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Liang Y, Yang X, Wang C, Wang Y. miRNAs: Primary modulators of plant drought tolerance. JOURNAL OF PLANT PHYSIOLOGY 2024; 301:154313. [PMID: 38991233 DOI: 10.1016/j.jplph.2024.154313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 06/17/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
Drought is a principal environmental factor that affects the growth and development of plants. Accordingly, plants have evolved adaptive mechanisms to cope with adverse environmental conditions. One of the mechanisms is gene regulation mediated by microRNAs (miRNAs). miRNAs are regarded as primary modulators of gene expression at the post-transcriptional level and have been shown to participate in drought stress response, including ABA response, auxin signaling, antioxidant defense, and osmotic regulation through downregulating the corresponding targets. miRNA-based genetic reconstructions have the potential to improve the tolerance of plants to drought. However, there are few precise classification and discussion of miRNAs in specific response behaviors to drought stress and their applications. This review summarized and discussed the specific response behaviors of miRNAs under drought stress and the role of miRNAs as regulators in the response of plants to drought and highlighted that the modification of miRNAs might effectively improve the tolerance of plants to drought.
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Affiliation(s)
- Yanting Liang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaoqian Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Chun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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Jiang C, Zhang X, Rao J, Luo S, Luo L, Lu W, Li M, Zhao S, Ren D, Liu J, Song Y, Zheng Y, Sun YB. Enhancing Pseudomonas syringae pv. Actinidiae sensitivity in kiwifruit by repressing the NBS-LRR genes through miRNA-215-3p and miRNA-29-3p identification. FRONTIERS IN PLANT SCIENCE 2024; 15:1403869. [PMID: 39086918 PMCID: PMC11288850 DOI: 10.3389/fpls.2024.1403869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024]
Abstract
Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (PSA), poses a grave threat to the global kiwifruit industry. In this study, we examined the role of microRNAs (miRNAs) in kiwifruit's response to PSA. Kiwifruit seedlings subjected to PSA treatment showed significant changes in both miRNA and gene expression compared to the control group. We identified 364 differentially expressed miRNAs (DEMs) and 7170 differentially expressed genes (DEGs). Further analysis revealed 180 miRNAs negatively regulating 641 mRNAs. Notably, two miRNAs from the miRNA482 family, miRNA-215-3p and miRNA-29-3p, were found to increase kiwifruit's sensitivity to PSA when overexpressed. These miRNAs were linked to the regulation of NBS-LRR target genes, shedding light on their role in kiwifruit's defence against PSA. This study offers insights into the miRNA482-NBS-LRR network as a crucial component in enhancing kiwifruit bioresistance to PSA infestation and provides promising candidate genes for further research.
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Affiliation(s)
- Chengyao Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoying Zhang
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Jiahui Rao
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Shu Luo
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Liang Luo
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Shumei Zhao
- Key Laboratory of Agricultural Engineering in Structure and Environment, China Agricultural University, Beijing, China
| | - Dan Ren
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Jiaming Liu
- Laboratory of Crop Immune Gene Editing Technology, Newsun Research Institute of Biotechnology, Chengdu, China
| | - Yu Song
- Research Institute of Crop Germplasm Resources, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yin-Biao Sun
- Randall Centre for Cell and Molecular Biophysics, School of Basic & Medical Biosciences, King’s College London, London, United Kingdom
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Kaur S, Seem K, Duhan N, Kumar S, Kaundal R, Mohapatra T. Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress. PLANTA 2024; 259:128. [PMID: 38639776 DOI: 10.1007/s00425-024-04399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
MAIN CONCLUSION Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
- ICAR-Research Complex for North Eastern Hill Region (NEH), Umiam, Meghalaya, 793103, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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Yadav A, Mathan J, Dubey AK, Singh A. The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling. Noncoding RNA 2024; 10:13. [PMID: 38392968 PMCID: PMC10893181 DOI: 10.3390/ncrna10010013] [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: 12/11/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.
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Affiliation(s)
- Amit Yadav
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Jyotirmaya Mathan
- Sashi Bhusan Rath Government Autonomous Women’s College, Brahmapur 760001, India;
| | - Arvind Kumar Dubey
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Anuradha Singh
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA
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Geng A, Lian W, Wang Y, Liu M, Zhang Y, Wang X, Chen G. Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice. Int J Mol Sci 2024; 25:1185. [PMID: 38256261 PMCID: PMC10817035 DOI: 10.3390/ijms25021185] [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: 12/24/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.
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Affiliation(s)
- Anjing Geng
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Wenli Lian
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yihan Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Minghao Liu
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yue Zhang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Guang Chen
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
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Zhang S, Han Y, Zeng Q, Wang C, Wang H, Zhang J, Cai M, Lu J, Chen T. Whole-Transcriptome Sequencing Reveals the Global Molecular Responses and NAC Transcription Factors Involved in Drought Stress in Dendrobium catenatum. Antioxidants (Basel) 2024; 13:94. [PMID: 38247518 PMCID: PMC10812421 DOI: 10.3390/antiox13010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
Dendrobium catenatum is a highly drought-tolerant herb, which usually grows on cliffs or in the branches of trees, yet the underlying molecular mechanisms for its tolerance remain poorly understood. We conducted a comprehensive study utilizing whole-transcriptome sequencing approaches to investigate the molecular response to extreme drought stress in D. catenatum. A large number of differentially expressed mRNAs, lncRNAs, and circRNAs have been identified, and the NAC transcription factor family was highly enriched. Meanwhile, 46 genes were significantly up-regulated in the ABA-activated signaling pathway. In addition to the 89 NAC family members accurately identified in this study, 32 members were found to have different expressions between the CK and extreme drought treatment. They may regulate drought stress through both ABA-dependent and ABA-independent pathways. Moreover, the 32 analyzed differentially expressed DcNACs were found to be predominantly expressed in the floral organs and roots. The ceRNA regulatory network showed that DcNAC87 is at the core of the ceRNA network and is regulated by miR169, miR393, and four lncRNAs. These investigations provided valuable information on the role of NAC transcription factors in D. catenatum's response to drought stress.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (S.Z.); (Y.H.); (Q.Z.); (C.W.); (H.W.); (J.Z.); (M.C.)
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (S.Z.); (Y.H.); (Q.Z.); (C.W.); (H.W.); (J.Z.); (M.C.)
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Lopos LC, Panthi U, Kovalchuk I, Bilichak A. Modulation of Plant MicroRNA Expression: Its Potential Usability in Wheat ( Triticum aestivum L.) Improvement. Curr Genomics 2023; 24:197-206. [PMID: 38169773 PMCID: PMC10758129 DOI: 10.2174/0113892029264886231016050547] [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: 05/31/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 01/05/2024] Open
Abstract
Wheat, a crucial crop for the pursuit of food security, is faced with a plateauing yield projected to fall short of meeting the demands of the exponentially increasing human population. To raise global wheat productivity levels, strong efforts must be made to overcome the problems of (1) climate change-induced heat and drought stress and (2) the genotype-dependent amenability of wheat to tissue culture, which limits the success of recovering genetically engineered plants, especially in elite cultivars. Unfortunately, the mainstream approach of genetically engineering plant protein-coding genes may not be effective in solving these problems as it is difficult to map, annotate, functionally verify, and modulate all existing homeologs and paralogs within wheat's large, complex, allohexaploid genome. Additionally, the quantitative, multi-genic nature of most agronomically important traits furthers the complications faced by this approach. miRNAs are small, noncoding RNAs (sncRNAs) that repress gene expression at the post-transcriptional level, regulating various aspects of plant growth and development. They are gaining popularity as alternative targets of genetic engineering efforts for crop improvement due to their (1) highly conserved nature, which facilitates reasonable prediction of their gene targets and phenotypic effects under different expression levels, and (2) the capacity to target multiple genes simultaneously, making them suitable for enhancing complex and multigenic agronomic traits. In this mini-review, we will discuss the biogenesis, manipulation, and potential applications of plant miRNAs in improving wheat's yield, somatic embryogenesis, thermotolerance, and drought-tolerance in response to the problems of plateauing yield, genotype-dependent amenability to tissue culture, and susceptibility to climate change-induced heat and drought stress. © His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food, 2023.
