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Junaid MD, Chaudhry UK, Şanlı BA, Gökçe AF, Öztürk ZN. A review of the potential involvement of small RNAs in transgenerational abiotic stress memory in plants. Funct Integr Genomics 2024; 24:74. [PMID: 38600306 DOI: 10.1007/s10142-024-01354-7] [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: 01/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Crop production is increasingly threatened by the escalating weather events and rising temperatures associated with global climate change. Plants have evolved adaptive mechanisms, including stress memory, to cope with abiotic stresses such as heat, drought, and salinity. Stress memory involves priming, where plants remember prior stress exposures, providing enhanced responses to subsequent stress events. Stress memory can manifest as somatic, intergenerational, or transgenerational memory, persisting for different durations. The chromatin, a central regulator of gene expression, undergoes modifications like DNA acetylation, methylation, and histone variations in response to abiotic stress. Histone modifications, such as H3K4me3 and acetylation, play crucial roles in regulating gene expression. Abiotic stresses like drought and salinity are significant challenges to crop production, leading to yield reductions. Plant responses to stress involve strategies like escape, avoidance, and tolerance, each influencing growth stages differently. Soil salinity affects plant growth by disrupting water potential, causing ion toxicity, and inhibiting nutrient uptake. Understanding plant responses to these stresses requires insights into histone-mediated modifications, chromatin remodeling, and the role of small RNAs in stress memory. Histone-mediated modifications, including acetylation and methylation, contribute to epigenetic stress memory, influencing plant adaptation to environmental stressors. Chromatin remodeling play a crucial role in abiotic stress responses, affecting the expression of stress-related genes. Small RNAs; miRNAs and siRNAs, participate in stress memory pathways by guiding DNA methylation and histone modifications. The interplay of these epigenetic mechanisms helps plants adapt to recurring stress events and enhance their resilience. In conclusion, unraveling the epigenetic mechanisms in plant responses to abiotic stresses provides valuable insights for developing resilient agricultural techniques. Understanding how plants utilize stress memory, histone modifications, chromatin remodeling, and small RNAs is crucial for designing strategies to mitigate the impact of climate change on crop production and global food security.
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Affiliation(s)
- Muhammad Daniyal Junaid
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey.
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
- Pakistan Environmental Protection Agency, Ministry of Climate Change & Environmental Coordination, Islamabad, Pakistan
| | - Beyazıt Abdurrahman Şanlı
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
| | - Ali Fuat Gökçe
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
| | - Zahide Neslihan Öztürk
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
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2
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Yadav S, Meena S, Kalwan G, Jain PK. DNA methylation: an emerging paradigm of gene regulation under drought stress in plants. Mol Biol Rep 2024; 51:311. [PMID: 38372841 DOI: 10.1007/s11033-024-09243-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Drought is an enormous threat to global crop production. In order to ensure food security for the burgeoning population, we must develop drought tolerant crop varieties. This necessitates the identification of drought-responsive genes and understanding the mechanisms involved in their regulation. DNA methylation is a widely studied mechanism of epigenetic regulation of gene expression, which is known to play vital role in conferring tolerance to various biotic and abiotic stress factors. The recent advances in next-generation sequencing (NGS) technologies, has allowed unprecedented access to genome-wide methylation marks, with single base resolution. The most important roles of DNA methylation have been studied in terms of gene body methylation (gbM), which is associated with regulation of both transcript abundance and its stability. The availability of mutants for the various genes encoding enzymes involved in methylation of DNA has allowed ascertainment of the biological significance of methylation. Even though a vast number of reports have emerged in the recent past, where both genome-wide methylation landscape and locus specific changes in DNA methylation have been studied, a conclusive picture with regards to the biological role of DNA methylation is still lacking. Compounding this, is the lack of sufficient evidence supporting the heritability of these epigenetic changes. Amongst the various epigenetic variations, the DNA methylation changes are observed to be the most stable. This review describes the drought-induced changes in DNA methylation identified across different plant species. We also briefly describe the stress memory contributed by these changes. The identification of heritable, drought-induced methylation marks would broaden the scope of crop improvement in the future.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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3
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Liu Y, Wang J, Liu B, Xu ZY. Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2252-2274. [PMID: 36149776 DOI: 10.1111/jipb.13368] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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4
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Nguyen NH, Vu NT, Cheong JJ. Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants. Int J Mol Sci 2022; 23:12918. [PMID: 36361708 PMCID: PMC9654142 DOI: 10.3390/ijms232112918] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2023] Open
Abstract
Plants respond to drought stress by producing abscisic acid, a chemical messenger that regulates gene expression and thereby expedites various physiological and cellular processes including the stomatal operation to mitigate stress and promote tolerance. To trigger or suppress gene transcription under drought stress conditions, the surrounding chromatin architecture must be converted between a repressive and active state by epigenetic remodeling, which is achieved by the dynamic interplay among DNA methylation, histone modifications, loop formation, and non-coding RNA generation. Plants can memorize chromatin status under drought conditions to enable them to deal with recurrent stress. Furthermore, drought tolerance acquired during plant growth can be transmitted to the next generation. The epigenetically modified chromatin architectures of memory genes under stressful conditions can be transmitted to newly developed cells by mitotic cell division, and to germline cells of offspring by overcoming the restraints on meiosis. In mammalian cells, the acquired memory state is completely erased and reset during meiosis. The mechanism by which plant cells overcome this resetting during meiosis to transmit memory is unclear. In this article, we review recent findings on the mechanism underlying transcriptional stress memory and the transgenerational inheritance of drought tolerance in plants.
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Affiliation(s)
- Nguyen Hoai Nguyen
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City 700000, Vietnam
| | - Nam Tuan Vu
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
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5
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Singh AK, Mishra P, Kashyap SP, Karkute SG, Singh PM, Rai N, Bahadur A, Behera TK. Molecular insights into mechanisms underlying thermo-tolerance in tomato. FRONTIERS IN PLANT SCIENCE 2022; 13:1040532. [PMID: 36388532 PMCID: PMC9645296 DOI: 10.3389/fpls.2022.1040532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Plant productivity is being seriously compromised by climate-change-induced temperature extremities. Agriculture and food safety are threatened due to global warming, and in many cases the negative impacts have already begun. Heat stress leads to significant losses in yield due to changes in growth pattern, plant phonologies, sensitivity to pests, flowering, grain filling, maturity period shrinkage, and senescence. Tomato is the second most important vegetable crop. It is very sensitive to heat stress and thus, yield losses in tomato due to heat stress could affect food and nutritional security. Tomato plants respond to heat stress with a variety of cellular, physiological, and molecular responses, beginning with the early heat sensing, followed by signal transduction, antioxidant defense, osmolyte synthesis and regulated gene expression. Recent findings suggest that specific plant organs are extremely sensitive to heat compared to the entire plant, redirecting the research more towards generative tissues. This is because, during sexual reproduction, developing pollens are the most sensitive to heat. Often, just a few degrees of temperature elevation during pollen development can have a negative effect on crop production. Furthermore, recent research has discovered certain genetic and epigenetic mechanisms playing key role in thermo-tolerance and have defined new directions for tomato heat stress response (HSR). Present challenges are to increase the understanding of molecular mechanisms underlying HS, and to identify superior genotypes with more tolerance to extreme temperatures. Several metabolites, genes, heat shock factors (HSFs) and microRNAs work together to regulate the plant HSR. The present review provides an insight into molecular mechanisms of heat tolerance and current knowledge of genetic and epigenetic control of heat-tolerance in tomato for sustainable agriculture in the future. The information will significantly contribute to improve breeding programs for development of heat tolerant cultivars.
