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Kaur G, Jain S, Bhushan S, Das N, Sharma M, Sharma D. Role of microRNAs and their putative mechanism in regulating potato (Solanum tuberosum L.) life cycle and response to various environmental stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108334. [PMID: 38219424 DOI: 10.1016/j.plaphy.2024.108334] [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: 02/26/2023] [Revised: 10/31/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
The exponentially increasing population and the demand for food is inextricably linked. This has shifted global attention to improving crop plant traits to meet global food demands. Potato (Solanum tuberosum L.) is a major non-grain food crop that is grown all over the world. Currently, some of the major global potato research work focuses on the significance of microRNAs (miRNAs) in potato. miRNAs are a type of non-coding RNAs that regulate the gene expression of their target mRNA genes by cleavage and/or their translational inhibition. This suggests an essential role of miRNAs in a multitude of plant biological processes, including maintenance of genome integrity, plant growth, development and maturation, and initiation of responses to various stress conditions. Therefore, engineering miRNAs to generate stress-resistant varieties of potato may result in high yield and improved nutritional qualities. In this review, we discuss the potato miRNAs specifically known to play an essential role in the various stages of the potato life cycle, conferring stress-resistant characteristics, and modifying gene expression. This review highlights the significance of the miRNA machinery in plants, especially potato, encouraging further research into engineering miRNAs to boost crop yields and tolerance towards stress.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Sahil Jain
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu and Kashmir (UT), India
| | - Niranjan Das
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Munish Sharma
- Department of Plant Science, Central University of Himachal Pradesh, Shahpur Parisar, Kangra, Himachal Pradesh, India.
| | - Deepak Sharma
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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2
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Deng K, Yin H, Xiong F, Feng L, Dong P, Ren M. Genome-wide miRNA expression profiling in potato ( Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway. PeerJ 2021; 9:e10704. [PMID: 33520467 PMCID: PMC7811781 DOI: 10.7717/peerj.10704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/14/2020] [Indexed: 12/29/2022] Open
Abstract
Target of rapamycin (TOR) operates as a hub of the signal transduction that integrates nutrient and energy signaling to promote cell proliferation and growth through mediating the transcriptional and post- transcriptional regulator networks in all eukaryotic species. MicroRNAs (miRNAs) are widespread classes of small, single-stranded, non-coding endogenous RNAs and are widely found in eukaryotes, which play a vital role in regulating gene expression by degrading targeted mRNAs or translational repression at post-transcriptional level. Recent studies found that there were necessarily close connections between miRNA and TOR pathways in mammals. However, there is little information about the interplay between the miRNA and TOR in plants. Thus, the aim of this study was to identify potential TOR-miRNA-mRNA regulatory networks in TOR signaling through global mRNA and microRNA expression profiling in potato. Based on the previous high-throughput transcriptome sequencing and filtering, a total of 2,899 genes were significantly differentially expressed in potato under TOR inhibitors treatment. Pathway analysis revealed that these genes were significantly enriched in multiple metabolic processes. Similarly, in the present study, suppression of TOR resulted in 41 miRNAs up-regulated and 45 down-regulated, revealing that TOR plays a crucial role in the regulation of miRNA regulatory network. Furthermore, integrated mRNA and miRNA expression profiling uncovered that these miRNAs participated in large-scale metabolic process in the TOR signal pathway in potato, such as regulation of autophagy and ubiquitination, and biosynthesis of secondary metabolites. Overall, the results shed new insight into TOR related post-transcriptional gene regulatory networks in potato and suggesting TOR-miRNA-targeting genes relevant networks as a potential genetic resource for potato improvement.