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Affiliation(s)
- Louie Cris Lopos
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
| | - Urbashi Panthi
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Andriy Bilichak
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
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Kumar D, Ramkumar MK, Dutta B, Kumar A, Pandey R, Jain PK, Gaikwad K, Mishra DC, Chaturvedi KK, Rai A, Solanke AU, Sevanthi AM. Integration of miRNA dynamics and drought tolerant QTLs in rice reveals the role of miR2919 in drought stress response. BMC Genomics 2023; 24:526. [PMID: 37674140 PMCID: PMC10481553 DOI: 10.1186/s12864-023-09609-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/20/2023] [Indexed: 09/08/2023] Open
Abstract
To combat drought stress in rice, a major threat to global food security, three major quantitative trait loci for 'yield under drought stress' (qDTYs) were successfully exploited in the last decade. However, their molecular basis still remains unknown. To understand the role of secondary regulation by miRNA in drought stress response and their relation, if any, with the three qDTYs, the miRNA dynamics under drought stress was studied at booting stage in two drought tolerant (Sahbaghi Dhan and Vandana) and one drought sensitive (IR 20) cultivars. In total, 53 known and 40 novel differentially expressed (DE) miRNAs were identified. The primary drought responsive miRNAs were Osa-MIR2919, Osa-MIR3979, Osa-MIR159f, Osa-MIR156k, Osa-MIR528, Osa-MIR530, Osa-MIR2091, Osa-MIR531a, Osa-MIR531b as well as three novel ones. Sixty-one target genes that corresponded to 11 known and 4 novel DE miRNAs were found to be co-localized with the three qDTYs, out of the 1746 target genes identified. We could validate miRNA-mRNA expression under drought for nine known and three novel miRNAs in eight different rice genotypes showing varying degree of tolerance. From our study, Osa-MIR2919, Osa-MIR3979, Osa-MIR528, Osa-MIR2091-5p and Chr01_11911S14Astr and their target genes LOC_Os01g72000, LOC_Os01g66890, LOC_Os01g57990, LOC_Os01g56780, LOC_Os01g72834, LOC_Os01g61880 and LOC_Os01g72780 were identified as the most promising candidates for drought tolerance at booting stage. Of these, Osa-MIR2919 with 19 target genes in the qDTYs is being reported for the first time. It acts as a negative regulator of drought stress tolerance by modulating the cytokinin and brassinosteroid signalling pathway.
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Affiliation(s)
- Deepesh Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, Indian Agricultural Research Institute, Pusa Campus New Delhi, New Delhi, 110012, India
| | - M K Ramkumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Bipratip Dutta
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, Indian Agricultural Research Institute, Pusa Campus New Delhi, New Delhi, 110012, India
| | - Ajay Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Rakesh Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep Kumar Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Dwijesh C Mishra
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - K K Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
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Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
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Kaur S, Seem K, Kumar S, Kaundal R, Mohapatra T. Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought. Genes (Basel) 2023; 14:1390. [PMID: 37510295 PMCID: PMC10379292 DOI: 10.3390/genes14071390] [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: 05/21/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Recurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food security. The root of a plant is primarily responsible to perceive drought stress and acquire sufficient water for the survival/optimal growth of the plant under extreme climatic conditions. Earlier studies reported the involvement/important roles of microRNAs (miRNAs) in plants' responses to environmental/abiotic stresses. A number (738) of miRNAs is known to be expressed in different tissues under varying environmental conditions in rice, but our understanding of the role, mode of action, and target genes of the miRNAs are still elusive. Using contrasting rice [IR-64 (reproductive-stage drought sensitive) and N-22 (drought-tolerant)] cultivars, imposed with terminal (reproductive-stage) drought stress, we demonstrate differential expression of 270 known and 91 novel miRNAs in roots of the contrasting rice cultivars in response to the stress. Among the known miRNAs, osamiR812, osamiR166, osamiR156, osamiR167, and osamiR396 were the most differentially expressed miRNAs between the rice cultivars. In the root of N-22, 18 known and 12 novel miRNAs were observed to be exclusively expressed, while only two known (zero novels) miRNAs were exclusively expressed in the roots of IR-64. The majority of the target gene(s) of the miRNAs were drought-responsive transcription factors playing important roles in flower, grain development, auxin signaling, root development, and phytohormone-crosstalk. The novel miRNAs identified in this study may serve as good candidates for the genetic improvement of rice for terminal drought stress towards developing climate-smart rice for sustainable food production.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
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11
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Rawal HC, Ali S, Mondal TK. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. Int J Biol Macromol 2023; 242:125172. [PMID: 37268077 DOI: 10.1016/j.ijbiomac.2023.125172] [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: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India; School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India; Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.
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12
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Balyan S, Kansal S, Jajo R, Behere PR, Chatterjee R, Raghuvanshi S. Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice. Funct Integr Genomics 2023; 23:187. [PMID: 37243818 DOI: 10.1007/s10142-023-01111-2] [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: 12/30/2022] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
Engineering drought tolerance in rice needs to focus on regulators that enhance tolerance while boosting plant growth and vigor. The present study delineated the concealed function and tissue-mediated interplay of the miR408/target module in imparting drought stress tolerance in rice. The plant miR408 family comprises three dominant mature forms (21 nt), including a distinct monocot variant (F-7 with 5' C) and is divided into six groups. miR408 majorly cleaves genes belonging to the blue copper protein in addition to several other species-specific targets in plants. Comparative sequence analysis in 4726 rice accessions identified 22 sequence variants (SNP and InDELs) in its promoter (15) and pre-miR408 region. Haplotype analysis of the sequence variants indicated eight haplotypes (three: Japonica-specific and five: Indica-specific) of the miR408 promoter. In drought-tolerant Nagina 22, miR408 follows flag leaf preferential expression. Under drought conditions, its levels are upregulated in flag leaf and roots which seems to be regulated by a differential fraction of methylated cytosines (mCs) in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of the miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice, out of which 12 genes, including four PLANTACYANINS (OsUCL6, 7, 9 and 30), PIRIN, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine-rich cell wall gene, OsDUT, and OsERF7, are among the high confidence targets. Further, overexpression of MIR408 in drought-sensitive rice cultivar (PB1) leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced dehydration stress tolerance. The above results suggest that miR408 is likely to act as a positive regulator of growth and vigor, as well as dehydration stress, making it a potential candidate for engineering drought tolerance in rice.
