affiliation(s)
- Yiling Miao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Weixuan Cong
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jingyao Mu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Tiansi Fu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Tingting Zhuang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China; Changchun Institute of Applied Chemistry Chinese Academy of Sciences, Changchun, 130024, China
| | - Yujia Yan
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Ying Kang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Lina Yu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Wenhao Zhao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Hebing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Yinhe Lv
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jiayu Zhang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC, 29506, USA.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China.
| | - Xiufang Ou
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China.
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12
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Tsaballa A, Sperdouli I, Avramidou EV, Ganopoulos I, Koukounaras A, Ntinas GK. Epigenetic and Physiological Responses to Varying Root-Zone Temperatures in Greenhouse Rocket. Genes (Basel) 2022; 13:364. [PMID: 35205409 PMCID: PMC8871717 DOI: 10.3390/genes13020364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Greenhouse production of baby leaf vegetables grown in hydroponic floating trays has become extremely popular in recent years. Rocket (Eruca sativa Mill.) can grow in temperatures varying between 10 and 20 °C; nevertheless, a root-zone temperature (RZT) range of 18-23 °C is considered optimal for high productivity, photosynthesis, and production of metabolites. Maintaining such temperatures in winter raises production costs and prevents sustainability. In this study, we tested the impact of lower RZT on plants' status and recorded their responses while providing energy for heating using photovoltaic solar panels. We used three hydroponic tanks for cultivation; a non-heated (control) tank (12 °C) and two heated tanks; a solar panel-powered one (16 °C) and a public grid-powered one (22 °C). Methylation-sensitive amplified polymorphisms (MSAP) analysis of global methylation profiles and chlorophyll fluorescence analysis were employed to assess methylation and physiology levels of rocket leaves. We found that there is demethylation at 16 °C RZT in comparison to 22 °C RZT. Reduction of temperature at 12 °C did not reduce methylation levels further but rather increased them. Furthermore, at 16 °C, the effective quantum yield of photosystem II (PSII) photochemistry (ΦPSII) was significantly higher, with a higher PSII electron transport rate (ETR) and a significantly decreased non-regulated energy loss (ΦΝO), suggesting a better light energy use by rocket plants with higher photosynthetic performance. ΦPSII was significantly negatively correlated with DNA methylation levels. Our results show that at 16 °C RZT, where plants grow efficiently without being affected by the cold, DNA methylation and photosynthesis apparatus systems are altered. These findings corroborate previous results where hydroponic production of rocket at RZT of 16 °C is accompanied by sufficient yield showing that rocket can effectively grow in suboptimal yet sustainable root-zone temperatures.
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Affiliation(s)
- Aphrodite Tsaballa
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO-Dimitra), Thermi, 57001 Thessaloniki, Greece; (I.S.); (I.G.); (G.K.N.)
| | - Ilektra Sperdouli
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO-Dimitra), Thermi, 57001 Thessaloniki, Greece; (I.S.); (I.G.); (G.K.N.)
| | - Evangelia V. Avramidou
- Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization (ELGO-Dimitra), Terma Alkmanos, Ilisia, 11528 Athens, Greece;
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO-Dimitra), Thermi, 57001 Thessaloniki, Greece; (I.S.); (I.G.); (G.K.N.)
| | - Athanasios Koukounaras
- Department of Horticulture, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Georgios K. Ntinas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO-Dimitra), Thermi, 57001 Thessaloniki, Greece; (I.S.); (I.G.); (G.K.N.)
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13
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Kourani M, Mohareb F, Rezwan FI, Anastasiadi M, Hammond JP. Genetic and Physiological Responses to Heat Stress in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:832147. [PMID: 35449889 PMCID: PMC9016328 DOI: 10.3389/fpls.2022.832147] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/04/2022] [Indexed: 05/07/2023]
Abstract
Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.
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Affiliation(s)
- Mariam Kourani
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Fady Mohareb
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
- *Correspondence: Fady Mohareb,
| | - Faisal I. Rezwan
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Maria Anastasiadi
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
- John P. Hammond,
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14
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Singh D, Chaudhary P, Taunk J, Kumar Singh C, Sharma S, Singh VJ, Singh D, Chinnusamy V, Yadav R, Pal M. Plant epigenomics for extenuation of abiotic stresses: challenges and future perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6836-6855. [PMID: 34302734 DOI: 10.1093/jxb/erab337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Climate change has escalated abiotic stresses, leading to adverse effects on plant growth and development, eventually having deleterious consequences on crop productivity. Environmental stresses induce epigenetic changes, namely cytosine DNA methylation and histone post-translational modifications, thus altering chromatin structure and gene expression. Stable epigenetic changes are inheritable across generations and this enables plants to adapt to environmental changes (epipriming). Hence, epigenomes serve as a good source of additional tier of variability for development of climate-smart crops. Epigenetic resources such as epialleles, epigenetic recombinant inbred lines (epiRILs), epigenetic quantitative trait loci (epiQTLs), and epigenetic hybrids (epihybrids) can be utilized in epibreeding for improving stress tolerance of crops. Epigenome engineering is also gaining momentum for developing sustainable epimarks associated with important agronomic traits. Different epigenome editing tools are available for creating, erasing, and reading such epigenetic codes in plant genomes. However, epigenome editing is still understudied in plants due to its complex nature. Epigenetic interventions such as epi-fingerprinting can be exploited in the near future for health and quality assessment of crops under stress conditions. Keeping in view the challenges and opportunities associated with this important technology, the present review intends to enhance understanding of stress-induced epigenetic changes in plants and its prospects for development of climate-ready crops.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Shristi Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Vikram Jeet Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajbir Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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15
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The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int J Mol Sci 2021; 22:ijms222111387. [PMID: 34768817 PMCID: PMC8583499 DOI: 10.3390/ijms222111387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.
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16
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Dalakouras A, Vlachostergios D. Epigenetic approaches to crop breeding: current status and perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5356-5371. [PMID: 34017985 DOI: 10.1093/jxb/erab227] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 05/10/2023]
Abstract
In order to tackle the cumulative adverse effects of global climate change, reduced farmland, and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued agronomical traits, but its potential is gradually being compromised by the menacing decline of genetic variation. Resorting to the epigenome as a source of variation could serve as a promising alternative. Here, we discuss current status of epigenetics-mediated crop breeding (epibreeding), highlight its advances and limitations, outline currently available methodologies, and propose novel RNA-based strategies to modify the epigenome in a gene-specific and transgene-free manner.
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Affiliation(s)
- Athanasios Dalakouras
- Institute of Industrial and Forage Crops, HAO-DEMETER, 41335 Larissa, Greece
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, 57001 Thessaloniki, Greece
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17
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Exploration of Epigenetics for Improvement of Drought and Other Stress Resistance in Crops: A Review. PLANTS 2021; 10:plants10061226. [PMID: 34208642 PMCID: PMC8235456 DOI: 10.3390/plants10061226] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 01/01/2023]
Abstract
Crop plants often have challenges of biotic and abiotic stresses, and they adapt sophisticated ways to acclimate and cope with these through the expression of specific genes. Changes in chromatin, histone, and DNA mostly serve the purpose of combating challenges and ensuring the survival of plants in stressful environments. Epigenetic changes, due to environmental stress, enable plants to remember a past stress event in order to deal with such challenges in the future. This heritable memory, called "plant stress memory", enables plants to respond against stresses in a better and efficient way, not only for the current plant in prevailing situations but also for future generations. Development of stress resistance in plants for increasing the yield potential and stability has always been a traditional objective of breeders for crop improvement through integrated breeding approaches. The application of epigenetics for improvements in complex traits in tetraploid and some other field crops has been unclear. An improved understanding of epigenetics and stress memory applications will contribute to the development of strategies to incorporate them into breeding for complex agronomic traits. The insight in the application of novel plant breeding techniques (NPBTs) has opened a new plethora of options among plant scientists to develop germplasms for stress tolerance. This review summarizes and discusses plant stress memory at the intergenerational and transgenerational levels, mechanisms involved in stress memory, exploitation of induced and natural epigenetic changes, and genome editing technologies with their future possible applications, in the breeding of crops for abiotic stress tolerance to increase the yield for zero hunger goals achievement on a sustainable basis in the changing climatic era.