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Affiliation(s)
- Kexuan Deng
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Huan Yin
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fangjie Xiong
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Li Feng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Pan Dong
- School of Life Sciences, Chongqing University, Chongqing, China.,Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
| | - Maozhi Ren
- School of Life Sciences, Chongqing University, Chongqing, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
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3
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Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Chakrabarti SK. Genome-wide identification and characterization of microRNAs by small RNA sequencing for low nitrogen stress in potato. PLoS One 2020; 15:e0233076. [PMID: 32428011 PMCID: PMC7237020 DOI: 10.1371/journal.pone.0233076] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/28/2020] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is an important nutrient for plant growth and tuber quality of potato. Since potato crop requires high dose of N, improving nitrogen use efficiency (NUE) of plant is an inevitable approach to minimize N fertilization. The aim of this study was to identify and characterize microRNAs (miRNAs) by small RNA sequencing in potato plants grown in aeroponic under two contrasting N (high and low) regimes. A total of 119 conserved miRNAs belonging to 41 miRNAs families, and 1002 putative novel miRNAs were identified. From total, 52 and 54 conserved miRNAs, and 404 and 628 putative novel miRNAs were differentially expressed in roots and shoots, respectively under low N stress. Of total 34,135 predicted targets, the gene ontology (GO) analysis indicated that maximum targets belong to biological process followed by molecular function and cellular component. Eexpression levels of the selected miRNAs and targets were validated by real time-quantitative polymerase chain reaction (RT-qPCR) analysis. Two predicted targets of potential miRNAs (miR397 and miR398) were validated by 5' RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). In general, predicted targets are associated with stress-related, kinase, transporters and transcription factors such as universal stress protein, heat shock protein, salt-tolerance protein, calmodulin binding protein, serine-threonine protein kinsae, Cdk10/11- cyclin dependent kinase, amino acid transporter, nitrate transporter, sugar transporter, transcription factor, F-box family protein, and zinc finger protein etc. Our study highlights that miR397 and miR398 play crucial role in potato during low N stress management. Moreover, study provides insights to modulate miRNAs and their predicted targets to develop N-use efficient potato using transgenic/genome-editing tools in future.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- * E-mail:
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Aastha Saraswati
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Shashi Rawat
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Swarup Kumar Chakrabarti
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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4
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Sangita Chowdhury Paul, Sharma A, Mehta R, Paul S. In silico Characterization of microRNAs and Their Target Transcripts from Cranberry (Vaccinium macrocarpon). CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720010120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Esposito S, Aversano R, Bradeen JM, Di Matteo A, Villano C, Carputo D. Deep-sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22 Suppl 1:133-142. [PMID: 30597710 DOI: 10.1111/plb.12955] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Among wild species used in potato breeding, Solanum commersonii displays the highest tolerance to low temperatures under both acclimated (ACC) and non-acclimated (NACC) conditions. It is also the first wild potato relative with a known whole genome sequence. Recent studies have shown that abiotic stresses induce changes in the expression of many small non-coding RNA (sncRNA). We determined the small non-coding RNA (sncRNAome) of two clones of S. commersonii contrasting in their cold response phenotypes via smRNAseq. Differential analysis provided evidence that expression of several miRNAs changed in response to cold stress conditions. Conserved miR408a and miR408b changed their expression under NACC conditions, whereas miR156 and miR169 were differentially expressed only under ACC conditions. We also report changes in tasiRNA and secondary siRNA expression under both stress conditions. Our results reveal possible roles of sncRNA in the regulatory networks associated with tolerance to low temperatures and provide useful information for a more strategic use of genomic resources in potato breeding.
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Affiliation(s)
- S Esposito
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - R Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - J M Bradeen
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - A Di Matteo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - C Villano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - D Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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Li J, Lei L, Ye F, Zhou Y, Chang H, Zhao G. Nutritive implications of dietary microRNAs: facts, controversies, and perspectives. Food Funct 2019; 10:3044-3056. [PMID: 31066412 DOI: 10.1039/c9fo00216b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As a group of non-coding RNA molecules, microRNAs have recently become more well-known due to their pivotal role in gene regulation. A large number of endogenous microRNAs naturally occur in the human body, and some of them act as regulatory targets of diet and its components. The wide presence of microRNAs in various food materials has inspired food scientists and nutritionists to explore their nutritive and bioactive significance. This article comprehensively reports updated insights into the accessibility, stability, absorbability, and bioactivity of dietary microRNAs by combining the current knowledge into figures and tables for reader's convenience. As one frontier in food science and nutrition, the research platform on dietary microRNAs is imperfect and even defective as indicated by the inconsistent and even contradictory results concluded by different investigations. The pros and cons as well as the limitations of current investigations have been critically discussed with attention chiefly paid to experimental designs and protocols. Moreover, future research directions have been recommended. Thus, this paper may not only provide a quick glance at the state-of-the-art of dietary microRNAs but also guide further research to clarify the present controversies and make the results more credible and persuasive.