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Affiliation(s)
- Sonia Balyan
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shivani Kansal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Ringyao Jajo
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Pratyush Rajiv Behere
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Rishika Chatterjee
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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13
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Kumar S, Seem K, Mohapatra T. Biochemical and Epigenetic Modulations under Drought: Remembering the Stress Tolerance Mechanism in Rice. Life (Basel) 2023; 13:life13051156. [PMID: 37240801 DOI: 10.3390/life13051156] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
A plant, being a sessile organism, needs to modulate biochemical, physiological, and molecular responses to the environment in a quick and efficient manner to be protected. Drought stress is a frequently occurring abiotic stress that severely affects plant growth, development, and productivity. Short- and long-term memories are well-known phenomena in animals; however, the existence of such remembrance in plants is still being discovered. In this investigation, different rice genotypes were imposed with drought stress just before flowering and the plants were re-watered for recovery from the stress. Seeds collected from the stress-treated (stress-primed) plants were used to raise plants for the subsequent two generations under a similar experimental setup. Modulations in physio-biochemical (chlorophyll, total phenolics and proline contents, antioxidant potential, lipid peroxidation) and epigenetic [5-methylcytosine (5-mC)] parameters were analyzed in the leaves of the plants grown under stress as well as after recovery. There was an increase in proline (>25%) and total phenolic (>19%) contents, antioxidant activity (>7%), and genome-wide 5-mC level (>56%), while a decrease (>9%) in chlorophyll content was recorded to be significant under the stress. Interestingly, a part of the increased proline content, total phenolics content, antioxidant activity, and 5-mC level was retained even after the withdrawal of the stress. Moreover, the increased levels of biochemical and epigenetic parameters were observed to be transmitted/inherited to the subsequent generations. These might help in developing stress-tolerant crops and improving crop productivity under the changing global climate for sustainable food production and global food security.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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14
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Xu C, Li J, Wang H, Liu H, Yu Z, Zhao Z. Whole-Transcriptome Sequencing Reveals a ceRNA Regulatory Network Associated with the Process of Periodic Albinism under Low Temperature in Baiye No. 1 ( Camellia sinensis). Int J Mol Sci 2023; 24:ijms24087162. [PMID: 37108322 PMCID: PMC10138444 DOI: 10.3390/ijms24087162] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
The young shoots of the tea plant Baiye No. 1 display an albino phenotype in the early spring under low environmental temperatures, and the leaves re-green like those of common tea cultivars during the warm season. Periodic albinism is precisely regulated by a complex gene network that leads to metabolic differences and enhances the nutritional value of tea leaves. Here, we identified messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) to construct competing endogenous RNA (ceRNA) regulatory networks. We performed whole-transcriptome sequencing of 12 samples from four periods (Bud, leaves not expanded; Alb, albino leaves; Med, re-greening leaves; and Gre, green leaves) and identified a total of 6325 differentially expressed mRNAs (DEmRNAs), 667 differentially expressed miRNAs (DEmiRNAs), 1702 differentially expressed lncRNAs (DElncRNAs), and 122 differentially expressed circRNAs (DEcircRNAs). Furthermore, we constructed ceRNA networks on the basis of co-differential expression analyses which comprised 112, 35, 38, and 15 DEmRNAs, DEmiRNAs, DElncRNAs, and DEcircRNAs, respectively. Based on the regulatory networks, we identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs during periodic albinism, including the ceRNA regulatory network centered on miR5021x, the GAMYB-miR159-lncRNA regulatory network, and the NAC035-miR319x-circRNA regulatory network. These regulatory networks might be involved in the response to cold stress, photosynthesis, chlorophyll synthesis, amino acid synthesis, and flavonoid accumulation. Our findings provide novel insights into ceRNA regulatory mechanisms involved in Baiye No. 1 during periodic albinism and will aid future studies of the molecular mechanisms underlying albinism mutants.
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Affiliation(s)
- Cunbin Xu
- College of Life Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
- College of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
| | - Jinling Li
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Hualei Wang
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Huijuan Liu
- College of Life Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Zhihai Yu
- College of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
| | - Zhi Zhao
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
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15
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Identification of microRNAs responsive to arbuscular mycorrhizal fungi in Panicum virgatum (switchgrass). BMC Genomics 2022; 23:688. [PMID: 36199042 PMCID: PMC9535954 DOI: 10.1186/s12864-022-08797-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important post-transcriptional regulators involved in the control of a range of processes, including symbiotic interactions in plants. MiRNA involvement in arbuscular mycorrhizae (AM) symbiosis has been mainly studied in model species, and our study is the first to analyze global miRNA expression in the roots of AM colonized switchgrass (Panicum virgatum), an emerging biofuel feedstock. AM symbiosis helps plants gain mineral nutrition from the soil and may enhance switchgrass biomass production on marginal lands. Our goals were to identify miRNAs and their corresponding target genes that are controlling AM symbiosis in switchgrass. RESULTS Through genome-wide analysis of next-generation miRNA sequencing reads generated from switchgrass roots, we identified 122 mature miRNAs, including 28 novel miRNAs. By comparing miRNA expression profiles of AM-inoculated and control switchgrass roots, we identified 15 AM-responsive miRNAs across lowland accession "Alamo", upland accession "Dacotah", and two upland/lowland F1 hybrids. We used degradome sequencing to identify target genes of the AM-responsive miRNAs revealing targets of miRNAs residing on both K and N subgenomes. Notably, genes involved in copper ion binding were targeted by downregulated miRNAs, while upregulated miRNAs mainly targeted GRAS family transcription factors. CONCLUSION Through miRNA analysis and degradome sequencing, we revealed that both upland and lowland switchgrass genotypes as well as upland-lowland hybrids respond to AM by altering miRNA expression. We demonstrated complex GRAS transcription factor regulation by the miR171 family, with some miR171 family members being AM responsive while others remained static. Copper miRNA downregulation was common amongst the genotypes tested and we identified superoxide dismutases and laccases as targets, suggesting that these Cu-miRNAs are likely involved in ROS detoxification and lignin deposition, respectively. Other prominent targets of the Cu miRNAs were blue copper proteins. Overall, the potential effect of AM colonization on lignin deposition pathways in this biofuel crop highlights the importance of considering AM and miRNA in future biofuel crop development strategies.
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16
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Fan B, Sun F, Yu Z, Zhang X, Yu X, Wu J, Yan X, Zhao Y, Nie L, Fang Y, Ma Y. Integrated analysis of small RNAs, transcriptome and degradome sequencing reveal the drought stress network in Agropyron mongolicum Keng. FRONTIERS IN PLANT SCIENCE 2022; 13:976684. [PMID: 36061788 PMCID: PMC9433978 DOI: 10.3389/fpls.2022.976684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Agropyron mongolicum (A. mongolicum) is an excellent gramineous forage with extreme drought tolerance, which lives in arid and semiarid desert areas. However, the mechanism that underlies the response of microRNAs (miRNAs) and their targets in A. mongolicum to drought stress is not well understood. In this study, we analyzed the transcriptome, small RNAome (specifically the miRNAome) and degradome to generate a comprehensive resource that focused on identifying key regulatory miRNA-target circuits under drought stress. The most extended transcript in each collection is known as the UniGene, and a total of 41,792 UniGenes and 1,104 miRNAs were identified, and 99 differentially expressed miRNAs negatively regulated 1,474 differentially expressed target genes. Among them, eight miRNAs were unique to A. mongolicum, and there were 36 target genes. A weighted gene co-expression network analysis identified five hub genes. The miRNAs of five hub genes were screened with an integration analysis of the degradome and sRNAs, such as osa-miR444a-3p.2-MADS47, bdi-miR408-5p_1ss19TA-CCX1, tae-miR9774_L-2R-1_1ss11GT-carC, ata-miR169a-3p-PAO2, and bdi-miR528-p3_2ss15TG20CA-HOX24. The functional annotations revealed that they were involved in mediating the brassinosteroid signal pathway, transporting and exchanging sodium and potassium ions and regulating the oxidation-reduction process, hydrolase activity, plant response to water deprivation, abscisic acid (ABA) and the ABA-activated signaling pathway to regulate drought stress. Five hub genes were discovered, which could play central roles in the regulation of drought-responsive genes. These results show that the combined analysis of miRNA, the transcriptome and degradation group provides a useful platform to investigate the molecular mechanism of drought resistance in A. mongolicum and could provide new insights into the genetic engineering of Poaceae crops in the future.