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In Response to Abiotic Stress, DNA Methylation Confers EpiGenetic Changes in Plants. PLANTS 2021; 10:plants10061096. [PMID: 34070712 PMCID: PMC8227271 DOI: 10.3390/plants10061096] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023]
Abstract
Epigenetics involves the heritable changes in patterns of gene expression determined by developmental and abiotic stresses, i.e., drought, cold, salinity, trace metals, and heat. Gene expression is driven by changes in DNA bases, histone proteins, the biogenesis of ncRNA, and changes in the nucleotide sequence. To cope with abiotic stresses, plants adopt certain changes driven by a sophisticated biological system. DNA methylation is a primary mechanism for epigenetic variation, which can induce phenotypic alterations in plants under stress. Some of the stress-driven changes in plants are temporary, while some modifications may be stable and inheritable to the next generations to allow them to cope with such extreme stress challenges in the future. In this review, we discuss the pivotal role of epigenetically developed phenotypic characteristics in plants as an evolutionary process participating in adaptation and tolerance responses to abiotic and biotic stresses that alter their growth and development. We emphasize the molecular process underlying changes in DNA methylation, differential variation for different species, the roles of non-coding RNAs in epigenetic modification, techniques for studying DNA methylation, and its role in crop improvement in tolerance to abiotic stress (drought, salinity, and heat). We summarize DNA methylation as a significant future research priority for tailoring crops according to various challenging environmental issues.
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Benincasa P, Bravi E, Marconi O, Lutts S, Tosti G, Falcinelli B. Transgenerational Effects of Salt Stress Imposed to Rapeseed ( Brassica napus var. oleifera Del.) Plants Involve Greater Phenolic Content and Antioxidant Activity in the Edible Sprouts Obtained from Offspring Seeds. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10050932. [PMID: 34066989 PMCID: PMC8151563 DOI: 10.3390/plants10050932] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022]
Abstract
Previous research has demonstrated that rapeseed sprouts obtained under salinity demonstrate greater phenolic content and antioxidant activity compared to those sprouted with distilled water. This work aimed to test the hypothesis that these effects of salinity may persist into the next generation, so that offspring seeds of plants grown under salt stress may give edible sprouts with increased phenolic content and antioxidant activity. Plants of one rapeseed cultivar were grown in pots with 0, 100 and 200 mM NaCl, isolated from each other at flowering to prevent cross-pollination. Offspring seeds harvested from each salinity treatment were then sprouted with distilled water. We performed the extraction of free and bound phenolic fractions of sprouts and, in each fraction (methanolic extract), we determined the total polyphenols (P), flavonoids, (F), and tannins (T) with Folin-Ciocalteu reagent, the phenolic acids (PAs) by ultra-high-performance liquid chromatographs (UHPLC) analysis, and the antioxidant activity with three tests (2,2-diphenyl-1-picrylhydrazyl-hydrate, DPPH; ferric reducing antioxidant power, FRAP; 2,2'-azino-bis[3-ethylbenzothiazoline-6-sulfonic acid] diammonium salt, ABTS). Individual seed weight was slightly decreased by salinity, whereas germination performance was improved, with a lower mean germination time for salted treatments. No significant differences were observed among treatments for P, F and T, except for bound P, while, in most cases, single PAs (as free, bound and total fractions) and antioxidant activity were significantly increased in salted treatments. Our results open new perspectives for the elicitation of secondary metabolites in the offspring seeds by growing parental plants under stressing conditions, imposed on purpose or naturally occurring.
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Affiliation(s)
- Paolo Benincasa
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06124 Perugia, Italy; (E.B.); (O.M.); (G.T.); (B.F.)
- Correspondence:
| | - Elisabetta Bravi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06124 Perugia, Italy; (E.B.); (O.M.); (G.T.); (B.F.)
| | - Ombretta Marconi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06124 Perugia, Italy; (E.B.); (O.M.); (G.T.); (B.F.)
| | - Stanley Lutts
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy (ELI-A), Université catholique de Louvain, 5 (Bte 7.07.13) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium;
| | - Giacomo Tosti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06124 Perugia, Italy; (E.B.); (O.M.); (G.T.); (B.F.)
| | - Beatrice Falcinelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06124 Perugia, Italy; (E.B.); (O.M.); (G.T.); (B.F.)
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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21
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Fang S, Hou X, Liang X. Response Mechanisms of Plants Under Saline-Alkali Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:667458. [PMID: 34149764 PMCID: PMC8213028 DOI: 10.3389/fpls.2021.667458] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/10/2021] [Indexed: 05/20/2023]
Abstract
As two coexisting abiotic stresses, salt stress and alkali stress have severely restricted the development of global agriculture. Clarifying the plant resistance mechanism and determining how to improve plant tolerance to salt stress and alkali stress have been popular research topics. At present, most related studies have focused mainly on salt stress, and salt-alkali mixed stress studies are relatively scarce. However, in nature, high concentrations of salt and high pH often occur simultaneously, and their synergistic effects can be more harmful to plant growth and development than the effects of either stress alone. Therefore, it is of great practical importance for the sustainable development of agriculture to study plant resistance mechanisms under saline-alkali mixed stress, screen new saline-alkali stress tolerance genes, and explore new plant salt-alkali tolerance strategies. Herein, we summarized how plants actively respond to saline-alkali stress through morphological adaptation, physiological adaptation and molecular regulation.
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Affiliation(s)
- Shumei Fang
- Department of Biotechnology, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
- *Correspondence: Shumei Fang,
| | - Xue Hou
- Department of Biotechnology, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xilong Liang
- Department of Environmental Science, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
- Heilongjiang Plant Growth Regulator Engineering Technology Research Center, Daqing, China
- Xilong Liang,
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22
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Sheeja TE, Kumar IPV, Giridhari A, Minoo D, Rajesh MK, Babu KN. Amplified Fragment Length Polymorphism: Applications and Recent Developments. Methods Mol Biol 2021; 2222:187-218. [PMID: 33301096 DOI: 10.1007/978-1-0716-0997-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.
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Affiliation(s)
- Thotten Elampilay Sheeja
- Indian Institute of Spices Research, Kozhikode, Kerala, India.
- Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India.