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Affiliation(s)
- Jianting Li
- College of Food Science, Southwest University, Chongqing 400715, People's Republic of China.
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Otsuka K, Yamamoto Y, Matsuoka R, Ochiya T. Maintaining good miRNAs in the body keeps the doctor away?: Perspectives on the relationship between food-derived natural products and microRNAs in relation to exosomes/extracellular vesicles. Mol Nutr Food Res 2017; 62. [PMID: 28594130 DOI: 10.1002/mnfr.201700080] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 12/21/2022]
Abstract
During the last decade, it has been uncovered that microRNAs (miRNAs), a class of small non-coding RNAs, are related to many diseases including cancers. With an increase in reports describing the dysregulation of miRNAs in various tumor types, it has become abundantly clear that miRNAs play significant roles in the formation and progression of cancers. Intriguingly, miRNAs are present in body fluids because they are packed in exosomes/extracellular vesicles and released from all types of cells. The miRNAs in the fluids are measured in a relatively simple way and the profile of miRNAs is likely to be an indicator of health condition. In recent years, various studies have demonstrated that some naturally occurring compounds can control tumor-suppressive and oncogenic miRNAs in a positive manner, suggesting that food-derived compounds could maintain the expression levels of miRNAs and help maintain good health. Therefore, our daily food and compounds in food are of great interest. In addition, exogenous diet-derived miRNAs have been indicated to function in the regulation of target mammalian transcripts in the body. These findings highlight the possibility of diet for good health through the regulation of miRNAs, and we also discuss the perspective of food application and health promotion.
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Affiliation(s)
- Kurataka Otsuka
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.,R&D Division, Kewpie Corporation Sengawa Kewport, Tokyo, Japan
| | - Yusuke Yamamoto
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | | | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
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8
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Paul S. Identification and characterization of microRNAs and their targets in high-altitude stress-adaptive plant maca (Lepidium meyenii Walp). 3 Biotech 2017; 7:103. [PMID: 28560642 DOI: 10.1007/s13205-017-0734-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/19/2017] [Indexed: 11/26/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous, short (~21-nucleotide), non-coding RNA molecules that play pivotal roles in plant growth, development, and stress response signaling. In this study using recently published draft genome sequence of a high-altitude plant maca (Lepidium meyenii Walp) and applying genome-wide computational-based approaches, a total of 62 potentially conserved miRNAs belonging to 28 families were identified and four (lme-miR160a, lme-miR164c, lme-miR 166a, and lme-miR 319a) of them further validated by RT-PCR. Deploying psRNATarget tool a total of 99 potential miRNA target transcripts were also identified in maca. Targets include a number of transcription factors like Squamosa promoter-binding, NAC, MYB, auxin response factor, APETALA, WRKY, and F-box protein. To the best of my knowledge, this is the first genome-based miRNA profiling of a high-altitude plant.
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Affiliation(s)
- Sujay Paul
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India.
- Laboratorio de Micología y Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, 12, Lima, Peru.