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Affiliation(s)
- Bobo Fan
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Fengcheng Sun
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Zhuo Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Xuefeng Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoxia Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Wu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiuxiu Yan
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Zhao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Lizhen Nie
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Yongyu Fang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Yanhong Ma
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
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17
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Molecular Aspects of MicroRNAs and Phytohormonal Signaling in Response to Drought Stress: A Review. Curr Issues Mol Biol 2022; 44:3695-3710. [PMID: 36005149 PMCID: PMC9406886 DOI: 10.3390/cimb44080253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Phytohormones play an essential role in plant growth and development in response to environmental stresses. However, plant hormones require a complex signaling network combined with other signaling pathways to perform their proper functions. Thus, multiple phytohormonal signaling pathways are a prerequisite for understanding plant defense mechanism against stressful conditions. MicroRNAs (miRNAs) are master regulators of eukaryotic gene expression and are also influenced by a wide range of plant development events by suppressing their target genes. In recent decades, the mechanisms of phytohormone biosynthesis, signaling, pathways of miRNA biosynthesis and regulation were profoundly characterized. Recent findings have shown that miRNAs and plant hormones are integrated with the regulation of environmental stress. miRNAs target several components of phytohormone pathways, and plant hormones also regulate the expression of miRNAs or their target genes inversely. In this article, recent developments related to molecular linkages between miRNAs and phytohormones were reviewed, focusing on drought stress.
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18
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Sun M, Shen Y, Chen Y, Wang Y, Cai X, Yang J, Jia B, Dong W, Chen X, Sun X. Osa-miR1320 targets the ERF transcription factor OsERF096 to regulate cold tolerance via JA-mediated signaling. PLANT PHYSIOLOGY 2022; 189:2500-2516. [PMID: 35522026 PMCID: PMC9342977 DOI: 10.1093/plphys/kiac208] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/09/2022] [Indexed: 05/08/2023]
Abstract
MicroRNAs play key roles in abiotic stress response. Rice (Oryza sativa L.) miR1320 is a species-specific miRNA that contributes to miR168-regulated immunity. However, it is still unknown whether miR1320 is involved in rice response to abiotic stress. In this study, we illustrated that the miR1320 precursor generated two mature miR1320s, miR1320-3p, and miR1320-5p, and they both displayed decreased expression under cold stress. Genetic evidence showed that miR1320 overexpression resulted in increased cold tolerance, while miR1320 knock down (KD) reduced cold tolerance. Furthermore, an APETALA2/ethylene-responsive factor (ERF) transcription factor OsERF096 was identified as a target of miR1320 via 5'-RACE and dual luciferase assays. OsERF096 expression was altered by miR1320 overexpression and KD and exhibited an opposite pattern to that of miR1320 in different tissues and under cold stress. Consistently, OsERF096 negatively regulated cold stress tolerance. Furthermore, we suggested that OsERF096 could bind to the GCC and DRE cis-elements and act as a transcriptional activator in the nucleus. Based on RNA-sequencing and targeted metabolomics assays, we found that OsERF096 modified hormone content and signaling pathways. Finally, phenotypic and reverse transcription-quantitative PCR assays showed that jasmonic acid (JA) methyl ester application recovered the cold-sensitive phenotype and JA-activated expression of three Dehydration Responsive Element Binding genes in the OsERF096-OE line. Taken together, our results strongly suggest that the miR1320-OsERF096 module regulates cold tolerance by repressing the JA-mediated cold signaling pathway.
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Affiliation(s)
- Mingzhe Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Yang Shen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Yue Chen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Yan Wang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaoxi Cai
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Junkai Yang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Bowei Jia
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Weifeng Dong
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xi Chen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
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19
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Li Y, Li T, He X, Zhu Y, Feng Q, Yang X, Zhou X, Li G, Ji Y, Zhao J, Zhao Z, Pu M, Zhou S, Zhang J, Huang Y, Fan J, Wang W. Blocking Osa-miR1871 enhances rice resistance against Magnaporthe oryzae and yield. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:646-659. [PMID: 34726307 PMCID: PMC8989506 DOI: 10.1111/pbi.13743] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/31/2021] [Accepted: 10/24/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) play vital roles in plant development and defence responses against various stresses. Here, we show that blocking miR1871 improves rice resistance against Magnaporthe oryzae and enhances grain yield simultaneously. The transgenic lines overexpressing miR1871 (OX1871) exhibit compromised resistance, suppressed defence responses and reduced panicle number resulting in slightly decreased yield. In contrast, the transgenic lines blocking miR1871 (MIM1871) show improved resistance, enhanced defence responses and significantly increased panicle number leading to enhanced yield per plant. The RNA-seq assay and defence response assays reveal that blocking miR1871 resulted in the enhancement of PAMP-triggered immunity (PTI). Intriguingly, miR1871 suppresses the expression of LOC_Os06g22850, which encodes a microfibrillar-associated protein (MFAP1) locating nearby the cell wall and positively regulating PTI responses. The mutants of MFAP1 resemble the phenotype of OX1871. Conversely, the transgenic lines overexpressing MFAP1 (OXMFAP1) or overexpressing both MFAP1 and miR1871 (OXMFAP1/OX1871) resemble the resistance of MIM1871. The time-course experiment data reveal that the expression of miR1871 and MFAP1 in rice leaves, panicles and basal internode is dynamic during the whole growth period to manipulate the resistance and yield traits. Our results suggest that miR1871 regulates rice yield and immunity via MFAP1, and the miR8171-MFAP1 module could be used in rice breeding to improve both immunity and yield.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Ting‐Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Xiao‐Rong He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yong Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Qin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Xue‐Mei Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Xin‐Hui Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Guo‐Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yun‐Peng Ji
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Jing‐Hao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Zhi‐Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Shi‐Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Ji‐Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yan‐Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Wen‐Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
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20
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Insight into gene regulatory networks involved in sesame (Sesamum indicum L.) drought response. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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21
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Rao S, Das JR, Balyan S, Verma R, Mathur S. Cultivar-biased regulation of HSFA7 and HSFB4a govern high-temperature tolerance in tomato. PLANTA 2022; 255:31. [PMID: 34982240 DOI: 10.1007/s00425-021-03813-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Cultivar-biased regulation of HSFB4a and HSFA7 mediates heat stress tolerance/sensitivity in tomato. Reduced HSFB4a repressor levels and enhanced HSFA7 activator levels govern thermo-tolerance in tolerant cultivars. Heat shock factors (HSFs) are at the core of heat stress (HS) response in plants. However, the contribution of HSFs governing the inherent thermo-tolerance mechanism in tomato from sub-tropical hot climates is poorly understood. With the above aim, comparative expression profiles of the HSF family in a HS-tolerant (CLN1621L) and -sensitive cultivars (CA4 and Pusa Ruby) of tomato under HS revealed cultivar-biased regulation of an activator (HSFA7) and a repressor (HSFB4a) class HSF. HSFA7 exhibited strong upregulation while HSFB4a showed downregulation in tolerant tomato cultivar upon HS. Functional characterization of HSFA7 and HSFB4a in a tolerant-sensitive cultivar pair by virus-induced gene silencing (VIGS)-based silencing and transient overexpression established them as a positive and a negative regulator of HS tolerance, respectively. Promoter:GUS reporter assays and promoter sequence analyses suggest heat-mediated transcriptional control of both the HSF genes in the contrasting cultivars. Moreover, degradome data highlighted HSFB4a is a probable target of microRNA Sly-miR4200. Transient in-planta Sly-MIR4200-effector:HSFB4a-reporter assays showed miRNA-dependent target down-regulation. Chelation of miRNA by short-tandem-target-mimic of Sly-miR4200 increased target abundance, highlighting a link between Sly-miR4200 and HSFB4a. This miRNA has induced several folds upon HS in the tolerant cultivar where HSFB4a levels are reduced, thus exhibiting the inverse miR:target expression. Thus, we speculate that the alleviation of HSFB4a and increased HSFA7 levels govern thermo-tolerance in the tolerant cultivar by regulating downstream heat stress-responsive genes.