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Liu J, He Z. Small DNA Methylation, Big Player in Plant Abiotic Stress Responses and Memory. FRONTIERS IN PLANT SCIENCE 2020; 11:595603. [PMID: 33362826 PMCID: PMC7758401 DOI: 10.3389/fpls.2020.595603] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/18/2020] [Indexed: 05/12/2023]
Abstract
DNA methylation is a conserved epigenetic mark that plays important roles in maintaining genome stability and regulating gene expression. As sessile organisms, plants have evolved sophisticated regulatory systems to endure or respond to diverse adverse abiotic environmental challenges, i.e., abiotic stresses, such as extreme temperatures (cold and heat), drought and salinity. Plant stress responses are often accompanied by changes in chromatin modifications at diverse responsive loci, such as 5-methylcytosine (5mC) and N 6-methyladenine (6mA) DNA methylation. Some abiotic stress responses are memorized for several hours or days through mitotic cell divisions and quickly reset to baseline levels after normal conditions are restored, which is referred to as somatic memory. In some cases, stress-induced chromatin marks are meiotically heritable and can impart the memory of stress exposure from parent plants to at least the next stress-free offspring generation through the mechanisms of transgenerational epigenetic inheritance, which may offer the descendants the potential to be adaptive for better fitness. In this review, we briefly summarize recent achievements regarding the establishment, maintenance and reset of DNA methylation, and highlight the diverse roles of DNA methylation in plant responses to abiotic stresses. Further, we discuss the potential role of DNA methylation in abiotic stress-induced somatic memory and transgenerational inheritance. Future research directions are proposed to develop stress-tolerant engineered crops to reduce the negative effects of abiotic stresses.
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Affiliation(s)
- Junzhong Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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24
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Varotto S, Tani E, Abraham E, Krugman T, Kapazoglou A, Melzer R, Radanović A, Miladinović D. Epigenetics: possible applications in climate-smart crop breeding. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5223-5236. [PMID: 32279074 PMCID: PMC7475248 DOI: 10.1093/jxb/eraa188] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/09/2020] [Indexed: 05/23/2023]
Abstract
To better adapt transiently or lastingly to stimuli from the surrounding environment, the chromatin states in plant cells vary to allow the cells to fine-tune their transcriptional profiles. Modifications of chromatin states involve a wide range of post-transcriptional histone modifications, histone variants, DNA methylation, and activity of non-coding RNAs, which can epigenetically determine specific transcriptional outputs. Recent advances in the area of '-omics' of major crops have facilitated identification of epigenetic marks and their effect on plant response to environmental stresses. As most epigenetic mechanisms are known from studies in model plants, we summarize in this review recent epigenetic studies that may be important for improvement of crop adaptation and resilience to environmental changes, ultimately leading to the generation of stable climate-smart crops. This has paved the way for exploitation of epigenetic variation in crop breeding.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals, and the Environment, University of Padova, Agripolis, Viale dell’Università, Padova, Italy
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Athens, Greece
| | - Eleni Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Demeter (HAO-Demeter), Lykovrysi, Greece
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
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25
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DNA Methylation Changes Induced by Cold in Psychrophilic and Psychrotolerant Naganishia Yeast Species. Microorganisms 2020; 8:microorganisms8020296. [PMID: 32093408 PMCID: PMC7074839 DOI: 10.3390/microorganisms8020296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
The involvement of DNA methylation in the response to cold stress of two different yeast species (Naganishia antarctica, psychrophilic, and Naganishia albida, psychrotolerant), exhibiting different temperature aptitudes, has been studied. Consecutive incubations at respective optimum temperatures, at 4 °C (cold stress) and at optimum temperatures again, were performed. After Methylation Sensitive Amplified Polymorphism (MSAP) fingerprints a total of 550 and 423 clear and reproducible fragments were amplified from N. antarctica and N. albida strains, respectively. The two Naganishia strains showed a different response in terms of level of DNA methylation during cold stress and recovery from cold stress. The percentage of total methylated fragments in psychrophilic N. antarctica did not show any significant change. On the contrary, the methylation of psychrotolerant N. albida exhibited a nonsignificant increase during the incubation at 4 °C and continued during the recovery step, showing a significant difference if compared with control condition, resembling an uncontrolled response to cold stress. A total of 12 polymorphic fragments were selected, cloned, and sequenced. Four fragments were associated to genes encoding for elongation factor G and for chitin synthase export chaperon. To the best of our knowledge, this is the first study on DNA methylation in the response to cold stress carried out by comparing a psychrophilic and a psychrotolerant yeast species.
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26
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Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem. Mol Biol Rep 2019; 47:1339-1360. [DOI: 10.1007/s11033-019-05236-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/08/2019] [Accepted: 12/07/2019] [Indexed: 11/26/2022]
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27
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Docimo T, De Stefano R, De Palma M, Cappetta E, Villano C, Aversano R, Tucci M. Transcriptional, metabolic and DNA methylation changes underpinning the response of Arundo donax ecotypes to NaCl excess. PLANTA 2019; 251:34. [PMID: 31848729 DOI: 10.1007/s00425-019-03325-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Arundo donax ecotypes react differently to salinity, partly due to differences in constitutive defences and methylome plasticity. Arundo donax L. is a C3 fast-growing grass that yields high biomass under stress. To elucidate its ability to produce biomass under high salinity, we investigated short/long-term NaCl responses of three ecotypes through transcriptional, metabolic and DNA methylation profiling of leaves and roots. Prolonged salt treatment discriminated the sensitive ecotype 'Cercola' from the tolerant 'Domitiana' and 'Canneto' in terms of biomass. Transcriptional and metabolic responses to NaCl differed between the ecotypes. In roots, constitutive expression of ion transporter and stress-related transcription factors' genes was higher in 'Canneto' and 'Domitiana' than 'Cercola' and 21-day NaCl drove strong up-regulation in all ecotypes. In leaves, unstressed 'Domitiana' confirmed higher expression of the above genes, whose transcription was repressed in 'Domitiana' but induced in 'Cercola' following NaCl treatment. In all ecotypes, salinity increased proline, ABA and leaf antioxidants, paralleled by up-regulation of antioxidant genes in 'Canneto' and 'Cercola' but not in 'Domitiana', which tolerated a higher level of oxidative damage. Changes in DNA methylation patterns highlighted a marked capacity of the tolerant 'Domitiana' ecotype to adjust DNA methylation to salt stress. The reduced salt sensitivity of 'Domitiana' and, to a lesser extent, 'Canneto' appears to rely on a complex set of constitutively activated defences, possibly due to the environmental conditions of the site of origin, and on higher plasticity of the methylome. Our findings provide insights into the mechanisms of adaptability of A. donax ecotypes to salinity, offering new perspectives for the improvement of this species for cultivation in limiting environments.
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Affiliation(s)
- Teresa Docimo
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Rosalba De Stefano
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Monica De Palma
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Elisa Cappetta
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Marina Tucci
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, via Università 133, 80055, Portici, Italy.
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28
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Vuković R, Liber Z, Ježić M, Sotirovski K, Ćurković-Perica M. Link between epigenetic diversity and invasive status of south-eastern European populations of phytopathogenic fungus Cryphonectria parasitica. Environ Microbiol 2019; 21:4521-4536. [PMID: 31314941 DOI: 10.1111/1462-2920.14742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022]
Abstract
Epigenetic modifications may play an important role in invasion and adaptation of clonal and invasive populations to different environments. The aim of this study was to analyse epigenetic diversity and structure within and among populations of invasive pathogenic fungus Cryphonectria parasitica from south-eastern Europe, where one haplotype S12 dominates. The highest level of epigenetic diversity was found in haplotype S1, followed by S2, while the lowest level of epigenetic diversity was found in haplotype S12. Similar pattern of epigenetic diversity was detected in the control, genetically diverse Croatian population where S1 haplotype dominates. In four south-eastern European populations, the highest level of epigenetic diversity was observed in the Italian population, the oldest population in the studied area, while the lowest diversity was found in most recently established Bulgarian population. This relationship between epigenetic diversity and population age implies the important role of epigenetic modifications on the process of invasion. Our data suggest that epigenetic differences might affect the success of expansion of certain haplotype into new regions. Understanding the role of epigenetic processes in expansion and (pre)adaptation of fungal plant pathogens, besides fundamental knowledge, can contribute to development of strategies for control of fungal spread and pathogenesis.