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Affiliation(s)
- Achuit K. Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Pallavi Mishra
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Suhas G. Karkute
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Nagendra Rai
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Anant Bahadur
- Division of Crop Production, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Tusar K. Behera
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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6
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Rajpal VR, Rathore P, Mehta S, Wadhwa N, Yadav P, Berry E, Goel S, Bhat V, Raina SN. Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions. Front Cell Dev Biol 2022; 10:1020958. [PMID: 36340045 PMCID: PMC9628676 DOI: 10.3389/fcell.2022.1020958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity in natural populations. Studies show that environmental changes induce epigenetic switches either independently or in complementation with the genetic variation. Although most of the induced epigenetic variability gets reset between generations and is short-lived, some variation becomes transgenerational and results in heritable phenotypic traits. The short-term epigenetic responses provide the first tier of transient plasticity required for local adaptations while transgenerational epigenetic changes contribute to stress memory and help the plants respond better to recurring or long-term stresses. These transgenerational epigenetic variations translate into an additional tier of diversity which results in stable epialleles. In recent years, studies have been conducted on epigenetic variation in natural populations related to various biological processes, ecological factors, communities, and habitats. With the advent of advanced NGS-based technologies, epigenetic studies targeting plants in diverse environments have increased manifold to enhance our understanding of epigenetic responses to environmental stimuli in facilitating plant fitness. Taking all points together in a frame, the present review is a compilation of present-day knowledge and understanding of the role of epigenetics and its fitness benefits in diverse ecological systems in natural populations.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | | | - Sahil Mehta
- School of Agricultural Sciences, K.R. Mangalam University, Gurugram, Haryana, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Eapsa Berry
- Maharishi Kanad Bhawan, Delhi School of Climate Change and Sustainability, University of Delhi, Delhi, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Vishnu Bhat
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
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7
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Xiao M, Wang J, Xu F. Methylation hallmarks on the histone tail as a linker of osmotic stress and gene transcription. FRONTIERS IN PLANT SCIENCE 2022; 13:967607. [PMID: 36035677 PMCID: PMC9399788 DOI: 10.3389/fpls.2022.967607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/25/2022] [Indexed: 06/12/2023]
Abstract
Plants dynamically manipulate their gene expression in acclimation to the challenging environment. Hereinto, the histone methylation tunes the gene transcription via modulation of the chromatin accessibility to transcription machinery. Osmotic stress, which is caused by water deprivation or high concentration of ions, can trigger remarkable changes in histone methylation landscape and genome-wide reprogramming of transcription. However, the dynamic regulation of genes, especially how stress-inducible genes are timely epi-regulated by histone methylation remains largely unclear. In this review, recent findings on the interaction between histone (de)methylation and osmotic stress were summarized, with emphasis on the effects on histone methylation profiles imposed by stress and how histone methylation works to optimize the performance of plants under stress.
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8
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Ge W, Luo M, Sun H, Wei B, Zhou X, Zhou Q, Ji S. The CaMYB340 transcription factor induces chilling injury in post-harvest bell pepper by inhibiting fatty acid desaturation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:800-818. [PMID: 35653257 DOI: 10.1111/tpj.15854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Bell pepper (Capsicum annuum L.) is a tradable and desirable crop; however, its perishable nature requires low-temperature handling. Paradoxically, cold causes chilling injury (CI) and post-harvest waste. Current knowledge about CI in pepper is limited. The mechanism of CI is multi-faceted; therefore, we focused on fatty acid (FA) desaturation. We identified an upstream nuclear transcription factor (TF), CaMYB340, belonging to the R2R3 MYB subfamily, that negatively regulates FA desaturation and CaCBF3 expression and whose gene and protein expression is induced by low temperature (4°C). Specifically, McrBC treatment and bisulfite sequencing PCR indicate that exposure to cold triggers DNA methylation on one of the CHH sites in the CaMYB340 promoter. This epigenetic event at least partly contributes to the upregulation of CaMYB340 transcript levels. Increased expression of CaMYB340 results in the formation of protein complexes with CabHLH93 and CaMYB1R1, which in turn downregulate the expression of downstream genes. For peppers held at low temperature, transient overexpression of CaMYB340 reduced unsaturated FA content and membrane fluidity, resulting in cold-induced poor peel texture. Transient CaMYB340 silencing increased FA desaturation and lowered electrolyte leakage, enhancing cold tolerance in CaMYB340 knockdown fruits. Overall, these results underscore the intricacy of transcriptional networks in plants and highlight the role of CaMYB340 in CI occurrence in pepper fruits.
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Affiliation(s)
- Wanying Ge
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Manli Luo
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Huajun Sun
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Baodong Wei
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xin Zhou
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qian Zhou
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shujuan Ji
- College of Food, Shenyang Agricultural University, Shenyang, 110866, China
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9
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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: 1] [Impact Index Per Article: 0.5] [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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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. Int J Genomics 2022; 2022:1092894. [PMID: 35747076 PMCID: PMC9213152 DOI: 10.1155/2022/1092894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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Zhao W, Wang X, Zhang Q, Zheng Q, Yao H, Gu X, Liu D, Tian X, Wang X, Li Y, Zhu Z. H3K36 demethylase JMJ710 negatively regulates drought tolerance by suppressing MYB48-1 expression in rice. PLANT PHYSIOLOGY 2022; 189:1050-1064. [PMID: 35253881 PMCID: PMC9157158 DOI: 10.1093/plphys/kiac095] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/31/2022] [Indexed: 05/14/2023]
Abstract
The homeostasis of histone methylation is maintained by histone methyltransferases and demethylases, which are important for the regulation of gene expression. Here, we report a histone demethylase from rice (Oryza sativa), Jumonji C domain-containing protein (JMJ710), which belongs to the JMJD6 group and plays an important role in the response to drought stress. Overexpression of JMJ710 causes a drought-sensitive phenotype, while RNAi and clustered regularly interspaced short palindromic repeats (CRISPR)-knockout mutant lines show drought tolerance. In vitro and in vivo assays showed that JMJ710 is a histone demethylase. It targets to MYB TRANSCRIPTION FACTOR 48 (MYB48-1) chromatin, demethylates H3K36me2, and negatively regulates the expression of MYB48-1, a positive regulator of drought tolerance. Under drought stress, JMJ710 is downregulated and the expression of MYB48-1 increases, and the subsequent activation of its downstream drought-responsive genes leads to drought tolerance. This research reports a negative regulator of drought stress-responsive genes, JMJ710, that ensures that the drought tolerance mechanism is not mis-activated under normal conditions but allows quick activation upon drought stress.
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Affiliation(s)
- Weijie Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiaoyan Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qian Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qian Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Haitao Yao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiangyang Gu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Dongliang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xuemin Tian
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiaoji Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Yongqing Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengge Zhu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
- Author for correspondence:
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12
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Grape ASR-Silencing Sways Nuclear Proteome, Histone Marks and Interplay of Intrinsically Disordered Proteins. Int J Mol Sci 2022; 23:ijms23031537. [PMID: 35163458 PMCID: PMC8835812 DOI: 10.3390/ijms23031537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/27/2023] Open
Abstract
In order to unravel the functions of ASR (Abscisic acid, Stress, Ripening-induced) proteins in the nucleus, we created a new model of genetically transformed grape embryogenic cells by RNAi-knockdown of grape ASR (VvMSA). Nuclear proteomes of wild-type and VvMSA-RNAi grape cell lines were analyzed by quantitative isobaric tagging (iTRAQ 8-plex). The most significantly up- or down-regulated nuclear proteins were involved in epigenetic regulation, DNA replication/repair, transcription, mRNA splicing/stability/editing, rRNA processing/biogenesis, metabolism, cell division/differentiation and stress responses. The spectacular up-regulation in VvMSA-silenced cells was that of the stress response protein VvLEA D-29 (Late Embryogenesis Abundant). Both VvMSA and VvLEA D-29 genes displayed strong and contrasted responsiveness to auxin depletion, repression of VvMSA and induction of VvLEA D-29. In silico analysis of VvMSA and VvLEA D-29 proteins highlighted their intrinsically disordered nature and possible compensatory relationship. Semi-quantitative evaluation by medium-throughput immunoblotting of eighteen post-translational modifications of histones H3 and H4 in VvMSA-knockdown cells showed significant enrichment/depletion of the histone marks H3K4me1, H3K4me3, H3K9me1, H3K9me2, H3K36me2, H3K36me3 and H4K16ac. We demonstrate that grape ASR repression differentially affects members of complex nucleoprotein structures and may not only act as molecular chaperone/transcription factor, but also participates in plant responses to developmental and environmental cues through epigenetic mechanisms.
