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Prakash V, Sharma V, Devendran R, Prajapati R, Ahmad B, Kumar R. A transition from enemies to allies: how viruses improve drought resilience in plants. STRESS BIOLOGY 2024; 4:33. [PMID: 38981936 PMCID: PMC11233480 DOI: 10.1007/s44154-024-00172-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/03/2024] [Indexed: 07/11/2024]
Abstract
Global crop production is severely affected by environmental factors such as drought, salinity, cold, flood etc. Among these stresses, drought is one of the major abiotic stresses reducing crop productivity. It is expected that drought conditions will further increase because of the increasing global temperature. In general, viruses are seen as a pathogen affecting the crop productivity. However, several researches are showing that viruses can induce drought tolerance in plants. This review explores the mechanisms underlying the interplay between viral infections and the drought response mechanisms in plants. We tried to address the molecular pathways and physiological changes induced by viruses that confer drought tolerance, including alterations in hormone signaling, antioxidant defenses, scavenging the reactive oxygen species, role of RNA silencing and miRNA pathway, change in the expression of several genes including heat shock proteins, cellulose synthase etc. Furthermore, we discuss various viruses implicated in providing drought tolerance and examine the range of plant species exhibiting this phenomenon. By applying current knowledge and identifying gaps in understanding, this review aims to provide valuable insights into the complex dynamics of virus-induced drought tolerance in plants, paving the way for future research directions and practical applications in sustainable agriculture.
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Affiliation(s)
- Ved Prakash
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| | - Veerendra Sharma
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Ramgopal Prajapati
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Bilal Ahmad
- Division of Biology, Kansas State University, Manhattan, KS, USA
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2
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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] [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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3
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Neysanian M, Iranbakhsh A, Ahmadvand R, Ardebili ZO, Ebadi M. Selenium nanoparticles conferred drought tolerance in tomato plants by altering the transcription pattern of microRNA-172 (miR-172), bZIP, and CRTISO genes, upregulating the antioxidant system, and stimulating secondary metabolism. PROTOPLASMA 2024; 261:735-747. [PMID: 38291258 DOI: 10.1007/s00709-024-01929-y] [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: 09/20/2023] [Accepted: 01/20/2024] [Indexed: 02/01/2024]
Abstract
Drought stress is one of the major limiting factors for the production of tomato in Iran. In this study, the efficiency of selenate and Se nanoparticle (SeNP) foliar application on tomato plants was assessed to vestigate mitigating the risk associated with water-deficit conditions. Tomato plants were treated with SeNPs at the concentrations of 0 and 4 mg L-1; after the third sprays, the plants were exposed to water-deficit conditions. The foliar spraying with SeNPs not only improved growth, yield, and developmental switch to the flowering phase but also noticeably mitigated the detrimental risk associated with the water-deficit conditions. Gene expression experiments showed a slight increase in expression of microRNA-172 (miR-172) in the SeNP-treated plants in normal irrigation, whereas miR-172 displayed a downregulation trend in response to drought stress. The bZIP transcription factor and CRTISO genes were upregulated following the SeNP and drought treatments. Drought stress significantly increased the H2O2 accumulation that is mitigated with SeNPs. The foliar spraying with Se or SeNPs shared a similar trend to alleviate the negative effect of drought stress on the membrane integrity. The applied supplements also conferred drought tolerance through noticeable improvements in the non-enzymatic (ascorbate and glutathione) and enzymatic (catalase and peroxidase) antioxidants. The SeNP-mediated improvement in drought stress tolerance correlated significantly with increases in the activity of phenylalanine ammonia-lyase, proline, non-protein thiols, and flavonoid concentrations. SeNPs also improved the fruit quality regarding K, Mg, Fe, and Se concentrations. It was concluded that foliar spraying with SeNPs could mitigate the detrimental risk associated with the water-deficit conditions.
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Affiliation(s)
- Maryam Neysanian
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Alireza Iranbakhsh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Rahim Ahmadvand
- Department of Vegetables Research, Seed and Plant Improvement Institute, Agricultural Research, Education & Extension Organization, Karaj, Iran
| | | | - Mostafa Ebadi
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
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Silva GCB, Camillo LR, Santos DB, Amorim MS, Gonçalves LP, Barbosa ACO, Rocha Junior DS, Alcântara GM, Costa MGC. Identification of DEMETER-like DNA demethylase gene family in citrus and their role in drought stress-adaptive responses. Comput Biol Chem 2024; 112:108128. [PMID: 38905900 DOI: 10.1016/j.compbiolchem.2024.108128] [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: 01/15/2024] [Revised: 05/17/2024] [Accepted: 06/10/2024] [Indexed: 06/23/2024]
Abstract
DEMETER-Like DNA demethylases (DMLs) are epigenetic regulators of many developmental and biological processes in plants. No comprehensive information about the DML gene family in citrus is available to date. Here, a total of three DML genes in the genomes of Citrus sinensis (named CsDML1-3) and C. clementina (named CcDML1-3) were identified and analyzed. They encode hydrophilic and relatively large proteins, with prediction of nuclear localization, containing the conserved domains and motifs typical of plant DMLs. Protein interaction network analysis suggested that they interact primarily with proteins related to the maintenance of DNA methylation and remodeling of chromatin. Analysis of their promoter regions led to the identification of several cis-acting regulatory elements involved in stress response, including drought, heat and cold stresses. The presence of several miRNA targets and potential phosphorylation sites suggest that their expression is also regulated at post-transcriptional and post-translational levels. RNA-Seq data and quantitative real-time PCR analysis showed a low and drought-regulated gene expression of the citrus DMLs in different plant tissues. CsDML1 and CsDML3 were also differentially regulated by deficit irrigation in fruits at different developmental stages, with a positive and significant correlation found between CsDML1 and PHYTOENE SYNTHASE (PSY) and between CsDML3 and ATP CITRATE LYASEs (ACLs) and ZETA-CAROTENE DESATURASE (ZDS) gene expression. These results indicate that the citrus DMLs are potentially functional enzymes involved in developmental processes and drought stress-adaptive responses, providing a useful reference for further investigation of their functions and applications on the citrus improvement.