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Affiliation(s)
- Rosemary Vuković
- Department of Biology, J. J. Strossmayer University of Osijek, Osijek, Croatia
| | - Zlatko Liber
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
| | - Marin Ježić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Kiril Sotirovski
- Faculty of Forestry, Ss. Cyril and Methodius University of Skopje, Skopje, North Macedonia
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29
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Jha UC, Bohra A, Jha R, Parida SK. Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes. PLANT CELL REPORTS 2019; 38:255-277. [PMID: 30637478 DOI: 10.1007/s00299-019-02374-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/04/2019] [Indexed: 05/21/2023]
Abstract
Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Rintu Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067, India
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30
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Mousavi S, Regni L, Bocchini M, Mariotti R, Cultrera NGM, Mancuso S, Googlani J, Chakerolhosseini MR, Guerrero C, Albertini E, Baldoni L, Proietti P. Physiological, epigenetic and genetic regulation in some olive cultivars under salt stress. Sci Rep 2019; 9:1093. [PMID: 30705308 PMCID: PMC6355907 DOI: 10.1038/s41598-018-37496-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022] Open
Abstract
Cultivated olive, a typical fruit crop species of the semi-arid regions, could successfully face the new scenarios driven by the climate change through the selection of tolerant varieties to salt and drought stresses. In the present work, multidisciplinary approaches, including physiological, epigenetic and genetic studies, have been applied to clarify the salt tolerance mechanisms in olive. Four varieties (Koroneiki, Royal de Cazorla, Arbequina and Picual) and a related form (O. europaea subsp. cuspidata) were grown in a hydroponic system under different salt concentrations from zero to 200 mM. In order to verify the plant response under salt stress, photosynthesis, gas exchange and relative water content were measured at different time points, whereas chlorophyll and leaf concentration of Na+, K+ and Ca2+ ions, were quantified at 43 and 60 days after treatment, when stress symptoms became prominent. Methylation sensitive amplification polymorphism (MSAP) technique was used to assess the effects of salt stress on plant DNA methylation. Several fragments resulted differentially methylated among genotypes, treatments and time points. Real time quantitative PCR (RT-qPCR) analysis revealed significant expression changes related to plant response to salinity. Four genes (OePIP1.1, OePetD, OePI4Kg4 and OeXyla) were identified, as well as multiple retrotransposon elements usually targeted by methylation under stress conditions.
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Affiliation(s)
- Soraya Mousavi
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
- CNR - Institute of Biosciences and Bioresources, Perugia, Italy
| | - Luca Regni
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| | - Marika Bocchini
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| | | | | | - Stefano Mancuso
- Università degli Studi di Firenze, Dept. Agrifood Production and Environmental Sciences, Florence, Italy
| | - Jalaladdin Googlani
- Università degli Studi di Firenze, Dept. Agrifood Production and Environmental Sciences, Florence, Italy
| | | | | | - Emidio Albertini
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources, Perugia, Italy.
| | - Primo Proietti
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
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31
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Komivi D, Marie AM, Rong Z, Qi Z, Mei Y, Ndiaga C, Diaga D, Linhai W, Xiurong Z. The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with transcript accumulation in sesame. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:207-217. [PMID: 30466587 DOI: 10.1016/j.plantsci.2018.09.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 05/07/2023]
Abstract
DNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, probably because of its origin in Africa or India. Understanding DNA methylation patterns under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying sesame contrasting responses to these abiotic stresses. We combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, transcript accumulation, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes. Drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging stress decreased the level of methylation but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the levels of the differentially accumulated transcripts (DATs) highly correlated with the methylation patterns. We observed that DM was associated with an increase of DAT levels while DNM was correlated with a decrease of DAT levels. Altogether, sesame has divergent epigenetic programs that respond to drought and waterlogging stresses and an interplay among DNA methylation and transcript accumulation may partly modulate the contrasting responses to these stresses.
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Affiliation(s)
- Dossa Komivi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China; Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal; Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal.
| | - Ali Mmadi Marie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China; Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal; Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal
| | - Zhou Rong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Zhou Qi
- College of Life Science, Hubei University, Wuhan, China
| | - Yang Mei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Cisse Ndiaga
- Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal
| | - Diouf Diaga
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal
| | - Wang Linhai
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Zhang Xiurong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China.
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32
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Parasyri A, Papazi A, Stamatis N, Zerveas S, Avramidou EV, Doulis AG, Pirintsos S, Kotzabasis K. Lichen as Micro-Ecosystem: Extremophilic Behavior with Astrobiotechnological Applications. ASTROBIOLOGY 2018; 18:1528-1542. [PMID: 30383392 DOI: 10.1089/ast.2017.1789] [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] [Indexed: 06/08/2023]
Abstract
This work demonstrates the tolerance of lichen Pleurosticta acetabulum under extreme conditions similar to those encountered in extraterrestrial environments. Specifically, the impact of three extreme Mars-like conditions-complete dehydration, extremely low temperature (-196°C/77K), and oxygen depletion-on lichens was investigated. The symbiosis of mycobiont and photobiont partners creates a micro-ecosystem that ensures viability of both symbiotic partners under prolonged desiccation and extremely low temperatures without any cultivation care. Changes in the molecular structure and function of the photosynthetic apparatus, in the level of chlorophylls, polyamines, fatty acids, carbohydrates, ergosterol, efflux of K+, and DNA methylation ensure the ecological integrity of the system and offer resistance of lichens to above-mentioned extreme environmental conditions. For the first time, we also demonstrate that the unprecedented polyextremophilic characteristic of lichens could be linked to biotechnological applications, following exposure to these extreme conditions, such that their ability to produce a high yield of hydrogen was unchanged. All these support that lichens are (a) ideal model systems for a space mission to inhabit other planets, supporting also the aspect that the panspermia theory could be extended to incorporate in the traveling entities not only single organisms but micro-ecosystems like lichens, and (b) ideal model systems for astrobiotechnological applications (hydrogen production), such as in the development of bioregeneration systems for extraterrestrial environments.