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Rashid MM, Vaishnav A, Verma RK, Sharma P, Suprasanna P, Gaur RK. Epigenetic regulation of salinity stress responses in cereals. Mol Biol Rep 2021; 49:761-772. [PMID: 34773178 DOI: 10.1007/s11033-021-06922-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/30/2021] [Indexed: 10/19/2022]
Abstract
Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.
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Affiliation(s)
- Md Mahtab Rashid
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India.,Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281121, India.,Agroecology and Environment, Agroscope (Reckenholz), 8046, Zürich, Switzerland
| | - Rakesh Kumar Verma
- Department of Biosciences, Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan, India
| | - Pradeep Sharma
- Department of Biotechnology, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - P Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - R K Gaur
- Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, India.
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Drosou V, Kapazoglou A, Letsiou S, Tsaftaris AS, Argiriou A. Drought induces variation in the DNA methylation status of the barley HvDME promoter. JOURNAL OF PLANT RESEARCH 2021; 134:1351-1362. [PMID: 34510287 DOI: 10.1007/s10265-021-01342-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Cytosine methylation is an epigenetic modification with essential roles in diverse plant biological processes including vegetative and reproductive development and responsiveness to environmental stimuli. A dynamic process involving DNA methyltransferases and DNA demethylases establishes cytosine DNA methylation levels and distribution along the genome. A DNA demethylase gene from barley (Hordeum vulgare), DEMETER (HvDME), the homologue of the Arabidopsis thaliana DME (AtDME), has been characterized previously and found to respond to drought conditions. Here, the promoter of the HvDME gene was analysed further by in silico and DNA methylation analysis. The effect of drought conditions on the DNA methylation status of HvDME was investigated at single-cytosine resolution using bisulfite sequencing. It was demonstrated that the HvDME promoter can be divided into two discrete regions, in terms of DNA methylation level and density; a relatively unmethylated region proximal to the translational start site that is depleted of non-CG (CHG, CHH) methylation and another distal region, approximately 1500 bp upstream of the translational start site, enriched in CG, as well as non-CG methylation. Drought stress provoked alterations in the methylation status of the HvDME promoter distal region, whereas the DNA methylation of the proximal region remained unaffected. Computational analysis of the HvDME promoter revealed the presence of several putative regulatory elements related to drought responsiveness, as well as transposable elements (TEs) that may affect DNA methylation. Overall, our results expand our investigations of the epigenetic regulation of the HvDME gene in response to drought stress in barley and may contribute to further understanding of the epigenetic mechanisms underlying abiotic stress responses in barley and other cereals.
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Affiliation(s)
- Victoria Drosou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thermi, 57001, Thessaloniki, Greece
| | - Aliki Kapazoglou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thermi, 57001, Thessaloniki, Greece.
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Lykovrysi, 14123, Athens, Greece.
| | - Sophia Letsiou
- Laboratory of Biochemistry, Department of Research and Development, APIVITA S.A., Industrial Park of Markopoulo Mesogaias, Markopoulo Attiki, 19003, Athens, Greece
| | | | - Anagnostis Argiriou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thermi, 57001, Thessaloniki, Greece
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15
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Kordyum E, Dubyna D. The role of epigenetic regulation in adaptive phenotypic plasticity of plants. UKRAINIAN BOTANICAL JOURNAL 2021. [DOI: 10.15407/ukrbotj78.05.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In recent decades, knowledge about the role of epigenetic regulation of gene expression in plant responses to external stimuli and in adaptation of plants to adverse environmental fluctuations have extended significantly. DNA methylation is considered as the main molecular mechanism that provides genomic information and contributes to the understanding of the molecular basis of phenotypic variations based on epigenetic modifications. Unfortunately, the vast majority of research in this area has been performed on the model species Arabidopsis thaliana. The development of the methylation-sensitive amplified polymorphism (MSAP) method has made it possible to implement the large-scale detection of DNA methylation alterations in wild non-model and agricultural plants with large and highly repetitive genomes in natural and manipulated habitats. The article presents current information on DNA methylation in species of natural communities and crops and its importance in plant development and adaptive phenotypic plasticity, along with brief reviews of current ideas about adaptive phenotypic plasticity and epigenetic regulation of gene expression. The great potential of further studies of the epigenetic role in phenotypic plasticity of a wide range of non-model species in natural populations and agrocenoses for understanding the molecular mechanisms of plant existence in the changing environment in onto- and phylogeny, directly related to the key tasks of forecasting the effects of global warming and crop selection, is emphasized. Specific taxa of the Ukrainian flora, which, in authors’ opinion, are promising and interesting for this type of research, are recommended.
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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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Wang Q, Liu P, Jing H, Zhou XF, Zhao B, Li Y, Jin JB. JMJ27-mediated histone H3K9 demethylation positively regulates drought-stress responses in Arabidopsis. THE NEW PHYTOLOGIST 2021; 232:221-236. [PMID: 34197643 DOI: 10.1111/nph.17593] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Dimethylation of histone H3 at lysine 9 (H3K9me2) is associated with heterochromatinization and transcriptional gene silencing in plants. The activation of sets of genes by drought stress is correlated with reduced H3K9me2 levels, but the role of H3K9 methylation in the regulation of drought-stress responses remains elusive. Here, we show that the Jumonji domain-containing H3K9 demethylase JMJ27 positively regulates drought-stress responses through its histone demethylase activity. RNA-seq analysis identified JMJ27-regulated genes, including positive regulators of drought stress GALACTINOL SYNTHASE 2 (GOLS2) and RESPONSE TO DESICCATION 20 (RD20). Genetic analysis demonstrated that JMJ27 positively regulates drought-stress responses at least partly through GOLS2 and RD20. JMJ27 directly associated with GOLS2 and RD20, and protected these loci from silencing by reducing H3K9me2 levels under normal conditions. REGULATORY PARTICLE NON-ATPASE 1a (RPN1a), a subunit of the 26S proteasome, interacted with JMJ27 and negatively regulated JMJ27 accumulation. Drought stress diminished RPN1a abundance, resulting in increased JMJ27 abundance. The drought stress-promoted occupancy of JMJ27 at GOLS2 and RD20 chromatin may reinforce their transcriptional induction by locally reducing the H3K9me2 levels. These results indicate that the RPN1a-JMJ27 module precisely regulates dynamic H3K9me2 deposition plasticity, ensuring proper adaptation to drought stress in Arabidopsis.
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Affiliation(s)
- Qiongli Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Peng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hua Jing
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Feng Zhou
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Bo Zhao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuan Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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Shen Q, Lin Y, Li Y, Wang G. Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues. PLANTS 2021; 10:plants10061165. [PMID: 34201297 PMCID: PMC8228231 DOI: 10.3390/plants10061165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and PRC1 implement and maintain the H3K27me3-mediated gene repression in most eukaryotic cells. Plants take advantage of this epigenetic machinery to reprogram gene expression in development and environmental adaption. Recent studies have uncovered a number of new players involved in the establishment, erasure, and regulation of H3K27me3 mark in plants, particularly highlighting new roles in plants’ responses to environmental cues. Here, we review current knowledge on PRC2-H3K27me3 dynamics occurring during plant growth and development, including its writers, erasers, and readers, as well as targeting mechanisms, and summarize the emerging roles of H3K27me3 mark in plant adaptation to environmental stresses.