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Affiliation(s)
- Gláucia C B Silva
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Luciana R Camillo
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Dalma B Santos
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Maurício S Amorim
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Luana P Gonçalves
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Ana C O Barbosa
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Dílson S Rocha Junior
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Grazielle M Alcântara
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Marcio G C Costa
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil.
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Chowdhury MR, Chatterjee C, Ghosh D, Mukherjee J, Shaw S, Basak J. Deciphering miRNA-lncRNA-mRNA interaction through experimental validation of miRNAs, lncRNAs, and miRNA targets on mRNAs in Cajanus cajan. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:560-567. [PMID: 38520244 DOI: 10.1111/plb.13639] [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: 06/27/2022] [Accepted: 02/14/2024] [Indexed: 03/25/2024]
Abstract
Pigeon pea (Cajanus cajan) is widely cultivated for its nutritional and medicinal value yet remains an orphan crop as productivity has not been improved because of a lack of genome and non-coding genome information. Non-coding RNAs, like miRNAs and long non-coding RNAs (lncRNAs), are involved in regulation of growth, metabolism, development, and stress response, and have a critical role in post-transcriptional gene regulation (PTGR). We attempted to elucidate the roles of miRNAs and lncRNAs in pigeon pea through experimental validation of computationally predicted miRNAs and lncRNAs and targets of miRNAs on mRNAs. We experimentally validated 20 miRNAs and 11 lncRNAs. We predicted cleavage sites of three miRNA targets: serine/threonine-protein kinase, polygalacturonase, beta-galactosidase. We identified 469 targets of 265 miRNAs and their functional annotations using computational methods. We built a miRNA-mRNA-lncRNA network model, with the miRNAs targeting both mRNAs and lncRNAs, to obtain information on the interplay of these three molecules. A confirmed interaction through experimental validation was established between miRNA, namely cca-miR1535a targeting the mRNA for beta-galactosidase, as well as the lncRNA cca-lnc-020033. Our findings increase knowledge of the non-coding genome of pigeon pea and their roles in PTGR and in improving agronomic traits of this pulse crop.
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Affiliation(s)
- M R Chowdhury
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, India
| | - C Chatterjee
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| | - D Ghosh
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| | - J Mukherjee
- Department of Computer Science and Engineering, Birla Institute of Technology, Mesra, India
| | - S Shaw
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| | - J Basak
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
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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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Akter N, Islam MSU, Rahman MS, Zohra FT, Rahman SM, Manirujjaman M, Sarkar MAR. Genome-wide identification and characterization of protein phosphatase 2C (PP2C) gene family in sunflower (Helianthus annuus L.) and their expression profiles in response to multiple abiotic stresses. PLoS One 2024; 19:e0298543. [PMID: 38507444 PMCID: PMC10954154 DOI: 10.1371/journal.pone.0298543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/25/2024] [Indexed: 03/22/2024] Open
Abstract
Plant protein phosphatase 2C (PP2C) plays vital roles in responding to various stresses, stimulating growth factors, phytohormones, and metabolic activities in many important plant species. However, the PP2C gene family has not been investigated in the economically valuable plant species sunflower (Helianthus annuus L.). This study used comprehensive bioinformatics tools to identify and characterize the PP2C gene family members in the sunflower genome (H. annuus r1.2). Additionally, we analyzed the expression profiles of these genes using RNA-seq data under four different stress conditions in both leaf and root tissues. A total of 121 PP2C genes were identified in the sunflower genome distributed unevenly across the 17 chromosomes, all containing the Type-2C phosphatase domain. HanPP2C genes are divided into 15 subgroups (A-L) based on phylogenetic tree analysis. Analyses of conserved domains, gene structures, and motifs revealed higher structural and functional similarities within various subgroups. Gene duplication and collinearity analysis showed that among the 53 HanPP2C gene pairs, 48 demonstrated segmental duplications under strong purifying selection pressure, with only five gene pairs showing tandem duplications. The abundant segmental duplication was observed compared to tandem duplication, which was the major factor underlying the dispersion of the PP2C gene family in sunflowers. Most HanPP2C proteins were localized in the nucleus, cytoplasm, and chloroplast. Among the 121 HanPP2C genes, we identified 71 miRNAs targeting 86 HanPP2C genes involved in plant developmental processes and response to abiotic stresses. By analyzing cis-elements, we identified 63 cis-regulatory elements in the promoter regions of HanPP2C genes associated with light responsiveness, tissue-specificity, phytohormone, and stress responses. Based on RNA-seq data from two sunflower tissues (leaf and root), 47 HanPP2C genes exhibited varying expression levels in leaf tissue, while 49 HanPP2C genes showed differential expression patterns in root tissue across all stress conditions. Transcriptome profiling revealed that nine HanPP2C genes (HanPP2C12, HanPP2C36, HanPP2C38, HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73) exhibited higher expression in leaf tissue, and five HanPP2C genes (HanPP2C13, HanPP2C47, HanPP2C48, HanPP2C54, and HanPP2C95) showed enhanced expression in root tissue in response to the four stress treatments, compared to the control conditions. These results suggest that these HanPP2C genes may be potential candidates for conferring tolerance to multiple stresses and further detailed characterization to elucidate their functions. From these candidates, 3D structures were predicted for six HanPP2C proteins (HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73), which provided satisfactory models. Our findings provide valuable insights into the PP2C gene family in the sunflower genome, which could play a crucial role in responding to various stresses. This information can be exploited in sunflower breeding programs to develop improved cultivars with increased abiotic stress tolerance.