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Affiliation(s)
- Athina Parasyri
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
| | - Aikaterini Papazi
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
| | | | - Sotirios Zerveas
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
| | | | | | - Stergios Pirintsos
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
- 3 Botanical Garden, University of Crete , Gallos Campus, Rethymnon, Greece
| | - Kiriakos Kotzabasis
- 1 Department of Biology, University of Crete, Voutes University Campus , Heraklion, Greece
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Busconi M, Soffritti G, Stagnati L, Marocco A, Marcos Martínez J, De Los Mozos Pascual M, Fernandez JA. Epigenetic stability in Saffron (Crocus sativus L.) accessions during four consecutive years of cultivation and vegetative propagation under open field conditions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:1-10. [PMID: 30466573 DOI: 10.1016/j.plantsci.2018.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 05/10/2023]
Abstract
Saffron (Crocus sativus L.) is a sterile species that is vegetatively propagated in the field, year by year, via the production of new corms. While Saffron's genetic variability is extremely low, phenotypic variation is frequently observed in the field and epigenetics could be a possible origin of these alternative phenotypes. Present day knowledge on Saffron epigenetics is very low or absent. In the present paper, to deepen existing knowledge, we focused on the epigenetic differences and stability among 17 Saffron accessions, of different geographic origin, during four consecutive years of vegetative propagation under open field conditions. Before the analysis, the selected accessions have been cultivated in the same field for at least three consecutive years. Despite the low genetic variability and the prolonged co-cultivation in the same environment, Methylation-Sensitive Amplified Fragment Length Polymorphism (MS-AFLP) analysis revealed a very high epigenetic difference among accessions, making it possible to discriminate them based on the epigenetic profiles. During the four years of the study, a little variation has been observed within accessions following different patterns, slightly modifying the accession epigenotypes but not enough to even them to a more uniform profile. These results confirm that, under natural conditions, Saffron epigenotypes are highly stable, supporting a role for epigenetics in phenotypic variability.
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Affiliation(s)
- Matteo Busconi
- Department of Sustainable Crop Production, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Giovanna Soffritti
- Department of Sustainable Crop Production, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Lorenzo Stagnati
- Department of Sustainable Crop Production, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Adriano Marocco
- Department of Sustainable Crop Production, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Javier Marcos Martínez
- Centro de Investigación Agroforestal de Albaladejito, Instituto Regional de Investigación y Desartrollo Agroalimentario y Forestal, Cuenca, Spain
| | - Marcelino De Los Mozos Pascual
- Centro de Investigación Agroforestal de Albaladejito, Instituto Regional de Investigación y Desartrollo Agroalimentario y Forestal, Cuenca, Spain
| | - José Antonio Fernandez
- IDR-Biotechnology and Natural Resources, Universidad de Castilla-La Mancha, Albacete, Spain
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DNA Methylation Analysis in Barley and Other Species with Large Genomes. Methods Mol Biol 2018. [PMID: 30460570 DOI: 10.1007/978-1-4939-8944-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Detailed DNA methylation analyses in plant species with large and highly repetitive genomes can be challenging as well as costly. Here, we describe a complete protocol for a high-throughput DNA methylation changes analysis using Methylation-Sensitive Amplification Polymorphism Sequencing (MSAP-Seq; Chwialkowska et al., Front Plant Sci. 8: 2056 (2017)). This method allows detailed information about DNA methylation changes in large and complex genomes to be obtained at a relatively low cost. MSAP-Seq is based on conventional MSAP marker analysis and employs all its basic steps such as restriction cleavage with methylation-sensitive restriction enzyme, ligation of universal adapters, and PCR amplification. However, the traditional gel-based amplicon separation is replaced by direct, global sequencing with next-generation sequencing (NGS) methods. Consequently, MSAP-Seq allows for parallel analysis of hundreds of thousands of different CCGG sites and evaluation of their DNA methylation state. This technique especially targets to genic regions, so it is well suited for large genomes with low gene density, such as barley and other plants with large genomes.
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Niedziela A. The influence of Al 3+ on DNA methylation and sequence changes in the triticale (× Triticosecale Wittmack) genome. J Appl Genet 2018; 59:405-417. [PMID: 30159773 PMCID: PMC7902597 DOI: 10.1007/s13353-018-0459-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/24/2018] [Accepted: 08/07/2018] [Indexed: 01/28/2023]
Abstract
Abiotic stressors such as drought, salinity, and exposure to heavy metals can induce epigenetic changes in plants. In this study, liquid chromatography (RP-HPLC), methylation amplified fragment length polymorphisms (metAFLP), and methylation-sensitive amplification polymorphisms (MSAP) analysis was used to investigate the effects of aluminum (Al) stress on DNA methylation levels in the crop species triticale. RP-HPLC, but not metAFLP or MSAP, revealed significant differences in methylation between Al-tolerant (T) and non-tolerant (NT) triticale lines. The direction of methylation change was dependent on phenotype and organ. Al treatment increased the level of global DNA methylation in roots of T lines by approximately 0.6%, whereas demethylation of approximately 1.0% was observed in NT lines. DNA methylation in leaves was not affected by Al stress. The metAFLP and MSAP approaches identified DNA alterations induced by Al3+ treatment. The metAFLP technique revealed sequence changes in roots of all analyzed triticale lines and few mutations in leaves. MSAP showed that demethylation of CCGG sites reached approximately 3.97% and 3.75% for T and NT lines, respectively, and was more abundant than de novo methylation, which was observed only in two tolerant lines affected by Al stress. Three of the MSAP fragments showed similarity to genes involved in abiotic stress.
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Affiliation(s)
- Agnieszka Niedziela
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute, National Research Institute, 05-870, Radzików, Błonie, Poland.
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36
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Analysis of sulphur and chlorine induced DNA cytosine methylation alterations in fresh corn (Zea mays L. saccharata and rugosa) leaf tissues by methylation sensitive amplification polymorphism (MSAP) approach. Genes Genomics 2018; 40:913-925. [PMID: 30155706 DOI: 10.1007/s13258-018-0685-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/26/2018] [Indexed: 01/24/2023]
Abstract
DNA (cytosine) methylation mechanism is another way through which plants respond to various cues including soil fertility amendments and abiotic stresses, and the mechanism has been used to infer some physiological, biochemical or adaptation processes. Despite numerous studies on global DNA methylation profiling in various crop species, however, researches on fresh corn (Zea mays L. saccharata or rugosa) remain largely unreported. The study aimed at investigating sulphur and chlorine induced DNA methylation changes in the fresh corn leaves of field-grown plants at the milk stage. Methylation sensitive amplification polymorphism (MSAP) technique was used to profile sulphur (S) and chlorine (Cl) induced DNA methylation patterns, levels and polymorphism alterations at the CCGG sites in fresh corn leaves of TDN21, JKN2000 and JKN928 hybrid cultivars. Twelve primer pairs used effectively detected 325 MSAP bands, exhibiting differentially methylated sites in the genomic DNA of all the three cultivars, with control showing higher (48.9-56.3%) type I bands as compared to sulphur (34.8-44.9%) and chlorine (40.9-47.4%) treatment samples. Consequently, total methylation levels were greater in S and Cl treatment samples than control; accounting for 43.7-59.7, 51.1-65.2 and 46.8-55.1% of total sites in TDN21, JKN2000 and JKN928, respectively. Full methylation of the internal cytosine was greater than hemi-methylation. Further, demethylation polymorphic loci significantly exceeded methylation polymorphic loci, being greater in S than Cl and control samples in all cultivars. Sulphur and chlorine have a profound influence on DNA methylation patterns and levels at the milk stage, principally by increasing the demethylation loci in the internal cytosine of the fresh corn genome. We speculate that these methylation alterations play an integral role in photosynthates assimilation and physiochemical pathways regulating quality parameters in kernels, as well as abiotic stress responses in fresh corn.
