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Kaya C, Uğurlar F, Adamakis IDS. Epigenetic Modifications of Hormonal Signaling Pathways in Plant Drought Response and Tolerance for Sustainable Food Security. Int J Mol Sci 2024; 25:8229. [PMID: 39125799 PMCID: PMC11311266 DOI: 10.3390/ijms25158229] [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: 06/08/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Drought significantly challenges global food security, necessitating a comprehensive understanding of plant molecular responses for effective mitigation strategies. Epigenetic modifications, such as DNA methylation and histone modifications, are key in regulating genes and hormones essential for drought response. While microRNAs (miRNAs) primarily regulate gene expression post-transcriptionally, they can also interact with epigenetic pathways as potential effectors that influence chromatin remodeling. Although the role of miRNAs in epigenetic memory is still being explored, understanding their contribution to drought response requires examining these indirect effects on epigenetic modifications. A key aspect of this exploration is epigenetic memory in drought-adapted plants, offering insights into the transgenerational inheritance of adaptive traits. Understanding the mechanisms that govern the maintenance and erasure of these epigenetic imprints provides nuanced insights into how plants balance stability and flexibility in their epigenomes. A major focus is on the dynamic interaction between hormonal pathways-such as those for abscisic acid (ABA), ethylene, jasmonates, and salicylic acid (SA)-and epigenetic mechanisms. This interplay is crucial for fine-tuning gene expression during drought stress, leading to physiological and morphological adaptations that enhance plant drought resilience. This review also highlights the transformative potential of advanced technologies, such as bisulfite sequencing and CRISPR-Cas9, in providing comprehensive insights into plant responses to water deficit conditions. These technologies pave the way for developing drought-tolerant crops, which is vital for sustainable agriculture.
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Affiliation(s)
- Cengiz Kaya
- Soil Science and Plant Nutrition Department, Harran University, Sanliurfa 63200, Turkey; (C.K.); (F.U.)
| | - Ferhat Uğurlar
- Soil Science and Plant Nutrition Department, Harran University, Sanliurfa 63200, Turkey; (C.K.); (F.U.)
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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Singroha G, Sharma P, Sunkur R. Current status of microRNA-mediated regulation of drought stress responses in cereals. PHYSIOLOGIA PLANTARUM 2021; 172:1808-1821. [PMID: 33956991 DOI: 10.1111/ppl.13451] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 04/20/2021] [Accepted: 05/04/2021] [Indexed: 05/03/2023]
Abstract
Drought is one of the most important abiotic stress factors impeding crop productivity. With the uncovering of their role as potential regulators of gene expression, microRNAs (miRNAs) have been recognized as new targets for developing stress resistance. MicroRNAs are small noncoding RNAs whose abundance is significantly altered under stress conditions. Interestingly, plant miRNAs predominantly targets transcription factors (TFs), and some of which are also the most critical drought-responsive genes that in turn could regulate the expression of numerous loci with drought-adaptive potential. The phytohormone ABA plays important roles in regulating stomatal conductance and in initiating an adaptive response to drought stress. miRNAs are implicated in regulating ABA-(abscisic acid) and non-ABA-mediated drought resistance pathways. For instance, miR159-MYB module and miR169-NFYA module participates in an ABA-dependent pathway, whereas several other ABA-independent miRNA-target modules (miR156-SPL; miR393-TIR1; miR160-ARF10, ARF16, ARF17; miR167-ARF6 and ARF8; miR390/TAS3siRNA-ARF2, ARF3, ARF4) collectively regulate drought responses in plants. Overall, miRNA-mediated drought response manifests diverse molecular, biochemical and physiological processes. Because of their immense role in controlling gene expression, miRNA manipulation has significant potential to augment plant tolerance to drought stress. This review compiles the current understanding of drought-responsive miRNAs in major cereals. Also, potential miRNA manipulation strategies currently in use along with the challenges and future perspectives are discussed.