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Kundu A, Paul S, Dey A, Pal A. High throughput sequencing reveals modulation of microRNAs in Vigna mungo upon Mungbean Yellow Mosaic India Virus inoculation highlighting stress regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 257:96-105. [PMID: 28224923 DOI: 10.1016/j.plantsci.2017.01.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/23/2017] [Accepted: 01/28/2017] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing. Sequencing followed by bioinformatics analysis of the small RNA reads indicated that the expression patterns of most of the known and novel miRNAs were altered in resistant line over mock-inoculated sample during the plant virus incompatible interaction. Highly altered miRNAs belong to the families of miR156, miR159, miR160, miR166, miR398, miR1511, miR1514, miR2118 and novel vmu-miRn7, vmu-miRn8, vmu-miRn13 and vmu-miRn14. These results were validated using qPCR, and most of the miRNAs showed similar pattern of expression like that of Illumina reads. The expression patterns of some selected known and novel miRNAs were also compared between the infected MYMIV-resistant and -susceptible genotypes and most of these were modulated after MYMIV-inoculation. Target transcripts like NB-LRR, NAC, MYB, Zinc finger, CCAAT-box transcription factor, fructose 2-6 bisphosphate, HDZIP protein that confers immune response were predicted as targets amongst identified miRNAs using psRNATarget server. Some selected target transcripts including NB-LRR, ARF, SOD, SPB, Basic blue copper protein were validated and their differential expression were demonstrated between MYMIV-resistant and -susceptible V. mungo by qPCR data analyses. In the present study we have identified miRNAs that implicate in the regulation of MYMIV-induced stress response in V. mungo; and generated genomic resources for a non-model legume with the aid of bioinformatics tools supplemented by experimental validation.
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Affiliation(s)
- Anirban Kundu
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India; Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata, 7000118, India
| | - Sujay Paul
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India; Laboratorio de Micología y Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima, 12, Peru.
| | - Avishek Dey
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India.
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Abstract
Foods provide fats, carbohydrates, and proteins as well as vitamins, minerals and trace elements. These dietary factors may influence cellular processes by regulating endogenous microRNA expression. MicroRNAs are non-coding regulatory molecules which affect gene expression at the post transcriptional level. It has been shown that plant and animal derived foods also contain microRNA. Yet, it is unclear if and to what extent plant and animal food derived microRNAs are absorbed by mammals. Thus, future studies need to better address absorption, tissue distribution and function of dietary plant and animal derived microRNAs in the context of human health and disease.
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Affiliation(s)
- Anika E Wagner
- Institute of Human Nutrition and Food Science, Christian-Albrechts-University, Hermann-Rodewald-Str. 6, 24118 Kiel, Germany.
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Xu X, Jiang Q, Ma X, Ying Q, Shen B, Qian Y, Song H, Wang H. Deep sequencing identifies tissue-specific microRNAs and their target genes involving in the biosynthesis of tanshinones in Salvia miltiorrhiza. PLoS One 2014; 9:e111679. [PMID: 25365305 PMCID: PMC4218800 DOI: 10.1371/journal.pone.0111679] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/29/2014] [Indexed: 11/19/2022] Open
Abstract
Salvia miltiorrhiza is one of the most popular traditional medicinal herbs in Asian nations. Its dried root contains a number of tanshinones, protocatechuic aldehyde, salvianolic acid B and rosmarinic, and is used for the treatment of various diseases. The finding of microRNAs (miRNAs) and their target genes will help understand their biological role on the biosynthesis of tanshinones in S. miltiorrhiza. In the present study, a total of 452 known miRNAs corresponding to 589 precursor miRNAs (pre-miRNAs), and 40 novel miRNAs corresponding to 24 pre-miRNAs were identified in different tissues of S. miltiorrhiza by high-throughput sequencing, respectively. Among them, 62 miRNAs express only in root, 95 miRNAs express only in stem, 19 miRNAs express only in leaf, and 71 miRNAs express only in flower, respectively. By the degradome analysis, 69 targets potentially cleaved by 25 miRNAs were identified. Among them, acetyl-CoA C-acetyltransferase was cleaved by miR5072, and involved in the biosynthesis of tanshinones. This study provided valuable information for understanding the tissue-specific expression patterns of miRNAs in S. miltiorrhiza, and offered a foundation for future studies of the miRNA-mediated biosynthesis of tanshinones.