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Kaleem F, Shabir G, Aslam K, Rasul S, Manzoor H, Shah SM, Khan AR. An Overview of the Genetics of Plant Response to Salt Stress: Present Status and the Way Forward. Appl Biochem Biotechnol 2018; 186:306-334. [PMID: 29611134 DOI: 10.1007/s12010-018-2738-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 03/15/2018] [Indexed: 01/24/2023]
Abstract
Salinity is one of the major threats faced by the modern agriculture today. It causes multidimensional effects on plants. These effects depend upon the plant growth stage, intensity, and duration of the stress. All these lead to stunted growth and reduced yield, ultimately inducing economic loss to the farming community in particular and to the country in general. The soil conditions of agricultural land are deteriorating at an alarming rate. Plants assess the stress conditions, transmit the specific stress signals, and then initiate the response against that stress. A more complete understanding of plant response mechanisms and their practical incorporation in crop improvement is an essential step towards achieving the goal of sustainable agricultural development. Literature survey shows that investigations of plant stresses response mechanism are the focus area of research for plant scientists. Although these efforts lead to reveal different plant response mechanisms against salt stress, yet many questions still need to be answered to get a clear picture of plant strategy to cope with salt stress. Moreover, these studies have indicated the presence of a complicated network of different integrated pathways. In order to work in a progressive way, a review of current knowledge is critical. Therefore, this review aims to provide an overview of our understanding of plant response to salt stress and to indicate some important yet unexplored dynamics to improve our knowledge that could ultimately lead towards crop improvement.
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Affiliation(s)
- Fawad Kaleem
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Ghulam Shabir
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Kashif Aslam
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Sumaira Rasul
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hamid Manzoor
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Shahid Masood Shah
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Abdul Rehman Khan
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
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Bocchini M, D’Amato R, Ciancaleoni S, Fontanella MC, Palmerini CA, Beone GM, Onofri A, Negri V, Marconi G, Albertini E, Businelli D. Soil Selenium (Se) Biofortification Changes the Physiological, Biochemical and Epigenetic Responses to Water Stress in Zea mays L. by Inducing a Higher Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2018; 9:389. [PMID: 29636765 PMCID: PMC5880925 DOI: 10.3389/fpls.2018.00389] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/09/2018] [Indexed: 05/08/2023]
Abstract
Requiring water and minerals to grow and to develop its organs, Maize (Zea mays L.) production and distribution is highly rainfall-dependent. Current global climatic changes reveal irregular rainfall patterns and this could represent for maize a stressing condition resulting in yield and productivity loss around the world. It is well known that low water availability leads the plant to adopt a number of metabolic alterations to overcome stress or reduce its effects. In this regard, selenium (Se), a trace element, can help reduce water damage caused by the overproduction of reactive oxygen species (ROS). Here we report the effects of exogenous Se supply on physiological and biochemical processes that may influence yield and quality of maize under drought stress conditions. Plants were grown in soil fertilized by adding 150 mg of Se (sodium selenite). We verified the effects of drought stress and Se treatment. Selenium biofortification proved more beneficial for maize plants when supplied at higher Se concentrations. The increase in proline, K concentrations and nitrogen metabolism in aerial parts of plants grown in Se-rich substrates, seems to prove that Se-biofortification increased plant resistance to water shortage conditions. Moreover, the increase of SeMeSeCys and SeCys2 forms in roots and aerial parts of Se-treated plants suggest resistance strategies to Se similar to those existing in Se-hyperaccumulator species. In addition, epigenetic changes in DNA methylation due to water stress and Se treatment were also investigated using methylation sensitive amplified polymorphism (MSAP). Results suggest that Se may be an activator of particular classes of genes that are involved in tolerance to abiotic stresses. In particular, PSY (phytoene synthase) gene, essential for maintaining leaf carotenoid contents, SDH (sorbitol dehydrogenase), whose activity regulates the level of important osmolytes during drought stress and ADH (alcohol dehydrogenase), whose activity plays a central role in biochemical adaptation to environmental stress. In conclusion, Se-biofortification could help maize plants to cope with drought stress conditions, by inducing a higher drought tolerance.
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Affiliation(s)
- Marika Bocchini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Roberto D’Amato
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Simona Ciancaleoni
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Maria C. Fontanella
- Department for Sustainable Food Process, Catholic University of the Sacred Heart, Piacenza, Italy
| | - Carlo A. Palmerini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Gian M. Beone
- Department for Sustainable Food Process, Catholic University of the Sacred Heart, Piacenza, Italy
| | - Andrea Onofri
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Valeria Negri
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Gianpiero Marconi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Daniela Businelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
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The vesicle trafficking regulator PN_SCD1 is demethylated and overexpressed in florets of apomictic Paspalum notatum genotypes. Sci Rep 2018; 8:3030. [PMID: 29445151 PMCID: PMC5812994 DOI: 10.1038/s41598-018-21220-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/31/2018] [Indexed: 01/01/2023] Open
Abstract
Apomixis (asexual reproduction through seeds) is considered a deviation of the sexual reproductive pathway leading to the development of clonal progenies genetically identical to the mother plant. Here we used the Methylation-Sensitive Amplification Polymorphism (MSAP) technique to characterize cytosine methylation patterns occurring in florets of sexual and aposporous Paspalum notatum genotypes, in order to identify epigenetically-controlled genes putatively involved in apomixis development. From twelve polymorphic MSAP-derived sequences, one (PN_6.6, later renamed PN_SCD1) was selected due to its relevant annotation and differential representation in apomictic and sexual floral transcriptome libraries. PN_SCD1 encodes the DENN domain/WD repeat-containing protein SCD1, which interacts with RAB GTPases- and/or MAPKs to promote specialized cell division, functions in clathrin-mediated membrane transport and acts as potential substrate receptor of CUL4 E3 ubiquitin ligases. Quantitative RT-PCR and comparative RNAseq analyses of laser microdissected nucellar cells confirmed PN_SCD1 upregulation in florets of apomictic plants and revealed that overexpression takes place just before the onset of apospory initials. Moreover, we found that several SCD1 molecular partners are expressed in P. notatum florets and upregulated in apomictic plants. Our results disclosed a specific vesicle trafficking molecular pathway epigenetically modulated during apomixis.
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40
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Epigenetics and Epigenomics of Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 164:237-261. [DOI: 10.1007/10_2017_51] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Yang C, Zhang Y, Liu W, Lu X, Li C. Genome-wide analysis of DNA methylation in five tissues of sika deer (Cervus nippon). Gene 2017; 645:48-54. [PMID: 29253609 DOI: 10.1016/j.gene.2017.12.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023]
Abstract
DNA methylation plays an important role in regulating gene expression during tissue development and differentiation in eukaryotes. In contrast to domestic animals, epigenetic studies have been seldom conducted in wild animals. In the present study, we conducted the genome-wide profiling of DNA methylation for five tissues of sika deer using the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) technique. Overall, a total of 104,131 fragments were amplified including 41,951 methylated fragments using 32 pairs of selected primers. The average incidence of DNA methylation was approximately 38.18% in muscle, 40.32% in heart, 41.86% in liver, 41.20% in lung, and 41.68% in kidney, respectively. Also, the significant differences of the DNA methylation levels were found between the different tissue types (P<0.05), which indicates that the differences of genome-wide DNA methylation levels may be related to gene expression during tissue development and differentiation. In addition, 37 tissue-specific differentially methylated regions (T-DMRs) were identified and recovered by MSAP in five tissues, and were further confirmed by Southern blot analysis. Our study presents the first look at the T-DMRs in sika deer and represents an initial step towards understanding of epigenetic regulatory mechanism underlying tissue development and differentiation in sika deer.
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Affiliation(s)
- Chun Yang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, PR China; State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun, PR China
| | - Yan Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, PR China
| | - Wenyuan Liu
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, PR China; State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun, PR China
| | - Xiao Lu
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, PR China; State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun, PR China
| | - Chunyi Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, PR China; State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun, PR China.