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Affiliation(s)
- Nasrin Akter
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Shohel Ul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - M. Manirujjaman
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana, LA, United States of America
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
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Ruan Q, Bai X, Wang Y, Zhang X, Wang B, Zhao Y, Zhu X, Wei X. Regulation of endogenous hormone and miRNA in leaves of alfalfa (Medicago sativa L.) seedlings under drought stress by endogenous nitric oxide. BMC Genomics 2024; 25:229. [PMID: 38429670 PMCID: PMC10908014 DOI: 10.1186/s12864-024-10024-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 01/17/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Alfalfa (Medicago sativa. L) is one of the best leguminous herbage in China and even in the world, with high nutritional and ecological value. However, one of the drawbacks of alfalfa is its sensitivity to dry conditions, which is a global agricultural problem. The objective of this study was to investigate the regulatory effects of endogenous nitric oxide (NO) on endogenous hormones and related miRNAs in alfalfa seedling leaves under drought stress. The effects of endogenous NO on endogenous hormones such as ABA, GA3, SA, and IAA in alfalfa leaves under drought stress were studied. In addition, high-throughput sequencing technology was used to identify drought-related miRNAs and endogenous NO-responsive miRNAs in alfalfa seedling leaves under drought stress. RESULT By measuring the contents of four endogenous hormones in alfalfa leaves, it was found that endogenous NO could regulate plant growth and stress resistance by inducing the metabolism levels of IAA, ABA, GA3, and SA in alfalfa, especially ABA and SA in alfalfa. In addition, small RNA sequencing technology and bioinformatics methods were used to analyze endogenous NO-responsive miRNAs under drought stress. It was found that most miRNAs were enriched in biological pathways and molecular functions related to hormones (ABA, ETH, and JA), phenylpropane metabolism, and plant stress tolerance. CONCLUSION In this study, the analysis of endogenous hormone signals and miRNAs in alfalfa leaves under PEG and PEG + cPTIO conditions provided an important basis for endogenous NO to improve the drought resistance of alfalfa at the physiological and molecular levels. It has important scientific value and practical significance for endogenous NO to improve plant drought resistance.
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Affiliation(s)
- Qian Ruan
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Pratacultural College, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaoming Bai
- Pratacultural College, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Yizhen Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of agronomy, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaofang Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Baoqiang Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Ying Zhao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaolin Zhu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of agronomy, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaohong Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China.
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China.
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Chang L, Jin X, Rao Y, Zhang X. Predicting abiotic stress-responsive miRNA in plants based on multi-source features fusion and graph neural network. PLANT METHODS 2024; 20:33. [PMID: 38402152 PMCID: PMC10894500 DOI: 10.1186/s13007-024-01158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/14/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND More and more studies show that miRNA plays a crucial role in plants' response to different abiotic stresses. However, traditional experimental methods are often expensive and inefficient, so it is important to develop efficient and economical computational methods. Although researchers have developed machine learning-based method, the information of miRNAs and abiotic stresses has not been fully exploited. Therefore, we propose a novel approach based on graph neural networks for predicting potential miRNA-abiotic stress associations. RESULTS In this study, we fully considered the multi-source feature information from miRNAs and abiotic stresses, and calculated and integrated the similarity network of miRNA and abiotic stress from different feature perspectives using multiple similarity measures. Then, the above multi-source similarity network and association information between miRNAs and abiotic stresses are effectively fused through heterogeneous networks. Subsequently, the Restart Random Walk (RWR) algorithm is employed to extract global structural information from heterogeneous networks, providing feature vectors for miRNA and abiotic stress. After that, we utilized the graph autoencoder based on GIN (Graph Isomorphism Networks) to learn and reconstruct a miRNA-abiotic stress association matrix to obtain potential miRNA-abiotic stress associations. The experimental results show that our model is superior to all known methods in predicting potential miRNA-abiotic stress associations, and the AUPR and AUC metrics of our model achieve 98.24% and 97.43%, respectively, under five-fold cross-validation. CONCLUSIONS The robustness and effectiveness of our proposed model position it as a valuable approach for advancing the field of miRNA-abiotic stress association prediction.