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Affiliation(s)
- Sombir Rao
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067, India
| | - Jaishri Rubina Das
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067, India
| | - Sonia Balyan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067, India
| | - Radhika Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067, India.
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22
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The Evolution and Functional Roles of miR408 and Its Targets in Plants. Int J Mol Sci 2022; 23:ijms23010530. [PMID: 35008962 PMCID: PMC8745667 DOI: 10.3390/ijms23010530] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
MicroRNA408 (miR408) is an ancient and highly conserved miRNA, which is involved in the regulation of plant growth, development and stress response. However, previous research results on the evolution and functional roles of miR408 and its targets are relatively scattered, and there is a lack of a systematic comparison and comprehensive summary of the detailed evolutionary pathways and regulatory mechanisms of miR408 and its targets in plants. Here, we analyzed the evolutionary pathway of miR408 in plants, and summarized the functions of miR408 and its targets in regulating plant growth and development and plant responses to various abiotic and biotic stresses. The evolutionary analysis shows that miR408 is an ancient and highly conserved microRNA, which is widely distributed in different plants. miR408 regulates the growth and development of different plants by down-regulating its targets, encoding blue copper (Cu) proteins, and by transporting Cu to plastocyanin (PC), which affects photosynthesis and ultimately promotes grain yield. In addition, miR408 improves tolerance to stress by down-regulating target genes and enhancing cellular antioxidants, thereby increasing the antioxidant capacity of plants. This review expands and promotes an in-depth understanding of the evolutionary and regulatory roles of miR408 and its targets in plants.
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Gour P, Kansal S, Agarwal P, Mishra BS, Sharma D, Mathur S, Raghuvanshi S. Variety-specific transcript accumulation during reproductive stage in drought-stressed rice. PHYSIOLOGIA PLANTARUM 2022; 174:e13585. [PMID: 34652858 DOI: 10.1111/ppl.13585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/23/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
The divergence of natural stress tolerance mechanisms between species is an intriguing phenomenon. To study it in rice, a comparative transcriptome analysis was carried out in 'heading' stage tissue (flag leaf, panicles and roots) of Nagina 22 (N22; drought-tolerant) and IR64 (drought-sensitive) plants subjected to field drought. Interestingly, N22 showed almost double the number of differentially expressed genes (DEGs) than IR64. Many DEGs colocalized within drought-related QTLs responsible for grain yield and drought tolerance and also associated with drought tolerance and critical drought-related plant traits such as leaf rolling, trehalose content, sucrose and cellulose content. Besides, co-expression analysis of the DEGs revealed several 'hub' genes known to actively regulate drought stress response. Strikingly, 1366 DEGs, including 21 'hub' genes, showed a distinct opposite regulation in the two rice varieties under similar drought conditions. Annotation of these variety-specific DEGs (VS-DEGs) revealed that they are distributed in various biological pathways. Furthermore, 103 VS-DEGs were found to physically interact with over 1300 genes, including 32 that physically interact with other VS-DEGs as well. The promoter region of these genes has sequence variations among the two rice varieties, which might be in part responsible for their unique expression pattern.
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Affiliation(s)
- Pratibha Gour
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Shivani Kansal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Priyanka Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Deepika Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, New Delhi, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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24
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Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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25
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Kansal S, Panwar V, Mutum RD, Raghuvanshi S. Investigations on Regulation of MicroRNAs in Rice Reveal [Ca 2+] cyt Signal Transduction Regulated MicroRNAs. FRONTIERS IN PLANT SCIENCE 2021; 12:720009. [PMID: 34733300 PMCID: PMC8558223 DOI: 10.3389/fpls.2021.720009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs) are critical components of the multidimensional regulatory networks in eukaryotic systems. Given their diverse spectrum of function, it is apparent that the transcription, processing, and activity of the miRNAs themselves, is very dynamically regulated. One of the most important and universally implicated signaling molecules is [Ca2+]cyt. It is known to regulate a plethora of developmental and metabolic processes in both plants and animals; however, its impact on the regulation of miRNA expression is relatively less explored. The current study employed a combination of internal and external calcium channel inhibitors to establishing that [Ca2+]cyt signatures actively regulate miRNA expression in rice. Involvement of [Ca2+]cyt in the regulation of miRNA expression was further confirmed by treatment with calcimycin, the calcium ionophore. Modulation of the cytosolic calcium levels was also found to regulate the drought-responsive expression as well as ABA-mediated response of miRNA genes in rice seedlings. The study further establishes the role of calmodulins and Calmodulin-binding Transcription Activators (CAMTAs) as important components of the signal transduction schema that regulates miRNA expression. Yeast one-hybrid assay established that OsCAMTA4 & 6 are involved in the transcriptional regulation of miR156a and miR167h. Thus, the study was able to establish that [Ca2+]cyt is actively involved in regulating the expression of miRNA genes both under control and stress conditions.
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Affiliation(s)
| | | | | | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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26
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Bhowal B, Bhattacharjee A, Goswami K, Sanan-Mishra N, Singla-Pareek SL, Kaur C, Sopory S. Serotonin and Melatonin Biosynthesis in Plants: Genome-Wide Identification of the Genes and Their Expression Reveal a Conserved Role in Stress and Development. Int J Mol Sci 2021; 22:ijms222011034. [PMID: 34681693 PMCID: PMC8538589 DOI: 10.3390/ijms222011034] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/29/2021] [Accepted: 10/07/2021] [Indexed: 01/04/2023] Open
Abstract
Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (SNAT) and acetyl-serotonin methyltransferase (ASMT) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of OsTDC5 and OsASMT18, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.
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Affiliation(s)
- Bidisha Bhowal
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (B.B.); (A.B.); (K.G.); (N.S.-M.); (S.L.S.-P.)
| | - Annapurna Bhattacharjee
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (B.B.); (A.B.); (K.G.); (N.S.-M.); (S.L.S.-P.)
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Kavita Goswami
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (B.B.); (A.B.); (K.G.); (N.S.-M.); (S.L.S.-P.)
| | - Neeti Sanan-Mishra
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (B.B.); (A.B.); (K.G.); (N.S.-M.); (S.L.S.-P.)
| | - Sneh L. Singla-Pareek
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (B.B.); (A.B.); (K.G.); (N.S.-M.); (S.L.S.-P.)
| | - Charanpreet Kaur
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (B.B.); (A.B.); (K.G.); (N.S.-M.); (S.L.S.-P.)
- Correspondence: (C.K.); (S.S.)
| | - Sudhir Sopory
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (B.B.); (A.B.); (K.G.); (N.S.-M.); (S.L.S.-P.)
- Correspondence: (C.K.); (S.S.)