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Affiliation(s)
- Xiangbin Xu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qinghua Jiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiuyan Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qicai Ying
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bo Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yongsheng Qian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hongmiao Song
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- * E-mail: (HMS); (HZW)
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- * E-mail: (HMS); (HZW)
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Identification of novel and conserved microRNAs related to drought stress in potato by deep sequencing. PLoS One 2014; 9:e95489. [PMID: 24748226 PMCID: PMC3991665 DOI: 10.1371/journal.pone.0095489] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/27/2014] [Indexed: 11/29/2022] Open
Abstract
MicroRNAs (miRNAs) are a group of small, non-coding RNAs that play important roles in plant growth, development and stress response. There have been an increasing number of investigations aimed at discovering miRNAs and analyzing their functions in model plants (such as Arabidopsis thaliana and rice). In this research, we constructed small RNA libraries from both polyethylene glycol (PEG 6,000) treated and control potato samples, and a large number of known and novel miRNAs were identified. Differential expression analysis showed that 100 of the known miRNAs were down-regulated and 99 were up-regulated as a result of PEG stress, while 119 of the novel miRNAs were up-regulated and 151 were down-regulated. Based on target prediction, annotation and expression analysis of the miRNAs and their putative target genes, 4 miRNAs were identified as regulating drought-related genes (miR811, miR814, miR835, miR4398). Their target genes were MYB transcription factor (CV431094), hydroxyproline-rich glycoprotein (TC225721), quaporin (TC223412) and WRKY transcription factor (TC199112), respectively. Relative expression trends of those miRNAs were the same as that predicted by Solexa sequencing and they showed a negative correlation with the expression of the target genes. The results provide molecular evidence for the possible involvement of miRNAs in the process of drought response and/or tolerance in the potato plant.
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Bhogale S, Mahajan AS, Natarajan B, Rajabhoj M, Thulasiram HV, Banerjee AK. MicroRNA156: a potential graft-transmissible microRNA that modulates plant architecture and tuberization in Solanum tuberosum ssp. andigena. PLANT PHYSIOLOGY 2014; 164:1011-27. [PMID: 24351688 PMCID: PMC3912076 DOI: 10.1104/pp.113.230714] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 12/13/2013] [Indexed: 05/18/2023]
Abstract
MicroRNA156 (miR156) functions in maintaining the juvenile phase in plants. However, the mobility of this microRNA has not been demonstrated. So far, only three microRNAs, miR399, miR395, and miR172, have been shown to be mobile. We demonstrate here that miR156 is a potential graft-transmissible signal that affects plant architecture and tuberization in potato (Solanum tuberosum). Under tuber-noninductive (long-day) conditions, miR156 shows higher abundance in leaves and stems, whereas an increase in abundance of miR156 has been observed in stolons under tuber-inductive (short-day) conditions, indicative of a photoperiodic control. Detection of miR156 in phloem cells of wild-type plants and mobility assays in heterografts suggest that miR156 is a graft-transmissible signal. This movement was correlated with changes in leaf morphology and longer trichomes in leaves. Overexpression of miR156 in potato caused a drastic phenotype resulting in altered plant architecture and reduced tuber yield. miR156 overexpression plants also exhibited altered levels of cytokinin and strigolactone along with increased levels of LONELY GUY1 and StCyclin D3.1 transcripts as compared with wild-type plants. RNA ligase-mediated rapid amplification of complementary DNA ends analysis validated SQUAMOSA PROMOTER BINDING-LIKE3 (StSPL3), StSPL6, StSPL9, StSPL13, and StLIGULELESS1 as targets of miR156. Gel-shift assays indicate the regulation of miR172 by miR156 through StSPL9. miR156-resistant SPL9 overexpression lines exhibited increased miR172 levels under a short-day photoperiod, supporting miR172 regulation via the miR156-SPL9 module. Overall, our results strongly suggest that miR156 is a phloem-mobile signal regulating potato development.