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Affiliation(s)
- Liming Chang
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Xiu Jin
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agricultural University, Hefei, 230036, China
| | - Yuan Rao
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaodan Zhang
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China.
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agricultural University, Hefei, 230036, China.
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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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11
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Kishore Sahoo R, Jeughale KP, Sarkar S, Selvaraj S, Singh NR, Swain N, Balasubramaniasai C, Chidambaranathan P, Katara JL, Nayak AK, Samantaray S. Growing Conditions and Varietal Ecologies Differently Regulates the Growth-regulating-factor (GRFs) Gene Family in Rice. IRANIAN JOURNAL OF BIOTECHNOLOGY 2024; 22:e3697. [PMID: 38827337 PMCID: PMC11139448 DOI: 10.30498/ijb.2024.394984.3697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/31/2023] [Indexed: 06/04/2024]
Abstract
Background Growth-regulating factors (GRFs) are crucial in rice for controlling plant growth and development. Among the rice cultivation practices, aerobic methods are water efficient but result in significant yield reduction relative to non-aerobic cultivation. Therefore, mechanistic insights into aerobic rice cultivation are important for improving the aerobic performance of rice. Objectives This study aimed to examine the evolution of GRFs in different rice species, analyse the phenotypic differences between aerobic and non-aerobic conditions in three rice varieties, and assess the expression of GRFs in these varieties under both aerobic and non-aerobic conditions. Materials and Methods This study comprehensively examined the GRFs gene family in 11 rice species (Oryza barthii, Oryza brachyantha, Oryza glaberrima, Oryza glumipatula, Oryza sativa subsp. indica, Oryza longistaminata, Oryza meridionalis, Oryza nivara, Oryza punctata, Oryza rufipogon, Oryza sativa subsp. japonica) focusing on phylogenetic analysis. Additionally, the expression patterns of 12 GRFs were investigated in three distinct genotypes of O. sativa subsp. indica rice, under both non-aerobic and aerobic conditions. Results Three major phylogenetic clades were formed based on conserved motifs in the 123 GRFs proteins in eleven rice species. Further, novel motifs were identified especially in O. longistaminata indicative of the species level evolutionary differences in rice. Among the trait performance, the number of tillers was reduced by ~ 36% under aerobic conditions, but the reduction was found to be less in CR Dhan 201, an aerobic variety. Besides, three GRFs namely GRF3, GRF4, and GRF7 were found to be distinct in expression between aerobic and non-aerobic conditions. Conclusion Three GRF genes namely GRF3, GRF4, and GRF7 could be associated with the aerobic adaptation in rice.
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Affiliation(s)
- Raj Kishore Sahoo
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
- Department of Botany, Ravenshaw University, Cuttack, India
| | | | - Suman Sarkar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | | | | | - Nibedita Swain
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | | | | | - Jawahar Lal Katara
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Amaresh Kumar Nayak
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, India
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12
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Ali S, Huang S, Zhou J, Bai Y, Liu Y, Shi L, Liu S, Hu Z, Tang Y. miR397-LACs mediated cadmium stress tolerance in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2023; 113:415-430. [PMID: 37566350 DOI: 10.1007/s11103-023-01369-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/04/2023] [Indexed: 08/12/2023]
Abstract
Cadmium (Cd) is a non-essential heavy metal, assimilated in plant tissue with other nutrients, disturbing the ions' homeostasis in plants. The plant develops different mechanisms to tolerate the hazardous environmental effects of Cd. Recently studies found different miRNAs that are involved in Cd stress. In the current study, miR397 mutant lines were constructed to explore the molecular mechanisms of miR397 underlying Cd tolerance. Compared with the genetically modified line of overexpressed miR397 (artificial miR397, amiR397), the lines of downregulated miR397 (Short Tandem Target Mimic miR397, STTM miR397) showed more substantial Cd tolerance with higher chlorophyll a & b, carotenoid and lignin content. ICP-OES revealed higher cell wall Cd and low total Cd levels in STTM miR397 than in the wild-type and amiR397 plants.Further, the STTM plants produced fewer reactive oxygen species (ROS) and lower activity of antioxidants enzymes (e.g., catalase [CAT], malondialdehyde [MDA]) compared with amiR397 and wild-type plants after stress, indicating that silencing the expression of miR397 can reduce oxidative damage. In addition, the different family transporters' gene expression was much higher in the amiR397 plants than in the wild type and STTM miRNA397. Our results suggest that miR397 plays a role in Cd tolerance in Arabidopsis thaliana. Overexpression of miR397 could decrease Cd tolerance in plants by regulating the expression of LAC 2/4/17, changing the lignin content, which may play an important role in inducing different stress-tolerant mechanisms and protecting the cell from a hazardous condition. This study provides a basis to elucidate the functions of miR397 and the Cd stress tolerance mechanism in Arabidopsis thaliana.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, Longhua Institute of Innovative Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, Guangdong Province, China
| | - Shili Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, Longhua Institute of Innovative Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China
| | - Jiajie Zhou
- Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, Longhua Institute of Innovative Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China
| | - Yongsheng Bai
- Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, Longhua Institute of Innovative Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China
| | - Yang Liu
- Guangdong Academy of Forestry, Guangzhou, 510520, Guangdong Province, China
| | - Liyu Shi
- Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, Longhua Institute of Innovative Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China
| | - Shuai Liu
- Shaanxi Academy of Traditional Chinese Medicine, Xi'an, 710003, Shaanxi, China
| | - Zhangli Hu
- Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, Longhua Institute of Innovative Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, Longhua Institute of Innovative Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China.