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42
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He S, Xu W, Li F, Wang Y, Liu A. Intraspecific DNA methylation polymorphism in the non-edible oilseed plant castor bean. PLANT DIVERSITY 2017; 39:300-307. [PMID: 30159523 PMCID: PMC6112301 DOI: 10.1016/j.pld.2017.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/25/2017] [Accepted: 05/27/2017] [Indexed: 05/05/2023]
Abstract
Investigation of the relationships of phenotypic and epigenetic variations might be a good way to dissect the genetic or molecular basis of phenotypic variation and plasticity in plants. Castor bean (Ricinus communis L.), an important non-edible oilseed crop, is a mono-species genus plant in the family Euphorbiaceae. Since it displays rich phenotypic variations with low genetic diversity, castor bean is a good model to investigate the molecular basis of phenotypic and epigenetic variations. Cytosine DNA methylation represents a major molecular mechanism of epigenetic occurrence. In this study, epigenetic diversity of sixty landrace accessions collected worldwide was investigated using the methylation-sensitive amplification polymorphism (MSAP) technique. Results showed that the epigenetic diversity (based on the polymorphism of DNA methylated loci) exhibited a medium variation (Ne = 1.395, He = 0.242, I = 0.366) at the population level though the variation was great, ranging from 3.80% to 34.31% among accessions. Both population structure analysis and the phylogenetic construction (using the neighbor-joining criteria) revealed that the two main clades were identified, but they did not display a distinct geographic structure. After inspecting the location of polymorphic methylated loci on genome we identified that the polymorphic methylated loci occur widely in nuclear and organelle genomes. This study provides new data to understand phenotypic and epigenetic variations in castor bean.
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Affiliation(s)
- Shan He
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fei Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yue Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Aizhong Liu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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The Variation Analysis of DNA Methylation in Wheat Carrying Gametocidal Chromosome 3C from Aegilops triuncialis. Int J Mol Sci 2017; 18:ijms18081738. [PMID: 28796162 PMCID: PMC5578128 DOI: 10.3390/ijms18081738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 12/16/2022] Open
Abstract
Gametocidal (Gc) chromosomes can ensure their preferential transmission by killing the gametes without themselves through causing chromosome breakage and therefore have been exploited as an effective tool for genetic breeding. However, to date very little is known about the molecular mechanism of Gc action. In this study, we used methylation-sensitive amplified polymorphism (MSAP) technique to assess the extent and pattern of cytosine methylation alterations at the whole genome level between two lines of wheat Gc addition line and their common wheat parent. The results indicated that the overall levels of cytosine methylation of two studied Gc addition lines (CS–3C and CS–3C3C, 48.68% and 48.65%, respectively) were significantly increased when compared to common wheat CS (41.31%) and no matter fully methylated or hemimethylated rates enhanced in Gc addition lines. A set of 30 isolated fragments that showed different DNA methylation or demethylation patterns between the three lines were sequenced and the results indicated that 8 fragments showed significant homology to known sequences, of which three were homologous to MITE transposon (Miniature inverted–repeat transposable elements), LTR-retrotransposon WIS-1p and retrotransposon Gypsy, respectively. Overall, our results showed that DNA methylation could play a role in the Gc action.
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Pandey G, Yadav CB, Sahu PP, Muthamilarasan M, Prasad M. Salinity induced differential methylation patterns in contrasting cultivars of foxtail millet (Setaria italica L.). PLANT CELL REPORTS 2017; 36:759-772. [PMID: 27999979 DOI: 10.1007/s00299-016-2093-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/07/2016] [Indexed: 05/18/2023]
Abstract
Genome-wide methylation analysis of foxtail millet cultivars contrastingly differing in salinity tolerance revealed DNA demethylation events occurring in tolerant cultivar under salinity stress, eventually modulating the expression of stress-responsive genes. Reduced productivity and significant yield loss are the adverse effects of environmental conditions on physiological and biochemical pathways in crop plants. In this context, understanding the epigenetic machinery underlying the tolerance traits in a naturally stress tolerant crop is imperative. Foxtail millet (Setaria italica) is known for its better tolerance to abiotic stresses compared to other cereal crops. In the present study, methylation-sensitive amplified polymorphism (MSAP) technique was used to quantify the salt-induced methylation changes in two foxtail millet cultivars contrastingly differing in their tolerance levels to salt stress. The study highlighted that the DNA methylation level was significantly reduced in tolerant cultivar compared to sensitive cultivar. A total of 86 polymorphic MSAP fragments were identified, sequenced and functionally annotated. These fragments showed sequence similarity to several genes including ABC transporter, WRKY transcription factor, serine threonine-protein phosphatase, disease resistance, oxidoreductases, cell wall-related enzymes and retrotransposon and transposase like proteins, suggesting salt stress-induced methylation in these genes. Among these, four genes were chosen for expression profiling which showed differential expression pattern between both cultivars of foxtail millet. Altogether, the study infers that salinity stress induces genome-wide DNA demethylation, which in turn, modulates expression of corresponding genes.
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Affiliation(s)
- Garima Pandey
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Chandra Bhan Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Pranav Pankaj Sahu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | | | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India.
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45
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Bednarek PT, Orłowska R, Niedziela A. A relative quantitative Methylation-Sensitive Amplified Polymorphism (MSAP) method for the analysis of abiotic stress. BMC PLANT BIOLOGY 2017; 17:79. [PMID: 28431570 PMCID: PMC5399823 DOI: 10.1186/s12870-017-1028-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/10/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND We present a new methylation-sensitive amplified polymorphism (MSAP) approach for the evaluation of relative quantitative characteristics such as demethylation, de novo methylation, and preservation of methylation status of CCGG sequences, which are recognized by the isoschizomers HpaII and MspI. We applied the technique to analyze aluminum (Al)-tolerant and non-tolerant control and Al-stressed inbred triticale lines. The approach is based on detailed analysis of events affecting HpaII and MspI restriction sites in control and stressed samples, and takes advantage of molecular marker profiles generated by EcoRI/HpaII and EcoRI/MspI MSAP platforms. METHODS Five Al-tolerant and five non-tolerant triticale lines were exposed to aluminum stress using the physiologicaltest. Total genomic DNA was isolated from root tips of all tolerant and non-tolerant lines before and after Al stress following metAFLP and MSAP approaches. Based on codes reflecting events affecting cytosines within a given restriction site recognized by HpaII and MspI in control and stressed samples demethylation (DM), de novo methylation (DNM), preservation of methylated sites (MSP), and preservation of nonmethylatedsites (NMSP) were evaluated. MSAP profiles were used for Agglomerative hierarchicalclustering (AHC) based on Squared Euclidean distance and Ward's Agglomeration method whereas MSAP characteristics for ANOVA. RESULTS Relative quantitative MSAP analysis revealed that both Al-tolerant and non-tolerant triticale lines subjected to Al stress underwent demethylation, with demethylation of CG predominating over CHG. The rate of de novo methylation in the CG context was ~3-fold lower than demethylation, whereas de novo methylation of CHG was observed only in Al-tolerant lines. CONCLUSIONS Our relative quantitative MSAP approach, based on methylation events affecting cytosines within HpaII-MspI recognition sequences, was capable of quantifying de novo methylation, demethylation, methylation, and non-methylated status in control and stressed Al-tolerant and non-tolerant triticale inbred lines. The method could also be used to analyze methylation events affecting CG and CHG contexts, which were differentially methylated under Al stress. We cannot exclude that the methylation changes revealed among lines as well as between Al-tolerant and non-tolerant groups of lines were due to some experimental errors or that the number of lines was too small for ANOVA to prove the influence of Al stress. Nevertheless, we suspect that Al tolerance in triticale could be partly regulated by epigenetic factors acting at the level of DNA methylation. This method provides a valuable tool for studies of abiotic stresses in plants.