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Tiwari RK, Lal MK, Kumar R, Chourasia KN, Naga KC, Kumar D, Das SK, Zinta G. Mechanistic insights on melatonin-mediated drought stress mitigation in plants. PHYSIOLOGIA PLANTARUM 2021; 172:1212-1226. [PMID: 33305363 DOI: 10.1111/ppl.13307] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/26/2020] [Accepted: 12/05/2020] [Indexed: 05/21/2023]
Abstract
Drought stress imposes a serious threat to crop productivity and nutritional security. Drought adaptation mechanisms involve complex regulatory network comprising of various sensory and signaling molecules. In this context, melatonin has emerged as a potential signaling molecule playing a crucial role in imparting stress tolerance in plants. Melatonin pretreatment regulates various plant physiological processes such as osmoregulation, germination, photosynthesis, senescence, primary/secondary metabolism, and hormonal cross-talk under water deficit conditions. Melatonin-mediated regulation of ascorbate-glutathione (AsA-GSH) cycle plays a crucial role to scavenge reactive oxygen species generated in the cells during drought. Here, in this review, the current knowledge on the role of melatonin to ameliorate adverse effects of drought by modulating morphological, physiological, and redox regulatory processes is discussed. The role of melatonin to improve water absorption capacity of roots by regulating aquaporin channels and hormonal cross-talk involved in drought stress mitigation are also discussed. Overall, melatonin is a versatile bio-molecule involved in growth promotion and yield enhancement under drought stress that makes it a suitable candidate for eco-friendly crop production to ensure food security.
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Affiliation(s)
- Rahul Kumar Tiwari
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Milan Kumar Lal
- Division of Crop Physiology, Biochemistry and Post-harvest Technology, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ravinder Kumar
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Kumar Nishant Chourasia
- Division of Crop Improvement, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Kailash Chandra Naga
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Dharmendra Kumar
- Division of Crop Physiology, Biochemistry and Post-harvest Technology, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Sourav Kumar Das
- Radiation Biology and Health Science Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
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Kumar J, Sen Gupta D, Djalovic I, Kumar S, Siddique KHM. Root-omics for drought tolerance in cool-season grain legumes. PHYSIOLOGIA PLANTARUM 2021; 172:629-644. [PMID: 33314181 DOI: 10.1111/ppl.13313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Root traits can be exploited to increase the physiological efficiency of crop water use under drought. Root length, root hairs, root branching, root diameter, and root proliferation rate are genetically defined traits that can help to improve the water productivity potential of crops. Recently, high-throughput phenotyping techniques/platforms have been used to screen the germplasm of major cool-season grain legumes for root traits and their impact on different physiological processes, including nutrient uptake and yield potential. Advances in omics approaches have led to the dissection of genomic, proteomic, and metabolomic structures of these traits. This knowledge facilitates breeders to improve the water productivity and nutrient uptake of cultivars under limited soil moisture conditions in major cool-season grain legumes that usually face terminal drought. This review discusses the advances in root traits and their potential for developing drought-tolerant cultivars in cool-season grain legumes.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Ivica Djalovic
- Maize Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Shiv Kumar
- Biodiversity and Crop Improvement Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
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Cuervo-Alarcon L, Arend M, Müller M, Sperisen C, Finkeldey R, Krutovsky KV. A candidate gene association analysis identifies SNPs potentially involved in drought tolerance in European beech (Fagus sylvatica L.). Sci Rep 2021; 11:2386. [PMID: 33504857 PMCID: PMC7840767 DOI: 10.1038/s41598-021-81594-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Studies of genetic variation underlying traits related to drought tolerance in forest trees are of great importance for understanding their adaptive potential under a climate change scenario. In this study, using a candidate gene approach, associations between SNPs and drought related traits were assessed in saplings of European beech (Fagus sylvatica L.) representing trees growing along steep precipitation gradients. The saplings were subjected to experimentally controlled drought treatments. Response of the saplings was assessed by the evaluation of stem diameter growth (SDG) and the chlorophyll fluorescence parameters FV/FM, PIabs, and PItot. The evaluation showed that saplings from xeric sites were less affected by the drought treatment. Five SNPs (7.14%) in three candidate genes were significantly associated with the evaluated traits; saplings with particular genotypes at these SNPs showed better performance under the drought treatment. The SNPs were located in the cytosolic class I small heat-shock protein, CTR/DRE binding transcription factor, and isocitrate dehydrogenase genes and explained 5.8-13.4% of the phenotypic variance. These findings provide insight into the genetic basis of traits related to drought tolerance in European beech and could support the development of forest conservation management strategies under future climatic conditions.
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Affiliation(s)
- Laura Cuervo-Alarcon
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Matthias Arend
- Physiological Plant Ecology, University of Basel, Schönbeinstrasse 6, 4056, Basel, Switzerland
| | - Markus Müller
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Christoph Sperisen
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Reiner Finkeldey
- University of Kassel, Mönchebergstrasse 19, 34109, Kassel, Germany
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., Moscow, Russia, 119333.
- Laboratory of Foresty Genomics, Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, Russia, 660036.
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.
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Salava H, Thula S, Mohan V, Kumar R, Maghuly F. Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects. Int J Mol Sci 2021; 22:E682. [PMID: 33445555 PMCID: PMC7827871 DOI: 10.3390/ijms22020682] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.
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Affiliation(s)
- Hymavathi Salava
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Sravankumar Thula
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic;
| | - Vijee Mohan
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA;
| | - Rahul Kumar
- Plant Translational Research Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Fatemeh Maghuly
- Plant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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Yang Y, Saand MA, Huang L, Abdelaal WB, Zhang J, Wu Y, Li J, Sirohi MH, Wang F. Applications of Multi-Omics Technologies for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:563953. [PMID: 34539683 PMCID: PMC8446515 DOI: 10.3389/fpls.2021.563953] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/06/2021] [Indexed: 05/19/2023]
Abstract
Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- *Correspondence: Yaodong Yang
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Department of Botany, Shah Abdul Latif University, Khairpur, Pakistan
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Walid Badawy Abdelaal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jun Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Fuyou Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Pecinka A, Chevalier C, Colas I, Kalantidis K, Varotto S, Krugman T, Michailidis C, Vallés MP, Muñoz A, Pradillo M. Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5205-5222. [PMID: 31626285 DOI: 10.1093/jxb/erz457] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.