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13
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Yuan J, Wang X, Qu S, Shen T, Li M, Zhu L. The roles of miR156 in abiotic and biotic stresses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108150. [PMID: 37922645 DOI: 10.1016/j.plaphy.2023.108150] [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: 08/02/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
MicroRNAs (miRNAs), known as a kind of non-coding RNA, can negatively regulate its target genes. To date, the roles of various miRNAs in plant development and resistance to abiotic and biotic stresses have been widely explored. The present review summarized and discussed the functions of miR156 or miR156-SPL module in abiotic and biotic stresses, such as drought, salt, heat, cold stress, UV-B radiation, heavy mental hazards, nutritional starvation, as well as plant viruses, plant diseases, etc. Based on this, the regulation of miR156-involved stress tolerance was better understood, thus, it would be much easier for plant biologists to carry out suitable strategies to help plants suffer from unfavorable living environments.
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Affiliation(s)
- Jing Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shengtao Qu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tian Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lingcheng Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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14
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Larran AS, Pajoro A, Qüesta JI. Is winter coming? Impact of the changing climate on plant responses to cold temperature. PLANT, CELL & ENVIRONMENT 2023; 46:3175-3193. [PMID: 37438895 DOI: 10.1111/pce.14669] [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: 05/03/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023]
Abstract
Climate change is causing alterations in annual temperature regimes worldwide. Important aspects of this include the reduction of winter chilling temperatures as well as the occurrence of unpredicted frosts, both significantly affecting plant growth and yields. Recent studies advanced the knowledge of the mechanisms underlying cold responses and tolerance in the model plant Arabidopsis thaliana. However, how these cold-responsive pathways will readjust to ongoing seasonal temperature variation caused by global warming remains an open question. In this review, we highlight the plant developmental programmes that depend on cold temperature. We focus on the molecular mechanisms that plants have evolved to adjust their development and stress responses upon exposure to cold. Covering both genetic and epigenetic aspects, we present the latest insights into how alternative splicing, noncoding RNAs and the formation of biomolecular condensates play key roles in the regulation of cold responses. We conclude by commenting on attractive targets to accelerate the breeding of increased cold tolerance, bringing up biotechnological tools that might assist in overcoming current limitations. Our aim is to guide the reflection on the current agricultural challenges imposed by a changing climate and to provide useful information for improving plant resilience to unpredictable cold regimes.
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Affiliation(s)
- Alvaro Santiago Larran
- Centre for Research in Agricultural Genomics (CRAG) IRTA-CSIC-UAB-UB, Campus UAB, Barcelona, Spain
| | - Alice Pajoro
- National Research Council, Institute of Molecular Biology and Pathology, Rome, Italy
| | - Julia I Qüesta
- Centre for Research in Agricultural Genomics (CRAG) IRTA-CSIC-UAB-UB, Campus UAB, Barcelona, Spain
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15
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Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
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16
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Inal B, Mirzapour M, Tufekci ED, Rustemoglu M, Kaba A, Albalawi MA, Alalawy AI, Sakran M, Alqurashi M, Ditta A. Drought-Induced miRNA Expression Correlated with Heavy Metal, Phenolic Acid, and Protein and Nitrogen Levels in Five Chickpea Genotypes. ACS OMEGA 2023; 8:35746-35754. [PMID: 37810661 PMCID: PMC10552140 DOI: 10.1021/acsomega.3c03003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Drought is a prime stress, drastically affecting plant growth, development, and yield. Plants have evolved various physiological, molecular, and biochemical mechanisms to cope with drought. Investigating specific biochemical pathways related to drought tolerance mechanisms of plants through biotechnology approaches is one of the quickest and most effective strategies for enhancing crop production. Among them, microRNAs (miRNAs) are the principal post-transcriptional regulators of gene expression in plants during plant growth under biotic and abiotic stresses. In this study, five different chickpea genotypes (İnci, Hasan bey, Arda, Seçkin, and Diyar 95) were grown under normal and drought stress. We recorded the expression levels of microRNAs in these genotypes and found differential expression (miRNA396, miR408, miRNA414, miRNA528, and miRNA1533) under contrasting conditions. Results revealed that miRNA414 and miRNA528 considerably increased in all genotypes under drought stress, and expression levels of miRNA418, miRNA1533, and miRNA396 (except for the Seçkin genotype) were found to be higher under the watered conditions. These genotypes were also investigated for heavy metal, phenolic acid, protein, and nitrogen concentrations under normal and drought stress conditions. The Arda genotype showed a significant increase in nitrogen (5.46%) and protein contents (28.3%), while protein contents were decreased in the Hasan bey and Seçkin genotypes subjected to drought stress. In the case of metals, iron was the most abundant element in all genotypes (İnci = 15.4 ppm, Hasan bey = 29.6 ppm, Seçkin = 37.8 ppm, Arda = 26.3 ppm, and Diyar 95 = 40.8 ppm) under normal conditions. Interestingly, these results were related to miRNA expression in the chickpea genotypes and hint at the regulation of multiple pathways under drought conditions. Overall, the present study will help us to understand the miRNA-mediated regulation of various pathways in chickpea genotypes.