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27
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Zhu Y, Liu Q, Xu W, Yao L, Wang X, Wang H, Xu Y, Li L, Duan C, Yi Z, Lin C. Identification of novel drought-responsive miRNA regulatory network of drought stress response in common vetch ( Vicia sativa). Open Life Sci 2021; 16:1111-1121. [PMID: 34712821 PMCID: PMC8511966 DOI: 10.1515/biol-2021-0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/06/2021] [Accepted: 08/19/2021] [Indexed: 11/15/2022] Open
Abstract
Drought is among the most important natural disasters with severe effects on animals and plants. MicroRNAs are a class of noncoding RNAs that play a crucial role in plant growth, development, and response to stress factors, including drought. However, the microRNAs in drought responses in common vetch (Vicia sativa), an annual herbaceous leguminous plant commonly used for forage by including it in mixed seeding during winter and spring, have not been characterized. To explore the microRNAs' response to drought in common vetch, we sequenced 10 small RNA (sRNA) libraries by the next-generation sequencing technology. We obtained 379 known miRNAs belonging to 38 families and 47 novel miRNAs. The two groups had varying numbers of differentially expressed miRNAs: 85 in the comparison group D5 vs C5 and 38 in the comparison group D3 vs C3. Combined analysis of mRNA and miRNA in the same samples under drought treatment identified 318 different target genes of 123 miRNAs. Functional annotation of the target genes revealed that the miRNAs regulate drought-responsive genes, such as leucine-rich repeat receptor-like kinase-encoding genes (LRR-RLKs), ABC transporter G family member 1 (ABCG1), and MAG2-interacting protein 2 (MIP2). The genes were involved in various pathways, including cell wall biosynthesis, reactive oxygen removal, and protein transport. The findings in this study provide new insights into the miRNA-mediated regulatory networks of drought stress response in common vetch.
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Affiliation(s)
- Yongqun Zhu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People’s Republic of China
| | - Qiuxu Liu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People’s Republic of China
| | - Wenzhi Xu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People’s Republic of China
| | - Li Yao
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People’s Republic of China
| | - Xie Wang
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People’s Republic of China
| | - Hong Wang
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People’s Republic of China
| | - Yalin Xu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People’s Republic of China
| | - Linxiang Li
- Bazhong Green Agriculture Innovation and Development Research Institute, Sichuan Academy of Agricultural Sciences, Bazhong, Sichuan 636000, People’s Republic of China
| | - Chunhua Duan
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People’s Republic of China
| | - Zhixin Yi
- Bazhong Green Agriculture Innovation and Development Research Institute, Sichuan Academy of Agricultural Sciences, Bazhong, Sichuan 636000, People’s Republic of China
| | - Chaowen Lin
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People’s Republic of China
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28
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Mehdi SMM, Krishnamoorthy S, Szczesniak MW, Ludwików A. Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis. Int J Mol Sci 2021; 22:7153. [PMID: 34281207 PMCID: PMC8268864 DOI: 10.3390/ijms22137153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5' RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.
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Affiliation(s)
- Syed Muhammad Muntazir Mehdi
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Sivakumar Krishnamoorthy
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Michal Wojciech Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland;
| | - Agnieszka Ludwików
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
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29
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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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30
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Hang N, Shi T, Liu Y, Ye W, Taier G, Sun Y, Wang K, Zhang W. Overexpression of Os-microRNA408 enhances drought tolerance in perennial ryegrass. PHYSIOLOGIA PLANTARUM 2021; 172:733-747. [PMID: 33215699 DOI: 10.1111/ppl.13276] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/26/2020] [Accepted: 11/10/2020] [Indexed: 05/29/2023]
Abstract
As a conserved microRNA (miRNA) family in plants, miR408 is known to be involved in different abiotic stress responses, including drought. Interestingly, some studies indicated a species- and/or cultivar-specific drought-responsive characteristic of miR408 in plant drought stress. Moreover, the functions of miR408 in perennial grass species are unknown. In this study, we investigated the role of miR408 in perennial ryegrass (Lolium perenne L.) by withholding water for 10 days for both wild type and transgenic plants with heterologous expression of rice (Oryza sativa L.) miR408 gene, Os-miR408. The results showed that transgenic perennial ryegrass plants displayed morphological changes under normal growth conditions, such as curl leaves and sunken stomata, which could be related to decreased leaf water loss. Moreover, transgenic perennial ryegrass exhibited improved drought tolerance, as demonstrated by maintaining higher leaf relative water content (RWC), lower electrolyte leakage (EL), and less lipid peroxidation compared to WT plants under drought stress. Furthermore, the transgenic plants showed higher antioxidative capacity under drought. These results showed that the improved drought tolerance in Os-miR408 transgenic plants could be due to leaf morphological changes favoring the maintenance of water status and to increased antioxidative capacity protecting against the reactive oxygen species damages under stress. These findings implied that miR408 could serve as a potential target for genetic manipulations to engineer perennial grass plants for improved water stress tolerance.
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Affiliation(s)
- Nan Hang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Tianran Shi
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yanrong Liu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenxin Ye
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Huhehaote, China
| | - Geli Taier
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yan Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Kehua Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- National Energy R&D Center for Biomass, China Agricultural University, Beijing, China
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31
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Giri J, Parida SK, Raghuvanshi S, Tyagi AK. Emerging Molecular Strategies for Improving Rice Drought Tolerance. Curr Genomics 2021; 22:16-25. [PMID: 34045921 PMCID: PMC8142347 DOI: 10.2174/1389202921999201231205024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/27/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
Rice occupies a pre-eminent position as a food crop in the world. Its production, how- ever, entails up to 3000 liters of water per kilogram of grain produced. Such high demand makes rice prone to drought easily. Sustainable rice cultivation with limited water resources requires the deployment of a suitable strategy for better water use efficiency and improved drought tolerance. Several drought-related genes have been evaluated in rice for their mode of action in conferring drought tolerance. Manipulation of components of abscisic acid signal transduction, stomatal density, deposition of cuticular wax, and protein modification pathways are emerging as priority targets. Gene reprogramming by microRNAs is also being explored to achieve drought tolerance. Genetically dissected Quantitative Trait Loci (QTLs) and their constituent genes are being deployed to develop drought-tolerant rice varieties. Progressive research and challenges include a better understanding of crucial components of drought response and search for new targets and the deployment of improved varieties in the field.
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Affiliation(s)
- Jitender Giri
- 1National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; 2Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Swarup K Parida
- 1National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; 2Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Saurabh Raghuvanshi
- 1National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; 2Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Akhilesh K Tyagi
- 1National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; 2Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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Tavanti TR, Melo AARD, Moreira LDK, Sanchez DEJ, Silva RDS, Silva RMD, Reis ARD. Micronutrient fertilization enhances ROS scavenging system for alleviation of abiotic stresses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:386-396. [PMID: 33556754 DOI: 10.1016/j.plaphy.2021.01.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/26/2021] [Indexed: 05/06/2023]
Abstract
Reactive oxygen species (ROS) such as hydrogen peroxide at low concentrations act as signaling of several abiotic stresses. Overproduction of hydrogen peroxide causes the oxidation of plant cell lipid phosphate layer promoting senescence and cell death. To mitigate the effect of ROS, plants develop antioxidant defense mechanisms (superoxide dismutase, catalase, guaiacol peroxidase), ascorbate-glutathione cycle enzymes (ASA-GSH) (ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase and glutathione reductase), which have the function of removing and transforming ROS into non-toxic substances to maintain cellular homeostasis. Foliar or soil application of fertilizers containing B, Cu, Fe, Mn, Mo, Ni, Se and Zn at low concentrations has the ability to elicit and activate antioxidative enzymes, non-oxidizing metabolism, as well as sugar metabolism to mitigate damage by oxidative stress. Plants treated with micronutrients show higher tolerance to abiotic stress and better nutritional status. In this review, we summarized results indicating micronutrient actions in order to reduce ROS resulting the increase of photosynthetic capacity of plants for greater crop yield. This meta-analysis provides information on the mechanism of action of micronutrients in combating ROS, which can make plants more tolerant to several types of abiotic stress such as extreme temperatures, salinity, heavy metals and excess light.