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Affiliation(s)
- Garima Singroha
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Ramanjulu Sunkur
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
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Pyo Y, Kim GM, Choi SW, Song CY, Yang SW, Jung IL. Strontium stress disrupts miRNA biogenesis by reducing HYL1 protein levels in Arabidopsis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 204:111056. [PMID: 32763566 DOI: 10.1016/j.ecoenv.2020.111056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 05/20/2023]
Abstract
Strontium (Sr) is an emerging environmental pollutant that has become a major global concern after the nuclear accident at the Fukushima Daiichi Nuclear Power Plant in 2011. Although many studies have demonstrated the harmful effects of Sr on plant growth and development at the physiological level, knowledge regarding how plants sense and respond to Sr stress at the molecular level is limited. Recent studies have suggested that microRNAs (miRNAs) function as key regulators of plant growth and development as well as in the responses of plants to environmental stresses, including salinity, drought, cold, nutrient starvation, and heavy metals. In this study, we examined the global expression profile of miRNAs under Sr stress using small RNA sequencing analysis in Arabidopsis to better understand the molecular basis of plant responses to Sr stress. To identify specific Sr-responsive miRNAs, we performed comparative miRNA expression profiling analysis using control, CaCl2-, and SrCl2-treated seedlings. Compared to the control treatment, the expressions of most miRNAs were considerably decreased in the Sr-treated seedlings. However, under Sr stress, the expressions of primary miRNAs (pri-miRNAs) and their target genes were significantly increased; the protein levels of HYPONASTIC LEAVES 1 (HYL1), one of the core components of the microprocessor complex, were strongly reduced despite the increased HYL1 mRNA expression. In addition, hyl1-2 mutant plants were shown to be more sensitive to Sr stress than wild-type plants. Collectively, our results strongly suggested that Sr stress may be associated with the disruption of miRNA biogenesis by reducing the protein level of HYL1, which is required to maintain proper growth and development for plants. Our findings further indicated that some miRNAs may play important roles in plant responses to Sr stress.
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Affiliation(s)
- Youngjae Pyo
- Department of Radiation Biology, Korea Atomic Energy Research Institute, Daejeon, 34057, Republic of Korea
| | - Gu Min Kim
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Suk Won Choi
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Chang Yeob Song
- Department of Radiation Biology, Korea Atomic Energy Research Institute, Daejeon, 34057, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Seong Wook Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea; UNIK Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, 2000, Frederiksberg, Copenhagen, Denmark.
| | - Il Lae Jung
- Department of Radiation Biology, Korea Atomic Energy Research Institute, Daejeon, 34057, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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Bakhshi B, Fard EM. Whole Aegilops tauschii Transcriptome Investigation Revealed Nine Novel miRNAs Involved in Stress Response. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191017151708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Aegilops tauschii is a wild relative of bread wheat. This species has been
reported as the donor of bread wheat D genome. There are also several reports that mentioned the
importance of Ae. tauschii in biotic and abiotic stress tolerance. On the other hands, miRNAs have
been reported as the essential regulatory elements in stress response.
Objective:
Therefore, it is important to discover novel miRNAs involved in stress tolerance in this
species. The aim of the current study was to predict novel miRNAs in Ae. tauschii and also
uncover their potential role in stress response.
Methods:
For this purpose, ESTs, TSAs, and miRBase databases were obtained and used to
predict new miRNAs.
Results:
Our results discovered nine novel stem-loop miRNAs. These predicted miRNAs could be
introduced as the new members of previously identified miRNA families in Ae. tauschii, including
miR156, miR168, miR169, and miR319. The result indicating that miR397 and miR530 are novel
families in this species. Furthermore, several novel stem-loop miRNAs predicted for T. aestivum
showed remarkable similarities to novel Ae. tauschii stem-loops.
Conclusion:
Our results demonstrated that predicted novel miRNAs could play a significant role
in stress response.