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Lakhotia N, Joshi G, Bhardwaj AR, Katiyar-Agarwal S, Agarwal M, Jagannath A, Goel S, Kumar A. Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing. BMC PLANT BIOLOGY 2014; 14:6. [PMID: 24397411 PMCID: PMC3913621 DOI: 10.1186/1471-2229-14-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/26/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are ubiquitous components of endogenous plant transcriptome. miRNAs are small, single-stranded and ~21 nt long RNAs which regulate gene expression at the post-transcriptional level and are known to play essential roles in various aspects of plant development and growth. Previously, a number of miRNAs have been identified in potato through in silico analysis and deep sequencing approach. However, identification of miRNAs through deep sequencing approach was limited to a few tissue types and developmental stages. This study reports the identification and characterization of potato miRNAs in three different vegetative tissues and four stages of tuber development by high throughput sequencing. RESULTS Small RNA libraries were constructed from leaf, stem, root and four early developmental stages of tuberization and subjected to deep sequencing, followed by bioinformatics analysis. A total of 89 conserved miRNAs (belonging to 33 families), 147 potato-specific miRNAs (with star sequence) and 112 candidate potato-specific miRNAs (without star sequence) were identified. The digital expression profiling based on TPM (Transcripts Per Million) and qRT-PCR analysis of conserved and potato-specific miRNAs revealed that some of the miRNAs showed tissue specific expression (leaf, stem and root) while a few demonstrated tuberization stage-specific expressions. Targets were predicted for identified conserved and potato-specific miRNAs, and predicted targets of four conserved miRNAs, miR160, miR164, miR172 and miR171, which are ARF16 (Auxin Response Factor 16), NAM (NO APICAL MERISTEM), RAP1 (Relative to APETALA2 1) and HAM (HAIRY MERISTEM) respectively, were experimentally validated using 5' RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). Gene ontology (GO) analysis for potato-specific miRNAs was also performed to predict their potential biological functions. CONCLUSIONS We report a comprehensive study of potato miRNAs at genome-wide level by high-throughput sequencing and demonstrate that these miRNAs have tissue and/or developmental stage-specific expression profile. Also, predicted targets of conserved miRNAs were experimentally confirmed for the first time in potato. Our findings indicate the existence of extensive and complex small RNA population in this crop and suggest their important role in pathways involved in diverse biological processes, including tuber development.
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Affiliation(s)
- Nisha Lakhotia
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Gopal Joshi
- Department of Botany, University of Delhi, Delhi 110007, India
| | | | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Arun Jagannath
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Amar Kumar
- Department of Botany, University of Delhi, Delhi 110007, India
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15
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Paul S, Kundu A, Pal A. Identification and expression profiling of Vigna mungo microRNAs from leaf small RNA transcriptome by deep sequencing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:15-23. [PMID: 24138283 DOI: 10.1111/jipb.12115] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 10/09/2013] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) represent a class of small non-coding RNA molecules that play a crucial role in post-transcriptional gene regulation. Several conserved and species-specific miRNAs have been characterized to date, predominantly from the plant species whose genome is well characterized. However, information on the variability of these regulatory RNAs in economically important but genetically less characterized crop species are limited. Vigna mungo is an important grain legume, which is grown primarily for its protein-rich edible seeds. miRNAs from this species have not been identified to date due to lack of genome sequence information. To identify miRNAs from V. mungo, a small RNA library was constructed from young leaves. High-throughput Illumina sequencing technology and bioinformatic analysis of the small RNA reads led to the identification of 66 miRNA loci represented by 45 conserved miRNAs belonging to 19 families and eight non-conserved miRNAs belonging to seven families. Besides, 13 novel miRNA candidates in V. mungo were also identified. Expression patterns of selected conserved, non-conserved, and novel miRNA candidates have been demonstrated in leaf, stem, and root tissues by quantitative polymerase chain reaction, and potential target genes were predicted for most of the conserved miRNAs. This information offers genomic resources for better understanding of miRNA mediated post-transcriptional gene regulation.
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Affiliation(s)
- Sujay Paul
- Division of Plant Biology, Bose Institute, Kolkata, 700054, West Bengal, India; Center for Genomic Sciences, National Autonomous University of Mexico, Morelos, 62431, Mexico
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16
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Zhang R, Marshall D, Bryan GJ, Hornyik C. Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS One 2013; 8:e57233. [PMID: 23437348 PMCID: PMC3578796 DOI: 10.1371/journal.pone.0057233] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/18/2013] [Indexed: 12/20/2022] Open
Abstract
Micro RNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. While the diverse functions of miRNAs in model plants have been well studied, the impact of miRNAs in crop plant biology is poorly understood. Here we used high-throughput sequencing and bioinformatics analysis to analyze miRNAs in the tuber bearing crop potato (Solanum tuberosum). Small RNAs were analysed from leaf and stolon tissues. 28 conserved miRNA families were found and potato-specific miRNAs were identified and validated by RNA gel blot hybridization. The size, origin and predicted targets of conserved and potato specific miRNAs are described. The large number of miRNAs and complex population of small RNAs in potato suggest important roles for these non-coding RNAs in diverse physiological and metabolic pathways.