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Affiliation(s)
- Tauan Rimoldi Tavanti
- São Paulo State University "Júlio de Mesquita Filho" (UNESP), 15385-000, Ilha Solteira, SP, Brazil
| | | | | | | | - Rafael Dos Santos Silva
- São Paulo State University "Júlio de Mesquita Filho" (UNESP), 15385-000, Ilha Solteira, SP, Brazil
| | - Ricardo Messias da Silva
- São Paulo State University "Júlio de Mesquita Filho" (UNESP), 15385-000, Ilha Solteira, SP, Brazil
| | - André Rodrigues Dos Reis
- São Paulo State University "Júlio de Mesquita Filho" (UNESP), Rua Domingos da Costa Lopes 780, 17602-496, Tupã, SP, Brazil.
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Balyan S, Rao S, Jha S, Bansal C, Das JR, Mathur S. Characterization of novel regulators for heat stress tolerance in tomato from Indian sub-continent. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2118-2132. [PMID: 32163647 PMCID: PMC7540533 DOI: 10.1111/pbi.13371] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 05/03/2023]
Abstract
The footprint of tomato cultivation, a cool region crop that exhibits heat stress (HS) sensitivity, is increasing in the tropics/sub-tropics. Knowledge of novel regulatory hot spots from varieties growing in the Indian sub-continent climatic zones could be vital for developing HS-resilient crops. Comparative transcriptome-wide signatures of a tolerant (CLN1621L) and sensitive (CA4) cultivar pair shortlisted from a pool of varieties exhibiting variable thermo-sensitivity using physiological-, survival- and yield-related traits revealed redundant to cultivar-specific HS regulation. The antagonistically expressing genes encode enzymes and proteins that have roles in plant defence and abiotic stresses. Functional characterization of three antagonistic genes by overexpression and silencing established Solyc09g014280 (Acylsugar acyltransferase) and Solyc07g056570 (Notabilis) that are up-regulated in tolerant cultivar, as positive regulators of HS tolerance and Solyc03g020030 (Pin-II proteinase inhibitor), that are down-regulated in CLN1621L, as negative regulator of thermotolerance. Transcriptional assessment of promoters of these genes by SNPs in stress-responsive cis-elements and promoter swapping experiments in opposite cultivar background showed inherent cultivar-specific orchestration of transcription factors in regulating transcription. Moreover, overexpression of three ethylene response transcription factors (ERF.C1/F4/F5) also improved HS tolerance in tomato. This study identifies several novel HS tolerance genes and provides proof of their utility in tomato thermotolerance.
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Affiliation(s)
- Sonia Balyan
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Sombir Rao
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Sarita Jha
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Chandni Bansal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Saloni Mathur
- National Institute of Plant Genome ResearchNew DelhiIndia
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Hernandez Y, Goswami K, Sanan‐Mishra N. Stress induced dynamic adjustment of conserved miR164:NAC module. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2020; 1:134-151. [PMID: 37283725 PMCID: PMC10168063 DOI: 10.1002/pei3.10027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 07/02/2020] [Accepted: 07/14/2020] [Indexed: 06/08/2023]
Abstract
Aims including the rationale Salinity and drought are the two major stresses limiting the productivity of economically important crops such as Glycine max (soybean). The incidence of these stresses during the pod development stages affects the quality and quantity of seeds, which compromise the yield of soybean. The miR164:NAC module has been shown to play a critical role in regulating the response to salt and drought stress in several plant species. However, biological role of miR164:NAC module in salt stress in soybean is not fully understood. Methods In this study, we identified 215 salt responsive miRNAs, using miScript miRNA array with a sensitive and a tolerant soybean genotype, William82 and INCASoy36, respectively. The targets of these salt regulated miRNAs were searched in the degradome datasets. Key results It was found that four salt stress deregulated miRNAs targeted the NAC transcription factor and among these miR164k and miR408d showed antagonistic expression in the two soybean genotypes. The expression of miR164k was higher in salt tolerant INCASoy36 as compared to salt sensitive William82, under unstressed conditions. However under salt stress, miR164k was downregulated in INCASoy36 (-2.65 fold), whereas it was upregulated in William82 (4.68 fold). A transient co-expression assay validated that gma-miR164k directs the cleavage of GmNAC1 transcript. Bioinformatics analysis revealed that the regulation of NAC transcription factor family by members of miR164 family is conserved across many species. The dynamic expression profiles of miR164 and NAC-TFs were captured in different tissues of rice, tobacco, and two soybean genotypes under drought and salt stress conditions. Main conclusion Collectively, our results suggest that genetically determined dynamic modulation of the conserved miR164:NAC-TF module may play an important role in determining the adaptive response of plants to stress.
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Affiliation(s)
- Yuniet Hernandez
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Kavita Goswami
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Neeti Sanan‐Mishra
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
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Rakhmetullina A, Pyrkova A, Aisina D, Ivashchenko A. In silico prediction of human genes as potential targets for rice miRNAs. Comput Biol Chem 2020; 87:107305. [PMID: 32570176 DOI: 10.1016/j.compbiolchem.2020.107305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Exogenous microRNAs (miRNAs) enter the human body through food, and their effects on metabolic processes can be considerable. It is important to determine which miRNAs from plants affect the expression of human genes and the extent of their influence. METHOD The binding sites of 738Oryza sativa miRNAs (osa-miRNAs) that interact with 17 508 mRNAs of human genes were determined using the MirTarget program. RESULT The characteristics of the binding of 46 single osa-miRNAs to 86 mRNAs of human genes with a value of free energy (ΔG) interaction equal 94%-100% from maximum ΔG were established. The findings showed that osa-miR2102-5p, osa-miR5075-3p, osa-miR2097-5p, osa-miR2919 targeted the largest number of genes at 38, 36, 23, 19 sites, respectively. mRNAs of 86 human genes were identified as targets for 93 osa-miRNAs of all family osa-miRNAs with ΔG values equal 94%-98% from maximum ΔG. Each miRNA of the osa-miR156-5p, osa-miR164-5p, osa-miR168-5p, osa-miR395-3p, osa-miR396-3p, osa-miR396-5p, osa-miR444-3p, osa-miR529-3p, osa-miR1846-3p, osa-miR2907-3p families had binding sites in mRNAs of several human target genes. The binding sites of osa-miRNAs in mRNAs of the target genes for each family of osa-miRNAs were conserved when compared to flanking nucleotide sequences. CONCLUSION Target mRNA human genes of osa-miRNAs are also candidate genes of cancer, cardiovascular and neurodegenerative diseases.
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Affiliation(s)
- Aizhan Rakhmetullina
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan
| | - Anna Pyrkova
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan
| | - Dana Aisina
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan
| | - Anatoliy Ivashchenko
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan.
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Xia H, Yu S, Kong D, Xiong J, Ma X, Chen L, Luo L. Temporal responses of conserved miRNAs to drought and their associations with drought tolerance and productivity in rice. BMC Genomics 2020; 21:232. [PMID: 32171232 PMCID: PMC7071783 DOI: 10.1186/s12864-020-6646-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Plant miRNAs play crucial roles in responses to drought and developmental processes. It is essential to understand the association of miRNAs with drought-tolerance (DT), as well as their impacts on growth, development, and reproduction (GDP). This will facilitate our utilization of rice miRNAs in breeding. RESULTS In this study, we investigated the time course of miRNA responses to a long-term drought among six rice genotypes by high-throughput sequencing. In total, 354 conserved miRNAs were drought responsive, representing obvious genotype- and stage-dependent patterns. The drought-responsive miRNAs (DRMs) formed complex regulatory network via their coexpression and direct/indirect impacts on the rice transcriptome. Based on correlation analyses, 211 DRMs were predicted to be associated with DT and/or GDP. Noticeably, 14.2% DRMs were inversely correlated with DT and GDP. In addition, 9 pairs of mature miRNAs, each derived from the same pre-miRNAs, were predicted to have opposite roles in regulating DT and GDP. This suggests a potential yield penalty if an inappropriate miRNA/pre-miRNA is utilized. miRNAs have profound impacts on the rice transcriptome reflected by great number of correlated drought-responsive genes. By regulating these genes, a miRNA could activate diverse biological processes and metabolic pathways to adapt to drought and have an influence on its GDP. CONCLUSION Based on the temporal pattern of miRNAs in response to drought, we have described the complex network between DRMs. Potential associations of DRMs with DT and/or GDP were disclosed. This knowledge provides valuable information for a better understanding in the roles of miRNAs play in rice DT and/or GDP, which can facilitate our utilization of miRNA in breeding.