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Affiliation(s)
- Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Agricultural and Biotechnological Research, Olomouc, Czech Republic
| | | | - Isabelle Colas
- James Hutton Institute, Cell and Molecular Science, Pr Waugh's Lab, Invergowrie, Dundee, UK
| | - Kriton Kalantidis
- Department of Biology, University of Crete, and Institute of Molecular Biology Biotechnology, FoRTH, Heraklion, Greece
| | - Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment (DAFNAE) University of Padova, Agripolis viale dell'Università, Legnaro (PD), Italy
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Christos Michailidis
- Institute of Experimental Botany, Czech Acad Sci, Praha 6 - Lysolaje, Czech Republic
| | - María-Pilar Vallés
- Department of Genetics and Plant Breeding, Estación Experimental Aula Dei (EEAD), Spanish National Research Council (CSIC), Zaragoza, Spain
| | - Aitor Muñoz
- Department of Plant Molecular Genetics, National Center of Biotechnology/Superior Council of Scientific Research, Autónoma University of Madrid, Madrid, Spain
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
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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: 52] [Impact Index Per Article: 13.0] [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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Turgut-Kara N, Arikan B, Celik H. Epigenetic memory and priming in plants. Genetica 2020; 148:47-54. [PMID: 32356021 DOI: 10.1007/s10709-020-00093-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/16/2020] [Indexed: 12/17/2022]
Abstract
In nature, plants are regularly exposed to biotic and abiotic stress conditions. These conditions create potential risks for survival. Plants have evolved in order to compete with these stress conditions through physiological adjustments that are based on epigenetic background. Thus, the ecological signals create different levels of stress memory. Recent studies have shown that this stress-induced environmental memory is mediated by epigenetic mechanisms that have fundamental roles in the aspect of controlling gene expression via DNA methylation, histone modifications and, small RNAs and these modifications could be transmitted to the next generations. Thus, they provide alternative mechanisms to constitute stress memories in plants. In this review, we summarized the epigenetic memory mechanisms related with biotic and abiotic stress conditions, and relationship between priming and epigenetic memory in plants by believing that it can be useful for analyzing memory mechanisms and see what is missing out in order to develop plants more resistant and productive under diverse environmental cues.
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Affiliation(s)
- Neslihan Turgut-Kara
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey.
| | - Burcu Arikan
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey
| | - Haluk Celik
- Program of Molecular Biology and Genetics, Institute of Science, Istanbul University, Istanbul, Turkey
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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
- *Correspondence: Junzhong Liu,
| | - 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
- Zuhua He,
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29
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Xing L, Li Y, Qi S, Zhang C, Ma W, Zuo X, Liang J, Gao C, Jia P, Shah K, Zhang D, An N, Zhao C, Han M, Zhao J. Comparative RNA-Sequencing and DNA Methylation Analyses of Apple (Malus domestica Borkh.) Buds with Diverse Flowering Capabilities Reveal Novel Insights into the Regulatory Mechanisms of Flower Bud Formation. PLANT & CELL PHYSIOLOGY 2019; 60:1702-1721. [PMID: 31077318 DOI: 10.1093/pcp/pcz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
In plants, DNA methylation (i.e. chromatin modification) is important for various biological processes, including growth, development and flowering. Because 'Fuji' apple trees are alternate bearing and have a long ripening period and poor-quality flower buds, we used bud types with diverse flowering capabilities to investigate the epigenetic regulatory mechanisms influencing flower bud formation. We examined the DNA methylation changes and the transcriptional responses in the selected apple bud types. We observed that in the apple genome, approximately 79.5%, 67.4% and 23.7% of the CG, CHG and CHH sequences are methylated, respectively. For each sequence context, differentially methylated regions exhibited distinct methylation patterns among the analyzed apple bud types. Global methylation and transcriptional analyses revealed that nonexpressed genes or genes expressed at low levels were highly methylated in the gene-body regions, suggesting that gene-body methylation is negatively correlated with gene expression. Moreover, genes with methylated promoters were more highly expressed than genes with unmethylated promoters, implying promoter methylation and gene expression are positively correlated. Additionally, flowering-related genes (e.g. SOC1, AP1 and SPLs) and some transcription factor genes (e.g. GATA, bHLH, bZIP and WOX) were highly expressed in spur buds (highest flowering rate), but were associated with low methylation levels in the gene-body regions. Our findings indicate a potential correlation between DNA methylation and gene expression in apple buds with diverse flowering capabilities, suggesting an epigenetic regulatory mechanism influences apple flower bud formation.
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Affiliation(s)
- Libo Xing
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Siyan Qi
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chenguang Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Wenchun Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xiya Zuo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jiayan Liang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Cai Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Pen Jia
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kamran Shah
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Na An
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Caiping Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Juan Zhao
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
- College of Mechanical and Electronic Engineering, Northwest A & F University, Yangling, Shaanxi, P. R. China
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30
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Cong W, Miao Y, Xu L, Zhang Y, Yuan C, Wang J, Zhuang T, Lin X, Jiang L, Wang N, Ma J, Sanguinet KA, Liu B, Rustgi S, Ou X. Transgenerational memory of gene expression changes induced by heavy metal stress in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2019; 19:282. [PMID: 31248374 PMCID: PMC6598230 DOI: 10.1186/s12870-019-1887-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/13/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Heavy metal toxicity has become a major threat to sustainable crop production worldwide. Thus, considerable interest has been placed on deciphering the mechanisms that allow plants to combat heavy metal stress. Strategies to deal with heavy metals are largely focused on detoxification, transport and/or sequestration. The P1B subfamily of the Heavy Metal-transporting P-type ATPases (HMAs) was shown to play a crucial role in the uptake and translocation of heavy metals in plants. Here, we report the locus-specific expression changes in the rice HMA genes together with several low-copy cellular genes and transposable elements upon the heavy metal treatment and monitored the transgenerational inheritance of the altered expression states. We reveal that plants cope with heavy metal stress by making heritable changes in gene expression and further determined gene-specific responses to heavy metal stress. RESULTS We found most HMA genes were upregulated in response to heavy metal stress, and furthermore found evidence of transgenerational memory via changes in gene regulation even after the removal of heavy metals. To explore whether DNA methylation was also altered in response to the heavy metal stress, we selected a Tos17 retrotransposon for bisulfite sequencing and studied its methylation state across three generations. We found the DNA methylation state of Tos17 was altered in response to the heavy metal stress and showed transgenerational inheritance. CONCLUSIONS Collectively, the present study elucidates heritable changes in gene expression and DNA methylation in rice upon exposure to heavy metal stress and discusses implications of this knowledge in breeding for heavy metal tolerant crops.
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Affiliation(s)
- Weixuan Cong
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Yiling Miao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Lei Xu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Yunhong Zhang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Chunlei Yuan
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Junmeng Wang
- 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
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences, Changchun, 130033 China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Ningning Wang
- Jilin Agriculture University, Changchun, 130000 China
| | - Jian Ma
- Jilin Agriculture University, Changchun, 130000 China
| | - Karen A. Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164 USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Sachin Rustgi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164 USA
- Department of Plant and Environmental Sciences, Clemson University, Pee Dee Research and Education Center, Florence, SC 29506 USA
| | - Xiufang Ou
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
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31
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O'Doherty AM, Rue-Albrecht KC, Magee DA, Ahting S, Irwin RE, Hall TJ, Browne JA, Nalpas NC, Walsh CP, Gordon SV, Wojewodzic MW, MacHugh DE. The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis. Sci Rep 2019; 9:1510. [PMID: 30728374 PMCID: PMC6365515 DOI: 10.1038/s41598-018-37618-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 12/07/2018] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is pivotal in orchestrating gene expression patterns in various mammalian biological processes. Perturbation of the bovine alveolar macrophage (bAM) transcriptome, due to Mycobacterium bovis (M. bovis) infection, has been well documented; however, the impact of this intracellular pathogen on the bAM epigenome has not been determined. Here, whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome. The methylomes of bAM infected with M. bovis were compared to those of non-infected bAM 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation of 33–66%). Gene ontology analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of genes in the IM category confirmed the WGBS observation. This study is the first in cattle examining genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model, providing evidence for IM promoter methylation in bAM.