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Affiliation(s)
- Behcet Inal
- Faculty
of Agriculture, Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
| | - Mohsen Mirzapour
- Faculty
of Agriculture, Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
| | - Ebru Derelli Tufekci
- Food
and Agriculture Vocational High School, Department of Field Crops, Cankiri Karatekin University, Cankiri 18100, Turkey
| | - Mustafa Rustemoglu
- Faculty
of Agriculture, Department of Plant Protection, Sirnak University, Sirnak 73000, Turkey
| | - Adem Kaba
- Faculty
of Agriculture, Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
| | - Marzough Aziz Albalawi
- Department
of Chemistry, University College at Alwajh, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Adel I. Alalawy
- Department
of Biochemistry, Faculty of Science, University
of Tabuk, Tabuk 73000, Kingdom
of Saudi Arabia
| | - Mohamed Sakran
- Department
of Biochemistry, Faculty of Science, University
of Tabuk, Tabuk 73000, Kingdom
of Saudi Arabia
- Biochemistry
Section, Chemistry Department, Faculty of Science, Tanta University, Tanta31527,Egypt
| | - Mohammed Alqurashi
- Department
of Biotechnology, Faculty of Science, Taif
University, Taif 21974, Saudi Arabia
| | - Allah Ditta
- Department
of Environmental Sciences, Shaheed Benazir
Bhutto University Sheringal, Dir (U), Khyber Pakhtunkhwa 18000, Pakistan
- School
of Biological Sciences, The University of
Western Australia, 35
Stirling Highway, Perth, WA 6009, Australia
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17
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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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18
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Riyazuddin R, Singh K, Iqbal N, Labhane N, Ramteke P, Singh VP, Gupta R. Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107978. [PMID: 37660607 DOI: 10.1016/j.plaphy.2023.107978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.
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Affiliation(s)
- Riyazuddin Riyazuddin
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary.
| | - Kalpita Singh
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary; Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, H-2462, Martonvásár, Hungary.
| | - Nadeem Iqbal
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, 6726, Szeged, Hungary; Doctoral School of Environmental Sciences, University of Szeged, Szeged, Hungary.
| | - Nitin Labhane
- Department of Botany, Bhavan's College Andheri West, Mumbai, 400058, India.
| | - Pramod Ramteke
- Department of Biotechnology, Dr. Ambedkar College, Nagpur, India.
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Ravi Gupta
- College of General Education, Kookmin University, 02707, Seoul, Republic of Korea.
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19
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Mittal M, Dhingra A, Dawar P, Payton P, Rock CD. The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea). THE PLANT GENOME 2023; 16:e20350. [PMID: 37351954 DOI: 10.1002/tpg2.20350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 06/24/2023]
Abstract
MicroRNAs (miRNAs) are 21-24 nt small RNAs (sRNAs) that negatively regulate protein-coding genes and/or trigger phased small-interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant-like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA-producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine-protein phosphatase7 and miRc20 and ahy-miR3514 targeting penta-tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS-like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought- and heat-regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta-analysis of an expression atlas and over representation of miRNA target genes in co-expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome-wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value-added traits.
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Affiliation(s)
- Meenakshi Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Anuradha Dhingra
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Paxton Payton
- USDA-ARS Plant Stress and Germplasm Lab, Lubbock, Texas, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
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20
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Singh A, Mazahar S, Chapadgaonkar SS, Giri P, Shourie A. Phyto-microbiome to mitigate abiotic stress in crop plants. Front Microbiol 2023; 14:1210890. [PMID: 37601386 PMCID: PMC10433232 DOI: 10.3389/fmicb.2023.1210890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Plant-associated microbes include taxonomically diverse communities of bacteria, archaebacteria, fungi, and viruses, which establish integral ecological relationships with the host plant and constitute the phyto-microbiome. The phyto-microbiome not only contributes in normal growth and development of plants but also plays a vital role in the maintenance of plant homeostasis during abiotic stress conditions. Owing to its immense metabolic potential, the phyto-microbiome provides the host plant with the capability to mitigate the abiotic stress through various mechanisms like production of antioxidants, plant growth hormones, bioactive compounds, detoxification of harmful chemicals and toxins, sequestration of reactive oxygen species and other free radicals. A deeper understanding of the structure and functions of the phyto-microbiome and the complex mechanisms of phyto-microbiome mediated abiotic stress mitigation would enable its utilization for abiotic stress alleviation of crop plants and development of stress-resistant crops. This review aims at exploring the potential of phyto-microbiome to alleviate drought, heat, salinity and heavy metal stress in crop plants and finding sustainable solutions to enhance the agricultural productivity. The mechanistic insights into the role of phytomicrobiome in imparting abiotic stress tolerance to plants have been summarized, that would be helpful in the development of novel bioinoculants. The high-throughput modern approaches involving candidate gene identification and target gene modification such as genomics, metagenomics, transcriptomics, metabolomics, and phyto-microbiome based genetic engineering have been discussed in wake of the ever-increasing demand of climate resilient crop plants.