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Affiliation(s)
- Behnam Bakhshi
- Horticulture Crops Research Department, Sistan Agricultural and Natural Resources Research and Education Center, AREEO, Zabol, Iran
| | - Ehsan Mohseni Fard
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
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OsmiR535, a Potential Genetic Editing Target for Drought and Salinity Stress Tolerance in Oryza sativa. PLANTS 2020; 9:plants9101337. [PMID: 33050518 PMCID: PMC7601473 DOI: 10.3390/plants9101337] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
OsmiR535 belongs to the miR156/miR529/miR535 superfamily, a highly conserved miRNA family in plants. OsmiR535 is involved in regulating the cold-stress response, modulating plant development, and determining panicle architecture and grain length. However, the role that OsmiR535 plays in plant responses to drought and salinity are elusive. In the current study, molecular and genetic engineering techniques were used to elucidate the possible role of OsmiR535 in response to NaCl, PEG(Poly ethylene glycol), ABA(Abscisic acid), and dehydration stresses. Our results showed that OsmiR535 is induced under stressed conditions as compared to control. With transgenic and CRISPR/Cas9 knockout system techniques, our results verified that either inhibition or knockout of OsmiR535 in rice could enhance the tolerance of plants to NaCl, ABA, dehydration and PEG stresses. In addition, the overexpression of OsmiR535 significantly reduced the survival rate of rice seedlings during PEG and dehydration post-stress recovery. Our results demonstrated that OsmiR535 negatively regulates the stress response in rice. Moreover, our practical application of CRISPR/Cas9 mediated genome editing created a homozygous 5 bp deletion in the coding sequence of OsmiR535, demonstrating that OsmiR535 could be a useful genetic editing target for drought and salinity tolerance and a new marker for molecular breeding of Oryza sativa.
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Qiu CW, Liu L, Feng X, Hao PF, He X, Cao F, Wu F. Genome-Wide Identification and Characterization of Drought Stress Responsive microRNAs in Tibetan Wild Barley. Int J Mol Sci 2020; 21:E2795. [PMID: 32316632 PMCID: PMC7216285 DOI: 10.3390/ijms21082795] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 11/16/2022] Open
Abstract
Drought stress is a major obstacle to agricultural production. Tibetan wild barley with rich genetic diversity is useful for drought-tolerant improvement of cereals. MicroRNAs (miRNAs) play critical roles in controlling gene expression in response to various environment perturbations in plants. However, the genome-wide expression profiles of miRNAs and their targets in response to drought stress are largely unknown in wild barley. In this study, a polyethylene glycol (PEG) induced drought stress hydroponic experiment was performed, and the expression profiles of miRNAs from the roots of two contrasting Tibetan wild barley genotypes XZ5 (drought-tolerant) and XZ54 (drought-sensitive), and one cultivated barley Tadmor (drought-tolerant) generated by high-throughput sequencing were compared. There were 69 conserved miRNAs and 1574 novel miRNAs in the dataset of three genotypes under control and drought conditions. Among them, seven conserved miRNAs and 36 novel miRNAs showed significantly genotype-specific expression patterns in response to drought stress. And 12 miRNAs were further regarded as drought tolerant associated miRNAs in XZ5, which mostly participate in gene expression, metabolism, signaling and transportation, suggesting that they and their target genes play important roles in plant drought tolerance. This is the first comparation study on the miRNA transcriptome in the roots of two Tibetan wild barley genotypes differing in drought tolerance and one drought tolerant cultivar in response to PEG treatment. Further results revealed the candidate drought tolerant miRNAs and target genes in the miRNA regulation mechanism in wild barley under drought stress. Our findings provide valuable understandings for the functional characterization of miRNAs in drought tolerance.