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Affiliation(s)
- Alan Mark O'Doherty
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.
| | - Kevin Christophe Rue-Albrecht
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Headington, Oxford, OX3 7FY, UK
| | - David Andrew Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Simone Ahting
- Institute of Molecular Medicine, Trinity College Dublin, Dublin, D08 W9RT, Ireland
| | - Rachelle Elizabeth Irwin
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA, UK
| | - Thomas Jonathan Hall
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - John Arthur Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Nicolas Claude Nalpas
- Quantitative Proteomics and Proteome Centre Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Colum Patrick Walsh
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA, UK
| | - Stephen Vincent Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | | | - David Evan MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
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32
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Beyrne CC, González RM, Iusem ND. Strategy for the analysis of tissue-specific methylation changes without physical isolation. Epigenetics 2019; 14:41-51. [PMID: 30632887 DOI: 10.1080/15592294.2019.1565589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
One common experimental hurdle that arises when explore patterns of cytosine methylation is the generation of data derived from a single specific tissue, often arduous to isolate from a heterogeneous biospecimen. Here we show a new strategy for exploring environment- or mutation-caused changes in cell type- or tissue-specific methylation landscapes, which requires neither transgenic reporter cell lines nor physical separation. This approach takes advantage of a known distinct methylation signature existing in only one of the tissues within an organ under a particular condition. From the information on such compared published methylomes, one can design a set of PCR primers that specifically amplify bisulfite-converted DNA of two nearby genomic regions of interest, thus allowing for tissue-specific DNA methylation data. To validate the performance of the approach, we designed primers able to amplify a portion of a gene in the context of root biology: the Arabidopsis homeotic gene Glabra-2 (Gl2), expressed only in epidermis during cell differentiation. We found that the extent of methylated cytosines appears remarkably different when root epidermis-specific primers were used vs. non-specific ones under three genetic backgrounds involving mutations in genes also associated with the establishment of cell identity. Although the genetic or environmental perturbations to be studied might modify methylation in the primer-annealing zone, leading to a possible misinterpretation of the data, the strategy presented here can become a useful first round screening tool to detect differences in tissue-specific epigenetic status under new conditions.
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Affiliation(s)
- Cecilia C Beyrne
- a Instituto de Fisiología , Biología Molecular y Neurociencias (IFIByNE); CONICET , Buenos Aires , Argentina
| | - Rodrigo M González
- a Instituto de Fisiología , Biología Molecular y Neurociencias (IFIByNE); CONICET , Buenos Aires , Argentina
| | - Norberto D Iusem
- a Instituto de Fisiología , Biología Molecular y Neurociencias (IFIByNE); CONICET , Buenos Aires , Argentina.,b Departamento de Fisiología, Biología Molecular y Celular (FBMC); Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
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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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Gaion LA, Monteiro CC, Cruz FJR, Rossatto DR, López-Díaz I, Carrera E, Lima JE, Peres LEP, Carvalho RF. Constitutive gibberellin response in grafted tomato modulates root-to-shoot signaling under drought stress. JOURNAL OF PLANT PHYSIOLOGY 2018; 221:11-21. [PMID: 29223878 DOI: 10.1016/j.jplph.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/21/2017] [Accepted: 12/02/2017] [Indexed: 05/07/2023]
Abstract
Plants are sessile organisms that must perceive and respond to various environmental constraints throughout their life cycle. Among these constraints, drought stress has become the main limiting factor to crop production around the world. Water deprivation is perceived primarily by the roots, which efficiently signal the shoot to trigger drought responses in order to maximize a plant's ability to survive. In this study, the tomato (Solanum lycopersicum L.) mutant procera (pro), with a constitutive response to gibberellin (GA), and its near isogenic line cv. Micro-Tom (MT), were used in reciprocal grafting under well-watered and water stress conditions to evaluate the role of GA signaling in root-to-shoot communication during drought stress. Growth, oxidative stress, gene expression, water relations and hormonal content were measured in order to provide insights into GA-mediated adjustments to water stress. All graft combinations with pro (i.e. pro/pro, MT/pro and pro/MT) prevented the reduction of growth under stress conditions without a reduction in oxidative stress. The increase of oxidative stress was followed by upregulation of SlDREB2, a drought-tolerance related gene, in all drought-stressed plants. Scions harboring the pro mutation tended to increase the abscisic acid (ABA) content, independent of the rootstock. Moreover, the GA sensitivity of the rootstock modulated stomatal conductance and water use efficiency under drought stress, indicating GA and ABA crosstalk in the adjustment of growth and water economy.
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Affiliation(s)
- Lucas Aparecido Gaion
- Department of Biology Applied to Agriculture, São Paulo State University, Via de Acesso Prof. Paulo Donato Castellane, 14884-900, Jaboticabal, Brazil
| | - Carolina Cristina Monteiro
- Department of Biology Applied to Agriculture, São Paulo State University, Via de Acesso Prof. Paulo Donato Castellane, 14884-900, Jaboticabal, Brazil
| | - Flávio José Rodrigues Cruz
- Department of Biology Applied to Agriculture, São Paulo State University, Via de Acesso Prof. Paulo Donato Castellane, 14884-900, Jaboticabal, Brazil
| | - Davi Rodrigo Rossatto
- Department of Biology Applied to Agriculture, São Paulo State University, Via de Acesso Prof. Paulo Donato Castellane, 14884-900, Jaboticabal, Brazil
| | - Isabel López-Díaz
- Institute for Plant Molecular and Cellular Biology (IBMCP), CSIC-UPV, Carrer de l'Enginyer Fausto Elio 46011, Valencia, Spain
| | - Esther Carrera
- Institute for Plant Molecular and Cellular Biology (IBMCP), CSIC-UPV, Carrer de l'Enginyer Fausto Elio 46011, Valencia, Spain
| | - Joni Esrom Lima
- Botany Department, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Minas Gerais, Brazil
| | | | - Rogério Falleiros Carvalho
- Department of Biology Applied to Agriculture, São Paulo State University, Via de Acesso Prof. Paulo Donato Castellane, 14884-900, Jaboticabal, Brazil.
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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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Crespo-Salvador Ó, Escamilla-Aguilar M, López-Cruz J, López-Rodas G, González-Bosch C. Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea. PLANT CELL REPORTS 2018; 37:153-166. [PMID: 29119291 DOI: 10.1007/s00299-017-2218-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/05/2017] [Indexed: 05/25/2023]
Abstract
Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea may contribute to find biomarkers of the early detection of this devastating pathogen. Recent studies have linked epigenetic modifications with plant responses to biotic stresses. Information about specific histone marks upon necrotrophic pathogens is scarce. Here we wondered whether the altered responsiveness of specific genes in plants infected with Botrytis cinerea was associated with changes in chromatin structure. We performed a chromatin immunoprecipitation analysis that obtained differential epigenetic signature of activating marks H3K4me3, H3K9ac, and the repressor one H3K27me3 on both the promoter and the body of the highly induced PR1 in Arabidopsis plants infected with B. cinerea at 24 and 33 h after inoculation. We also determined the histone marks' profile in two differentially expressed genes in response to B. cinerea, as well as to oxidative stress, given its relevance in this infection. These are both the induced CYP71A13, which encodes a cytochrome P450 involved in camalexin synthesis, and is essential against this necrotroph and the repressed EXL7 (Exordium-like 1). We also adapted our protocol in tomato plants infected with B. cinerea. At 24 hpi, H3K4me3 level increased on the promoter and at different locations of the body of the genes induced upon B. cinerea, including DES (divinyl ethyl synthase), LoxD (lipoxygenase D), DOX1 (α-dioxygenase 1), PR2 (pathogenesis-related protein2), WRKY53 and WRKY33. The histone modifications determined herein will allow future studies on epigenetic marks and their transgenerational inheritance in plants infected with B. cinerea. In addition, the analyzed genes are potential biomarkers of B. cinerea infection that could contribute to its early detection in tomato and related crops.