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Affiliation(s)
- Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai, China.
| | - Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Deyan Kong
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jie Xiong
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China.
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Balyan S, Joseph SV, Jain R, Mutum RD, Raghuvanshi S. Investigation into the miRNA/5' isomiRNAs function and drought-mediated miRNA processing in rice. Funct Integr Genomics 2020; 20:509-522. [DOI: 10.1007/s10142-020-00731-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/04/2019] [Accepted: 01/02/2020] [Indexed: 11/28/2022]
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Pareek A, Dhankher OP, Foyer CH. Mitigating the impact of climate change on plant productivity and ecosystem sustainability. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:451-456. [PMID: 31909813 PMCID: PMC6945998 DOI: 10.1093/jxb/erz518] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, UK
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Biswal AK, Mangrauthia SK, Reddy MR, Yugandhar P. CRISPR mediated genome engineering to develop climate smart rice: Challenges and opportunities. Semin Cell Dev Biol 2019; 96:100-106. [DOI: 10.1016/j.semcdb.2019.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022]
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Nadarajah K, Kumar IS. Drought Response in Rice: The miRNA Story. Int J Mol Sci 2019; 20:ijms20153766. [PMID: 31374851 PMCID: PMC6696311 DOI: 10.3390/ijms20153766] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 01/07/2023] Open
Abstract
As a semi-aquatic plant, rice requires water for proper growth, development, and orientation of physiological processes. Stress is induced at the cellular and molecular level when rice is exposed to drought or periods of low water availability. Plants have existing defense mechanisms in planta that respond to stress. In this review we examine the role played by miRNAs in the regulation and control of drought stress in rice through a summary of molecular studies conducted on miRNAs with emphasis on their contribution to drought regulatory networks in comparison to other plant systems. The interaction between miRNAs, target genes, transcription factors and their respective roles in drought-induced stresses is elaborated. The cross talk involved in controlling drought stress responses through the up and down regulation of targets encoding regulatory and functional proteins is highlighted. The information contained herein can further be explored to identify targets for crop improvement in the future.
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Affiliation(s)
- Kalaivani Nadarajah
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia.
| | - Ilakiya Sharanee Kumar
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
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Awasthi JP, Chandra T, Mishra S, Parmar S, Shaw BP, Nilawe PD, Chauhan NK, Sahoo S, Panda SK. Identification and characterization of drought responsive miRNAs in a drought tolerant upland rice cultivar KMJ 1-12-3. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 137:62-74. [PMID: 30738218 DOI: 10.1016/j.plaphy.2019.01.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Shortfall of rain that creates drought like situation in non-irrigated agriculture system often limits rice production, necessitating introduction of drought tolerance trait into the cultivar of interest. The mechanism governing drought tolerance is, however, largely unknown, particularly the involvement of miRNAs, the master regulators of biochemical events. In this regard, response study on a drought tolerant rice variety KMJ 1-12-3 to 20% PEG (osmolality- 315 mOsm/kg) as drought stress revealed significant changes in abundance of several conserved miRNAs targeting transcription factors like homeodomain-leucine zipper, MADS box family protein, C2H2 zinc finger protein and Myb, well known for their importance in drought tolerance in plants. The response study also revealed significant PEG-induced decrease in abundance of the miRNAs targeting cyclin A, cyclin-dependent kinase, guanine nucleotide exchange factor, GTPase-activating protein, 1-aminocyclopropane-1-carboxylic acid oxidase and indole-3-acetic beta-glucosyl transferase indicating miRNA-regulated role of the cell cycle regulators, G-protein signalling and the plant hormones ethylene and IAA in drought tolerance in plants. The study confirmed the existence of four novel miRNAs, including osa-miR12470, osa-miR12471, osa-miR12472 and osa-miR12473, and the targets of three of them could be successfully validated. The PEG-induced decrease in abundance of the novel miRNAs osa-miR12470 and osa-miR12473 targeting RNA dependent RNA polymerase and equilibrative nucleoside transporter, respectively suggested an overall increase in both degradation and synthesis of nucleic acids in plants challenged with drought stress. The drought-responsive miRNAs identified in the study may be proved useful in introducing the trait in the rice cultivars of choice by manipulation of their cellular abundance.
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Affiliation(s)
- Jay Prakash Awasthi
- Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, Assam, India.
| | - Tilak Chandra
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Sagarika Mishra
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Shaifaly Parmar
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Birendra Prasad Shaw
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Pravin Daulat Nilawe
- Thermo Fisher Scientific India Pvt. Ltd, 403/404 B-Wing, Delphi, Hiranandani Business Park, Powai, Mumbai, 400076, India.
| | - Neeraj Kumar Chauhan
- Thermo Fisher Scientific India Pvt. Ltd, 403/404 B-Wing, Delphi, Hiranandani Business Park, Powai, Mumbai, 400076, India.
| | - Smita Sahoo
- Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, Assam, India.
| | - Sanjib Kumar Panda
- Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, Assam, India.
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Multiple Regression Analysis Reveals MicroRNA Regulatory Networks in Oryza sativa under Drought Stress. Int J Genomics 2018; 2018:9395261. [PMID: 30402456 PMCID: PMC6196795 DOI: 10.1155/2018/9395261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/14/2018] [Accepted: 09/10/2018] [Indexed: 01/17/2023] Open
Abstract
Drought is a major abiotic stress that reduces rice development and yield. miRNAs (microRNAs) are known to mediate posttranscriptional regulation under drought stress. Although the importance of individual miRNAs has been established, the crosstalks between miRNAs and mRNAs remain unearthed. Here we performed microarray analysis of miRNAs and matched mRNA expression profiles of drought-treated rice cultivar Nipponbare. Drought-responsive miRNA-mRNA regulations were identified by a combination of a partial least square (PLS) regression approach and sequence-based target prediction. A drought-induced network with 13 miRNAs and 58 target mRNAs was constructed, and four miRNA coregulatory modules were revealed. Functional analysis suggested that drought-response miRNA targets are enriched in hormone signaling, lipid and carbohydrate metabolism, and antioxidant defense. 13 candidate miRNAs and target genes were validated by RT-qPCR, hierarchical clustering, and ROC analysis. Two target genes (DWARF-3 and P0651G05.2) of miRNA coregulatory modules were further verified by RLM-5' RACE. Together, our integrative study of miRNA-mRNA interaction provided attractive candidates that will help elucidate the drought-response mechanisms in Oryza sativa.
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Islam W, Noman A, Qasim M, Wang L. Plant Responses to Pathogen Attack: Small RNAs in Focus. Int J Mol Sci 2018; 19:E515. [PMID: 29419801 PMCID: PMC5855737 DOI: 10.3390/ijms19020515] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/04/2018] [Accepted: 02/05/2018] [Indexed: 12/25/2022] Open
Abstract
Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.
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Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38040, Pakistan.
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Qasim
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Liande Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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