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Affiliation(s)
- Cheng-Wei Qiu
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Li Liu
- Department of Applied Engineering, Zhejiang Economic and Trade Polytechnic, Hangzhou 310018, China;
| | - Xue Feng
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Peng-Fei Hao
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Xiaoyan He
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Fangbin Cao
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
| | - Feibo Wu
- Institute of Crop Science, Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (C.-W.Q.); (X.F.); (P.-F.H.); (X.H.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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Ye C, Zhou Q, Wu X, Ji G, Li QQ. Genome-wide alternative polyadenylation dynamics in response to biotic and abiotic stresses in rice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 183:109485. [PMID: 31376807 DOI: 10.1016/j.ecoenv.2019.109485] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 05/24/2023]
Abstract
Alternative polyadenylation (APA) is an important way to regulate gene expression at the post-transcriptional level, and is extensively involved in plant stress responses. However, the systematic roles of APA regulation in response to abiotic and biotic stresses in rice at the genome scale remain unknown. To take advantage of available RNA-seq datasets, using a novel tool APAtrap, we identified thousands of genes with significantly differential usage of polyadenylation [poly(A)] sites in response to the abiotic stress (drought, heat shock, and cadmium) and biotic stress [bacterial blight (BB), rice blast, and rice stripe virus (RSV)]. Genes with stress-responsive APA dynamics commonly exhibited higher expression levels when their isoforms with short 3' untranslated region (3' UTR) were more abundant. The stress-responsive APA events were widely involved in crucial stress-responsive genes and pathways: e.g. APA acted as a negative regulator in heat stress tolerance; APA events were involved in DNA repair and cell wall formation under Cd stress; APA regulated chlorophyll metabolism, being associated with the pathogenesis of leaf diseases under RSV and BB challenges. Furthermore, APA events were found to be involved in glutathione metabolism and MAPK signaling pathways, mediating a crosstalk among the abiotic and biotic stress-responsive regulatory networks in rice. Analysis of large-scale datasets revealed that APA may regulate abiotic and biotic stress-responsive processes in rice. Such post-transcriptome diversities contribute to rice adaption to various environmental challenges. Our study would supply useful resource for further molecular assisted breeding of multiple stress-tolerant cultivars for rice.
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Affiliation(s)
- Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Qian Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China; Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA.
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China.
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China.
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China; Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA.
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9
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Kord H, Fakheri B, Ghabooli M, Solouki M, Emamjomeh A, Khatabi B, Sepehri M, Salekdeh GH, Ghaffari MR. Salinity-associated microRNAs and their potential roles in mediating salt tolerance in rice colonized by the endophytic root fungus Piriformospora indica. Funct Integr Genomics 2019; 19:659-672. [PMID: 30903405 DOI: 10.1007/s10142-019-00671-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/24/2019] [Accepted: 02/25/2019] [Indexed: 12/23/2022]
Abstract
Piriformospora indica (P. indica), an endophytic root fungus, supports the growth and enhanced tolerance of plants to biotic and abiotic stresses. Several recent studies showed the significant role of small RNA (sRNA) molecules including microRNAs (miRNAs) in plant adaption to environmental stress, but little is known concerning the symbiosis-mediated salt stress tolerance regulated at miRNAs level. The overarching goal of this research is to elucidate the impact of miRNAs in regulating the P. indica-mediated salt tolerance in rice. Applying sRNA-seq analysis led to identify a set of 547 differentially abundant miRNAs in response to P. indica inoculation and salt stress. These included 206 rice-specific and 341 previously known miRNAs from other plant species. In silico analysis of miRNAs predictions of the differentially abundant miRNAs led to identifying of 193 putatively target genes, most of which were encoded either genes or transcription factors involved in nutrient uptake, sodium ion transporters, growth regulators, and auxin- responsive proteins. The rice-specific miRNAs targeted the transcription factors involved in the import of potassium ions into the root cells, the export of sodium ions, and plant growth and development. Interestingly, P. indica affected the differential abundance of miRNAs regulated genes and transcription factors linked to salt stress tolerance. Our data helps to understand the molecular basis of salt stress tolerance mediated by symbionts in plant and the potential impact of miRNAs for genetic improvement of rice varieties for tolerance to salt stress.
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Affiliation(s)
- Hadis Kord
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Baratali Fakheri
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mehdi Ghabooli
- Department of Agronomy, Faculty of Agriculture, Malayer University, Malayer, Iran
| | - Mahmood Solouki
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Abbasali Emamjomeh
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Behnam Khatabi
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Mozhgan Sepehri
- Department of Soil Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran.
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