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Affiliation(s)
- Runxuan Zhang
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - David Marshall
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Glenn J. Bryan
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Csaba Hornyik
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
- * E-mail:
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17
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Wang B, Dong M, Chen W, Liu X, Feng R, Xu T. Microarray identification of conserved microRNAs in Pinellia pedatisecta. Gene 2012; 498:36-40. [DOI: 10.1016/j.gene.2012.01.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 11/29/2011] [Accepted: 01/27/2012] [Indexed: 12/13/2022]
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18
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Mao W, Li Z, Xia X, Li Y, Yu J. A combined approach of high-throughput sequencing and degradome analysis reveals tissue specific expression of microRNAs and their targets in cucumber. PLoS One 2012; 7:e33040. [PMID: 22479356 PMCID: PMC3316546 DOI: 10.1371/journal.pone.0033040] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 02/08/2012] [Indexed: 11/30/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs playing an important regulatory function in plant development and stress responses. Among them, some are evolutionally conserved in plant and others are only expressed in certain species, tissue or developmental stages. Cucumber is among the most important greenhouse species in the world, but only a limited number of miRNAs from cucumber have been identified and the experimental validation of the related miRNA targets is still lacking. In this study, two independent small RNA libraries from cucumber leaves and roots were constructed, respectively, and sequenced with the high-throughput Illumina Solexa system. Based on sequence similarity and hairpin structure prediction, a total of 29 known miRNA families and 2 novel miRNA families containing a total of 64 miRNA were identified. QRT-PCR analysis revealed that some of the cucumber miRNAs were preferentially expressed in certain tissues. With the recently developed 'high throughput degradome sequencing' approach, 21 target mRNAs of known miRNAs were identified for the first time in cucumber. These targets were associated with development, reactive oxygen species scavenging, signaling transduction and transcriptional regulation. Our study provides an overview of miRNA expression profile and interaction between miRNA and target, which will help further understanding of the important roles of miRNAs in cucumber plants.
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Affiliation(s)
- Weihua Mao
- Department of Horticulture, Zhejiang University, Hangzhou, China
- Center of Analysis and Measurement, Zhejiang University, Hangzhou, China
| | - Zeyun Li
- Center of Analysis and Measurement, Zhejiang University, Hangzhou, China
| | - Xiaojian Xia
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yadan Li
- Hunan Agricultural Bioengineering Research Institute, Hunan Agricultural University, Changsha, China
| | - Jingquan Yu
- Department of Horticulture, Zhejiang University, Hangzhou, China
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19
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Microarray-based identification of conserved microRNAs from Pinellia ternata. Gene 2011; 493:267-72. [PMID: 22166543 DOI: 10.1016/j.gene.2011.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/25/2011] [Indexed: 12/23/2022]
Abstract
A large number of microRNAs (miRNAs) reportedly play important roles in plant development; however, scarcely any of these have been found in Pinellia ternata, a herbaceous plant with special physiologic characteristics and important medicinal value. To detect P. ternata miRNAs, an in situ synthesized custom microarray of plant miRNAs was employed, following verification of the presence of the miRNAs through reverse transcription polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR) in the current study. A total of 54 miRNAs belonging to 23 miRNA families were identified. RT-PCR applied to the eight miRNAs validated the microarray results. qRT-PCR that targeted eleven miRNAs showed the presence of miRNAs in different tissues with different expression levels, especially, miRNA319 expression level in the tubers is nearly 10 times higher than that in the stalks and leaves. This is the first report on the miRNAs in P. ternata, which will enable further investigation of their roles in P. ternata.