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Affiliation(s)
- Piotr T. Bednarek
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Renata Orłowska
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Agnieszka Niedziela
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870 Błonie, Poland
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Santos AP, Ferreira LJ, Oliveira MM. Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses. BIOLOGY 2017; 6:biology6010003. [PMID: 28275209 PMCID: PMC5371996 DOI: 10.3390/biology6010003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/05/2017] [Accepted: 01/10/2017] [Indexed: 12/12/2022]
Abstract
The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs) or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants) are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to “communicate” past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
| | - Liliana J Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
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Chwialkowska K, Korotko U, Kosinska J, Szarejko I, Kwasniewski M. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes. FRONTIERS IN PLANT SCIENCE 2017; 8:2056. [PMID: 29250096 PMCID: PMC5714927 DOI: 10.3389/fpls.2017.02056] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/16/2017] [Indexed: 05/14/2023]
Abstract
Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop plants with large and complex genomes.
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Affiliation(s)
- Karolina Chwialkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Urszula Korotko
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Kosinska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Szarejko
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
- *Correspondence: Miroslaw Kwasniewski
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Pandey G, Sharma N, Sahu PP, Prasad M. Chromatin-Based Epigenetic Regulation of Plant Abiotic Stress Response. Curr Genomics 2016; 17:490-498. [PMID: 28217005 PMCID: PMC5282600 DOI: 10.2174/1389202917666160520103914] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 12/15/2022] Open
Abstract
Plants are continuously exposed to various abiotic and biotic factors limiting their growth and reproduction. In response, they need various sophisticated ways to adapt to adverse environmental conditions without compromising their proper development, reproductive success and eventually survival. This requires an intricate network to regulate gene expression at transcriptional and post-transcriptional levels, including epigenetic switches. Changes in chromatin modifications such as DNA and histone methylation have been observed in plants upon exposure to several abiotic stresses. In the present review, we highlight the changes of DNA methylation in diverse plants in response to several abiotic stresses such as salinity, drought, cold and heat. We also discuss the progresses made in understanding how these DNA methylation changes might contribute to the abiotic stress tolerance.
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Affiliation(s)
- Garima Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Pranav Pankaj Sahu
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India,Address correspondence to this author at the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India; Tel: 91-11-26735160; Fax: 91-11-26741658; 26741146;, E-mails: ,
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Feng SJ, Liu XS, Tao H, Tan SK, Chu SS, Oono Y, Zhang XD, Chen J, Yang ZM. Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium. PLANT, CELL & ENVIRONMENT 2016; 39:2629-2649. [PMID: 27412910 DOI: 10.1111/pce.12793] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 06/23/2016] [Accepted: 07/05/2016] [Indexed: 05/17/2023]
Abstract
We report genome-wide single-base resolution maps of methylated cytosines and transcriptome change in Cd-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between Cd-exposed and Cd-free rice genomes. There are 2320 non-redundant differentially methylated regions detected in the genome. RNA sequencing revealed 2092 DNA methylation-modified genes differentially expressed under Cd exposure. More genes were found hypermethylated than those hypomethylated in CG, CHH and CHG (where H is A, C or T) contexts in upstream, gene body and downstream regions. Many of the genes were involved in stress response, metal transport and transcription factors. Most of the DNA methylation-modified genes were transcriptionally altered under Cd stress. A subset of loss of function mutants defective in DNA methylation and histone modification activities was used to identify transcript abundance of selected genes. Compared with wide type, mutation of MET1 and DRM2 resulted in general lower transcript levels of the genes under Cd stress. Transcripts of OsIRO2, OsPR1b and Os09g02214 in drm2 were significantly reduced. A commonly used DNA methylation inhibitor 5-azacytidine was employed to investigate whether DNA demethylation affected physiological consequences. 5-azacytidine provision decreased general DNA methylation levels of selected genes, but promoted growth of rice seedlings and Cd accumulation in rice plant.
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Affiliation(s)
- Sheng Jun Feng
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Song Liu
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Tao
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shang Kun Tan
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shan Shan Chu
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Youko Oono
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Xian Duo Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Chen
- Institute of Food Safety and Quality, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
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Urban MO, Vašek J, Klíma M, Krtková J, Kosová K, Prášil IT, Vítámvás P. Proteomic and physiological approach reveals drought-induced changes in rapeseeds: Water-saver and water-spender strategy. J Proteomics 2016; 152:188-205. [PMID: 27838467 DOI: 10.1016/j.jprot.2016.11.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/21/2016] [Accepted: 11/03/2016] [Indexed: 01/05/2023]
Abstract
The cultivar-dependent differences in Brassica napus L. seed yield are significantly affected by drought stress. Here, the response of leaf proteome to long-term drought (28days) was studied in cultivars (cvs): Californium (C), Cadeli (D), Navajo (N), and Viking (V). Analysis of twenty-four 2-D DIGE gels revealed 134 spots quantitatively changed at least 2-fold; from these, 79 proteins were significantly identified by MALDI-TOF/TOF. According to the differences in water use, the cultivars may be assigned to two categories: water-savers or water-spenders. In the water-savers group (cvs C+D), proteins related to nitrogen assimilation, ATP and redox homeostasis were increased under stress, while in the water-spenders category (cvs N+V), carbohydrate/energy, photosynthesis, stress related and rRNA processing proteins were increased upon stress. Taking all data together, we indicated cv C as a drought-adaptable water-saver, cv D as a medium-adaptable water-saver, cv N as a drought-adaptable water-spender, and cv V as a low-adaptable drought sensitive water-spender rapeseed. Proteomic data help to evaluate the impact of drought and the extent of genotype-based adaptability and contribute to the understanding of their plasticity. These results provide new insights into the provenience-based drought acclimation/adaptation strategy of contrasting winter rapeseeds and link data at gasometric, biochemical, and proteome level. SIGNIFICANCE Soil moisture deficit is a real problem for every crop. The data in this study demonstrates for the first time that in stem-prolongation phase cultivars respond to progressive drought in different ways and at different levels. Analysis of physiological and proteomic data showed two different water regime-related strategies: water-savers and spenders. However, not only water uptake rate itself, but also individual protein abundances, gasometric and biochemical parameters together with final biomass accumulation after stress explained genotype-based responses. Interestingly, under a mixed climate profile, both water-use patterns (savers or spenders) can be appropriate for drought adaptation. These data suggest, than complete "acclimation image" of rapeseeds in stem-prolongation phase under drought could be reached only if these characteristics are taken, explained and understood together.
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Affiliation(s)
- Milan Oldřich Urban
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic; Charles University, Department of Experimental Plant Biology, Viničná 5, Prague, Czech Republic.
| | - Jakub Vašek
- Czech University of Life Sciences Prague, Department of Genetics and Breeding, Kamýcká 129, Prague, Czech Republic
| | - Miroslav Klíma
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
| | - Jana Krtková
- Charles University, Department of Experimental Plant Biology, Viničná 5, Prague, Czech Republic
| | - Klára Kosová
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
| | - Ilja Tom Prášil
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
| | - Pavel Vítámvás
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
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