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Affiliation(s)
- Óscar Crespo-Salvador
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46980, Paterna, Valencia, Spain
| | - Mónica Escamilla-Aguilar
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46980, Paterna, Valencia, Spain
| | - Jaime López-Cruz
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46980, Paterna, Valencia, Spain
| | - Gerardo López-Rodas
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Dr. Moliner 50, Burjassot, Valencia, Spain
- Institute of health research INCLIVA, Valencia, Spain
| | - Carmen González-Bosch
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46980, Paterna, Valencia, Spain.
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Gallusci P, Dai Z, Génard M, Gauffretau A, Leblanc-Fournier N, Richard-Molard C, Vile D, Brunel-Muguet S. Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues. TRENDS IN PLANT SCIENCE 2017; 22:610-623. [PMID: 28587758 DOI: 10.1016/j.tplants.2017.04.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/12/2017] [Accepted: 04/28/2017] [Indexed: 05/21/2023]
Abstract
Epigenetic variations are involved in the control of plant developmental processes and participate in shaping phenotypic plasticity to the environment. Intense breeding has eroded genetic diversity, and epigenetic diversity now emerge as a new source of phenotypic variations to improve adaptation to changing environments and ensure the yield and quality of crops. Here, we review how the characterization of the stability and heritability of epigenetic variations is required to drive breeding strategies, which can be assisted by process-based models. We propose future directions to hasten the elucidation of complex epigenetic regulatory networks that should help crop modelers to take epigenetic modifications into account and assist breeding strategies for specific agronomical traits.
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Affiliation(s)
- Philippe Gallusci
- EGFV, Bordeaux Sciences Agro, INRA, Univ. Bordeaux, 33140 Villenave d'Ornon, France.
| | - Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Univ. Bordeaux, 33140 Villenave d'Ornon, France.
| | | | - Arnaud Gauffretau
- UMR Agronomie, AgroParisTech, INRA, 78850, Thiverval-Grignon, France
| | | | - Céline Richard-Molard
- UMR ECOSYS, INRA AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Denis Vile
- LEPSE, INRA-SupAgro, 34060, Montpellier, France
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Fortes AM, Gallusci P. Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:82. [PMID: 28220131 PMCID: PMC5292615 DOI: 10.3389/fpls.2017.00082] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/16/2017] [Indexed: 05/20/2023]
Abstract
Epigenetic marks include Histone Post-Translational Modifications and DNA methylation which are known to participate in the programming of gene expression in plants and animals. These epigenetic marks may be subjected to dynamic changes in response to endogenous and/or external stimuli and can have an impact on phenotypic plasticity. Studying how plant genomes can be epigenetically shaped under stressed conditions has become an essential issue in order to better understand the molecular mechanisms underlying plant stress responses and enabling epigenetic in addition to genetic factors to be considered when breeding crop plants. In this perspective, we discuss the contribution of epigenetic mechanisms to our understanding of plant responses to biotic and abiotic stresses. This regulation of gene expression in response to environment raises important biological questions for perennial species such as grapevine which is asexually propagated and grown worldwide in contrasting terroirs and environmental conditions. However, most species used for epigenomic studies are annual herbaceous plants, and epigenome dynamics has been poorly investigated in perennial woody plants, including grapevine. In this context, we propose grape as an essential model for epigenetic and epigenomic studies in perennial woody plants of agricultural importance.
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Affiliation(s)
- Ana M. Fortes
- Faculdade de Ciências, Instituto de Biossistemas e Ciências Integrativas, Universidade de LisboaLisboa, Portugal
| | - Philippe Gallusci
- UMR EGFV, Université de Bordeaux, Institut national de la recherche agronomique, Institut des Sciences de la Vigne et du VinVillenave-d’Ornon, France
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Kalinka A, Achrem M, Poter P. The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L. PeerJ 2017; 5:e2889. [PMID: 28149679 PMCID: PMC5267573 DOI: 10.7717/peerj.2889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/08/2016] [Indexed: 01/05/2023] Open
Abstract
Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue.
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Affiliation(s)
- Anna Kalinka
- Department of Cell Biology, Faculty of Biology, University of Szczecin, Szczecin, Poland; Molecular Biology and Biotechnology Center, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Magdalena Achrem
- Department of Cell Biology, Faculty of Biology, University of Szczecin, Szczecin, Poland; Molecular Biology and Biotechnology Center, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Paulina Poter
- Department of Cell Biology, Faculty of Biology, University of Szczecin , Szczecin , 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: 11] [Impact Index Per Article: 1.6] [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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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: 49] [Impact Index Per Article: 6.1] [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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Candar-Cakir B, Arican E, Zhang B. Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1727-46. [PMID: 26857916 PMCID: PMC5067666 DOI: 10.1111/pbi.12533] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 12/15/2015] [Accepted: 12/26/2015] [Indexed: 05/03/2023]
Abstract
Drought stress has adverse impacts on plant production and productivity. MicroRNAs (miRNAs) are one class of noncoding RNAs regulating gene expression post-transcriptionally. In this study, we employed small RNA and degradome sequencing to systematically investigate the tissue-specific miRNAs responsible to drought stress, which are understudied in tomato. For this purpose, root and upground tissues of two different drought-responsive tomato genotypes (Lycopersicon esculentum as sensitive and L. esculentum var. cerasiforme as tolerant) were subjected to stress with 5% polyethylene glycol for 7 days. A total of 699 conserved miRNAs belonging to 578 families were determined and 688 miRNAs were significantly differentially expressed between different treatments, tissues and genotypes. Using degradome sequencing, 44 target genes were identified associated with 36 miRNA families. Drought-related miRNAs and their targets were enriched functionally by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Totally, 53 miRNAs targeted 23 key drought stress- and tissue development-related genes, including DRP (dehydration-responsive protein), GTs (glycosyltransferases), ERF (ethylene responsive factor), PSII (photosystem II) protein, HD-ZIP (homeodomain-leucine zipper), MYB and NAC-domain transcription factors. miR160, miR165, miR166, miR171, miR398, miR408, miR827, miR9472, miR9476 and miR9552 were the key miRNAs functioning in regulation of these genes and involving in tomato response to drought stress. Additionally, plant hormone signal transduction pathway genes were differentially regulated by miR169, miR172, miR393, miR5641, miR5658 and miR7997 in both tissues of both sensitive and tolerant genotypes. These results provide new insight into the regulatory role of miRNAs in drought response with plant hormone signal transduction and drought-tolerant tomato breeding.
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Affiliation(s)
- Bilgin Candar-Cakir
- Programme of Molecular Biology and Genetics, Institute of Science, Istanbul University, Vezneciler, Istanbul, Turkey
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Ercan Arican
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, Istanbul, Turkey
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, USA
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Abstract
Environmental conditions can change the activity of plant genes via epigenetic effects that alter the competence of genetic information to be expressed. This may provide a powerful strategy for plants to adapt to environmental change. However, as epigenetic changes do not modify DNA sequences and are therefore reversible, only those epi-mutations that are transmitted through the germline can be expected to contribute to a long-term adaptive response. The major challenge for the investigation of epigenetic adaptation theories is therefore to identify genomic loci that undergo epigenetic changes in response to environmental conditions, which alter their expression in a heritable way and which improve the plant's ability to adapt to the inducing conditions. This review focuses on the role of DNA methylation as a prominent epigenetic mark that controls chromatin conformation, and on its potential in mediating expression changes in response to environmental signals.