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20
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Discovering numerical laws of plant microRNA by evolution. Biochem Biophys Res Commun 2011; 415:313-8. [PMID: 22033408 DOI: 10.1016/j.bbrc.2011.10.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 10/09/2011] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules with important post-transcriptional regulatory roles. They are found in most eukaryotic cell types, including a diverse range of plant species. Previous research has demonstrated that numerical features of miRNA genes, based on sequence and structure, can be indicative of a particular miRNA's specialty. We carried out a large-scale analysis to discover the laws of the relationship between numerical features and evolution. Basic statistical methods were applied to 132 numerical features of 3343 miRNA genes from phylum levels to family levels. Results demonstrated that there were three significant classes among candidate numerical features, the conserved, the increased and the decreased with evolutionary time based on phylum levels. Furthermore, the conserved numerical features among families are usually also conserved among phyla and the features increasing with evolutionary time tended to be related to A or U nucleotides, while the features decreasing with evolutionary time tended to be related to G or C nucleotides. Our results confirm the strong relationship between numerical features of miRNA and species evolution. This research will greatly assist in elucidating the numerical laws of plant miRNA based on evolution.
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21
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LIU YX, CHANG W, HAN YP, ZOU Q, GUO MZ, LI WB. In silico Detection of Novel MicroRNAs Genes in Soybean Genome. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/s1671-2927(11)60126-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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22
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Characterization of novel small RNAs from tea (Camellia sinensis L.). Mol Biol Rep 2011; 39:3977-86. [DOI: 10.1007/s11033-011-1178-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/02/2011] [Indexed: 11/26/2022]
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23
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Lang Q, Jin C, Lai L, Feng J, Chen S, Chen J. Tobacco microRNAs prediction and their expression infected with Cucumber mosaic virus and Potato virus X. Mol Biol Rep 2011; 38:1523-31. [PMID: 20853150 DOI: 10.1007/s11033-010-0260-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 09/02/2010] [Indexed: 11/27/2022]
Abstract
MicroRNAs (miRNAs) are a newly identified class of non-coding small RNAs of about 21-24 nucleotides. They play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. To date, a total of 2,043 plant miRNAs are present in the miRNA Registry database (miRBase Release 14.0), and none for tobacco (Nicotiana tabacum). In this research, we used known plant miRNAs against both genomic survey sequence (GSS) and expressed sequence tags (EST) databases to search for potential miRNAs in tobacco. A total of 25 potential miRNAs were identified following a range of strict filtering criteria, and 33 potential targets of miRNAs were predicted by searching the tobacco Unigene database. Most of these miRNA targeting genes were predicted to encode transcription factors which play important roles in tobacco development. Additionally, real-time PCR assays were performed to profile the expression levels of 10 miRNAs after the infection of Cucumber mosaic virus (CMV) and Potato virus X (PVX). The results showed that symptom severity is correlated to the miRNA accumulation, and increased miR168 expression during virus infection is a common, plant- and virus-independent response.
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Affiliation(s)
- Qiulei Lang
- College of Life Sciences, Zhejiang University, Hangzhou, China
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24
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osa-MIR393: a salinity- and alkaline stress-related microRNA gene. Mol Biol Rep 2010; 38:237-42. [PMID: 20336383 DOI: 10.1007/s11033-010-0100-8] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 03/16/2010] [Indexed: 10/19/2022]
Abstract
Salinity and alkalinity are the two main environmental factors that limit rice production. Better understanding of the mechanisms responsible for salinity and alkaline stress tolerance would allow researchers to modify rice to increase its resistance to salinity and alkaline stress. MicroRNAs (miRNAs) are ~21-nucleotide RNAs that are ubiquitous regulators of gene expression in eukaryotic organisms. Some miRNAs acts as an important endogenous regulator in plant responses to abiotic stressors. miR393 is a conservative miRNA family that occurs in a variety of different plants. The two members of the miR393 family found in rice are named osa-MIR393 and osa-MIR393b. We found that the osa-MIR393 expression level changed under salinity and alkaline stress, whereas that of osa-MIR393b did not. Target genes of osa-MIR393 were predicted, and some of these putative targets are abiotic related genes. Furthermore, we generated transgenic rice and Arabidopsis thaliana that over-expressed osa-MIR393, and the phenotype analysis showed that these transgenic plants were more sensitive to salt and alkali treatment compared to wild-type plants. These results illustrate that over-expression of osa-MIR393 can negatively regulate rice salt-alkali stress tolerance.
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