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Affiliation(s)
- Anamika Singh
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Samina Mazahar
- Department of Botany, Dyal Singh College, University of Delhi, New Delhi, India
| | - Shilpa Samir Chapadgaonkar
- Department of Biosciences and Technology, Dr. Vishwanath Karad MIT World Peace University, Pune, Maharashtra, India
| | - Priti Giri
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Abhilasha Shourie
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, India
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21
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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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22
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Pasandideh Arjmand M, Samizadeh Lahiji H, Mohsenzadeh Golfazani M, Biglouei MH. Evaluation of protein's interaction and the regulatory network of some drought-responsive genes in Canola under drought and re-watering conditions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1085-1102. [PMID: 37829706 PMCID: PMC10564702 DOI: 10.1007/s12298-023-01345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/14/2023]
Abstract
Drought stress is one of the most important environmental stresses that severely limits the growth and yield of Canola. The re-watering can compensate for the damage caused by drought stress. Investigation of protein's interaction of genes involved in important drought-responsive pathways and their regulatory network by microRNAs (miRNAs) under drought and re-watering conditions are helpful approaches to discovering drought-stress tolerance and recovery mechanisms. In this study, the protein's interaction and functional enrichment analyses of glycolysis, pentose phosphate, glyoxylate cycle, fatty acid biosynthesis, heat shock factor main genes, and the regulatory network of key genes by miRNAs were investigated by in silico analysis. Then, the relative expression of key genes and their related miRNAs were investigated in tolerant and susceptible genotypes of Canola under drought and re-watering conditions by Real-time PCR technique. The bna-miR156b/c/g, bna-miR395d/e/f, bna-miR396a, and all the studied key genes except HSFA1E and PK showed changes in expression levels in one or both genotypes after re-watering. The PPC1 and HSFB2B expression decreased, whereas the MLS and CAC3 expression increased in both genotypes under re-watering treatment after drought stress. It could cause the regulation of oxaloacetate production, the increase of the glyoxylate cycle, lipid biosynthesis, and the reduction of the negative regulation of HSFs under re-watering conditions. It seems that PPC1, G6PD2, MLS, CAC3, and HSFB2B were involved in the recovery mechanisms after drought stress of Canola. They were regulated by drought-responsive miRNAs to respond appropriately to drought stress. Therefore, regulating these genes could be important in plant recovery mechanisms. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01345-1.
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Affiliation(s)
- Maryam Pasandideh Arjmand
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | | | - Mohammad Hassan Biglouei
- Department of Water Engineering, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
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23
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Hassan MA, Dahu N, Hongning T, Qian Z, Yueming Y, Yiru L, Shimei W. Drought stress in rice: morpho-physiological and molecular responses and marker-assisted breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1215371. [PMID: 37534289 PMCID: PMC10391551 DOI: 10.3389/fpls.2023.1215371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023]
Abstract
Rice (Oryza Sativa L.) is an essential constituent of the global food chain. Drought stress significantly diminished its productivity and threatened global food security. This review concisely discussed how drought stress negatively influenced the rice's optimal growth cycle and altered its morpho-physiological, biochemical, and molecular responses. To withstand adverse drought conditions, plants activate their inherent drought resistance mechanism (escape, avoidance, tolerance, and recovery). Drought acclimation response is characterized by many notable responses, including redox homeostasis, osmotic modifications, balanced water relations, and restored metabolic activity. Drought tolerance is a complicated phenomenon, and conventional breeding strategies have only shown limited success. The application of molecular markers is a pragmatic technique to accelerate the ongoing breeding process, known as marker-assisted breeding. This review study compiled information about quantitative trait loci (QTLs) and genes associated with agronomic yield-related traits (grain size, grain yield, harvest index, etc.) under drought stress. It emphasized the significance of modern breeding techniques and marker-assisted selection (MAS) tools for introgressing the known QTLs/genes into elite rice lines to develop drought-tolerant rice varieties. Hence, this study will provide a solid foundation for understanding the complex phenomenon of drought stress and its utilization in future crop development programs. Though modern genetic markers are expensive, future crop development programs combined with conventional and MAS tools will help the breeders produce high-yielding and drought-tolerant rice varieties.
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Affiliation(s)
- Muhammad A. Hassan
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ni Dahu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Tong Hongning
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhu Qian
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yi Yueming
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Li Yiru
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Wang Shimei
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
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24
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Pei LL, Zhang LL, Liu X, Jiang J. Role of microRNA miR171 in plant development. PeerJ 2023; 11:e15632. [PMID: 37456878 PMCID: PMC10340099 DOI: 10.7717/peerj.15632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNA with 19-24 nucleotides (nts) in length, which play an essential role in regulating gene expression at the post-transcriptional level. As one of the first miRNAs found in plants, miR171 is a typical class of conserved miRNAs. The miR171 sequences among different species are highly similar, and the vast majority of them have both "GAGCCG" and "CAAUAU" fragments. In addition to being involved in plant growth and development, hormone signaling and stress response, miR171 also plays multiple and important roles in plants through interactions with microbe and other small-RNAs. The miRNA functions by regulating the expression of target genes. Most of miR171's target genes are in the GRAS gene family, but also include some NSP, miRNAs, lncRNAs, and other genes. This review is intended to summarize recent updates on miR171 regarding its function in plant life and hopefully provide new ideas for understanding miR171 function and regulatory mechanisms.