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Affiliation(s)
- Peter Meyer
- Centre for Plant Sciences, University of Leeds, Leeds, UK
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45
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O'Doherty AM, McGettigan PA. Epigenetic processes in the male germline. Reprod Fertil Dev 2015; 27:725-38. [DOI: 10.1071/rd14167] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/01/2014] [Indexed: 12/12/2022] Open
Abstract
Sperm undergo some of the most extensive chromatin modifications seen in mammalian biology. During male germline development, paternal DNA methylation marks are erased and established on a global scale through waves of demethylation and de novo methylation. As spermatogenesis progresses, the majority of the histones are removed and replaced by protamines, enabling a tighter packaging of the DNA and transcriptional shutdown. Following fertilisation, the paternal genome is rapidly reactivated, actively demethylated, the protamines are replaced with histones and the embryonic genome is activated. The development of new assays, made possible by high-throughput sequencing technology, has resulted in the revisiting of what was considered settled science regarding the state of DNA packaging in mammalian spermatozoa. Researchers have discovered that not all histones are replaced by protamines and, in certain experiments, various species of RNA have been detected in what was previously considered transcriptionally quiescent spermatozoa. Most controversially, several groups have suggested that environmental modifications of the epigenetic state of spermatozoa may operate as a non-DNA-based form of inheritance, a process known as ‘transgenerational epigenetic inheritance’. Other developments in the field include the increased focus on the involvement of short RNAs, such as microRNAs, long non-coding RNAs and piwi-interacting RNAs. There has also been an accumulation of evidence illustrating associations between defects in sperm DNA packaging and disease and fertility. In this paper we review the literature, recent findings and areas of controversy associated with epigenetic processes in the male germline, focusing on DNA methylation dynamics, non-coding RNAs, the biology of sperm chromatin packaging and transgenerational inheritance.
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O'Doherty AM, O'Gorman A, al Naib A, Brennan L, Daly E, Duffy P, Fair T. Negative energy balance affects imprint stability in oocytes recovered from postpartum dairy cows. Genomics 2014; 104:177-85. [PMID: 25084396 DOI: 10.1016/j.ygeno.2014.07.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 12/27/2022]
Abstract
Ovarian follicle development in post-partum, high-producing dairy cows, occurs in a compromised endogenous metabolic environment (referred to as negative energy balance, NEB). Key events that occur during oocyte/follicle growth, such as the vital process of genomic imprinting, may be detrimentally affected by this altered ovarian environment. Imprinting is crucial for placental function and regulation of fetal growth, therefore failure to establish and maintain imprints during oocyte growth may contribute to early embryonic loss. Using ovum pick-up (OPU), oocytes and follicular fluid samples were recovered from cows between days 20 and 115 post-calving, encompassing the NEB period. In a complimentary study, cumulus oocyte complexes were in vitro matured under high non-esterified fatty acid (NEFA) concentrations and in the presence of the methyl-donor S-adenosylmethionine (SAM). Pyrosequencing revealed the loss of methylation at several imprinted loci in the OPU derived oocytes. The loss of DNA methylation was observed at the PLAGL1 locus in oocytes, following in vitro maturation (IVM) in the presence of elevated NEFAs and SAM. Finally, metabolomic analysis of postpartum follicular fluid samples revealed significant differences in several branched chain amino acids, with fatty acid profiles bearing similarities to those characteristic of lactating dairy cows. These results provide the first evidence that (1) the postpartum ovarian environment may affect maternal imprint acquisition and (2) elevated NEFAs during IVM can lead to the loss of imprinted gene methylation in bovine oocytes.
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Affiliation(s)
- Alan M O'Doherty
- School of Agriculture & Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aoife O'Gorman
- School of Agriculture & Food Science, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Abdullah al Naib
- Lyons Research Farm, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lorraine Brennan
- School of Agriculture & Food Science, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Edward Daly
- Lyons Research Farm, University College Dublin, Belfield, Dublin 4, Ireland
| | - Pat Duffy
- Lyons Research Farm, University College Dublin, Belfield, Dublin 4, Ireland
| | - Trudee Fair
- School of Agriculture & Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
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Bloomfield JA, Rose TJ, King GJ. Sustainable harvest: managing plasticity for resilient crops. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:517-33. [PMID: 24891039 PMCID: PMC4207195 DOI: 10.1111/pbi.12198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/14/2014] [Indexed: 05/18/2023]
Abstract
Maintaining crop production to feed a growing world population is a major challenge for this period of rapid global climate change. No consistent conceptual or experimental framework for crop plants integrates information at the levels of genome regulation, metabolism, physiology and response to growing environment. An important role for plasticity in plants is assisting in homeostasis in response to variable environmental conditions. Here, we outline how plant plasticity is facilitated by epigenetic processes that modulate chromatin through dynamic changes in DNA methylation, histone variants, small RNAs and transposable elements. We present examples of plant plasticity in the context of epigenetic regulation of developmental phases and transitions and map these onto the key stages of crop establishment, growth, floral initiation, pollination, seed set and maturation of harvestable product. In particular, we consider how feedback loops of environmental signals and plant nutrition affect plant ontogeny. Recent advances in understanding epigenetic processes enable us to take a fresh look at the crosstalk between regulatory systems that confer plasticity in the context of crop development. We propose that these insights into genotype × environment (G × E) interaction should underpin development of new crop management strategies, both in terms of information-led agronomy and in recognizing the role of epigenetic variation in crop breeding.
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Affiliation(s)
- Justin A Bloomfield
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Terry J Rose
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
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González RM, Iusem ND. Twenty years of research on Asr (ABA-stress-ripening) genes and proteins. PLANTA 2014; 239:941-949. [PMID: 24531839 DOI: 10.1007/s00425-014-2039-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 01/29/2014] [Indexed: 05/29/2023]
Abstract
Investigating how plants cope with different abiotic stresses-mainly drought and extreme temperatures-is pivotal for both understanding the underlying signaling pathways and improving genetically engineered crops. Plant cells are known to react defensively to mild and severe dehydration by initiating several signal transduction pathways that result in the accumulation of different proteins, sugar molecules and lipophilic anti-oxidants. Among the proteins that build up under these adverse conditions are members of the ancestral ASR (ABA-stress-ripening) family, which is conserved in the plant kingdom but lacks orthologs in Arabidopsis. This review provides a comprehensive summary of the state of the art regarding ASRs, going back to the original description and cloning of the tomato ASR cDNA. That seminal discovery sparked worldwide interest amongst research groups spanning multiple fields: biochemistry, cell biology, evolution, physiology and epigenetics. As these proteins function as both chaperones and transcription factors; this review also covers the progress made on relevant molecular features that account for these dual roles-including the recent identification of their target genes-which may inspire future basic research. In addition, we address reports of drought-tolerant ASR-transgenic plants of different species, highlighting the influential work of authors taking more biotechnological approaches.
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Affiliation(s)
- Rodrigo M González
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE)-CONICET, Buenos Aires, Argentina
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Shanker AK, Maheswari M, Yadav SK, Desai S, Bhanu D, Attal NB, Venkateswarlu B. Drought stress responses in crops. Funct Integr Genomics 2014; 14:11-22. [PMID: 24408129 DOI: 10.1007/s10142-013-0356-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/04/2013] [Accepted: 12/18/2013] [Indexed: 01/09/2023]
Abstract
Among the effects of impending climate change, drought will have a profound impact on crop productivity in the future. Response to drought stress has been studied widely, and the model plant Arabidopsis has guided the studies on crop plants with genome sequence information viz., rice, wheat, maize and sorghum. Since the value of functions of genes, dynamics of pathways and interaction of networks for drought tolerance in plants can only be judged by evidence from field performance, this mini-review provides a research update focussing on the current developments on the response to drought in crop plants. Studies in Arabidopsis provide the basis for interpreting the available information in a systems biology perspective. In particular, the elucidation of the mechanism of drought stress response in crops is considered from evidence-based outputs emerging from recent omic studies in crops.
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Affiliation(s)
- Arun K Shanker
- Division of Crop Sciences, Central Research Institute for Dryland Agriculture (CRIDA), Santoshnagar, Saidabad P.O, Hyderabad, 500-059, India,
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