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Affiliation(s)
- Ling Ling Pei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Ling Ling Zhang
- College of Horticulture, Shenyang Agriculture University, Shenyang, Shenhe District, China
| | - Xin Liu
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Jing Jiang
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
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25
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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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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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27
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Hassani SB, Latifi M, Aliniaeifard S, Sohrabi Bonab S, Nasiri Almanghadim N, Jafari S, Mohebbifar E, Ahangir A, Seifikalhor M, Rezadoost H, Bosacchi M, Rastogi A, Bernard F. Response to Cadmium Toxicity: Orchestration of Polyamines and microRNAs in Maize Plant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1991. [PMID: 37653908 PMCID: PMC10223431 DOI: 10.3390/plants12101991] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/13/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Cadmium (Cd) is a heavy metal that is widely contaminating the environment due to its uses in industries as corrosive reagents, paints, batteries, etc. Cd can easily be absorbed through plant roots and may have serious negative impacts on plant growth. To investigate the mechanisms utilized by plants to cope with Cd toxicity, an experiment was conducted on maize seedlings. We observed that the plant growth and photosynthetic mechanism were negatively influenced during 20 days of Cd stress. The expression levels of ornithine decarboxylase (ORDC) increased in the six seedlings under Cd exposure compared to the control. However, Cd toxicity led to an increase in putrescine (Put) content only on day 15 when compared to the control plants. In fact, with the exception of day 15, the increases in the ORDC transcript levels did not show a direct correlation with the observed increases in Put content. Spermidine and Spermine levels were reduced on day 6 by Cd application, which was parallel with suppressed Spermidine synthase gene. However, an increase in Spermidine and Spermine levels was observed on day 12 along with a significant elevation in Spermidine synthase expression. On day 6, Cd was observed to start accumulating in the root with an increase in the expression of microRNA 528; while on day 15, Cd started to be observed in the shoot part with an increase in microRNA 390 and microRNA 168. These results imply that different miRNAs may regulate polyamines (PAs) in maize under Cd toxicity, suggesting a plant-derived strategy to commit a PAs/miRNA-regulated mechanism/s in different developmental stages (time points) in response to Cd exposure.
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Affiliation(s)
- Seyedeh Batool Hassani
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 19839-69411, Iran; (S.B.H.)
| | - Mojgan Latifi
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 19839-69411, Iran; (S.B.H.)
| | - Sasan Aliniaeifard
- Photosynthesis Laboratory, Department of Horticulture, College of Agricultural Technology (Aburaihan), University of Tehran, Tehran 33916-53755, Iran
| | - Shabnam Sohrabi Bonab
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 19839-69411, Iran; (S.B.H.)
| | - Neda Nasiri Almanghadim
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 19839-69411, Iran; (S.B.H.)
| | - Sara Jafari
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 19839-69411, Iran; (S.B.H.)
| | - Elham Mohebbifar
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 19839-69411, Iran; (S.B.H.)
| | - Anahita Ahangir
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 19839-69411, Iran; (S.B.H.)
| | | | - Hassan Rezadoost
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran 19839-69411, Iran
| | - Massimo Bosacchi
- Park at the Danforth Plant Science Center, KWS Gateway Research Center, LLC, BRDG, Saint Louis, MO 95618, USA
| | - Anshu Rastogi
- Laboratory of Bioclimatology, Department of Ecology and Environmental Protection, Faculty of Environmental Engineering and Mechanical Engineering, Poznan University of Life Sciences, Piątkowska 94, 60-649 Poznań, Poland
| | - Françoise Bernard
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 19839-69411, Iran; (S.B.H.)
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28
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Mishra S, Chaudhary R, Sharma P. Temporal expression analysis of microRNAs and their target GRAS genes induced by osmotic stress in two contrasting wheat genotypes. Mol Biol Rep 2023:10.1007/s11033-023-08486-2. [PMID: 37179268 DOI: 10.1007/s11033-023-08486-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are important nonprotein-coding genes in plants which participate in almost all biological processes during abiotic and biotic stresses. Understanding how plants respond to various environmental conditions requires the identification of stress-related miRNAs. In recent years, there has been an increased interest in studying miRNA genes and gene expression. Drought is one of the common environmental stresses limiting plant growth and development. Stress-specific miRNAs and their GRAS gene targets were validated to understand the role of miRNAs in response to osmotic stress. RESULTS In this study, expression patterns of the ten stress-responsive miRNAs involved in osmotic stress adaptation were examined in order to undertand the regulation behavior of abiotic stress and miRNAs in two contrasting wheat genotype C-306 (drought tolerant) and WL-711 (drought sensitive). Three miRNAs were discovered to be upregulated under stress, whereas seven miRNAs were showed to be down-regulated as a consequence of the study. In contrast to miRNA, it was also discovered that GRAS genes as their targets were up-regulated during osmotic stress. In addition, the expression level of miR159, miR408 along with their targets, TaGRAS178 and TaGRAS84 increased in response to osmotic stress. Nevertheless, miR408 is highly conserved miRNA that regulates plant growth, development and stress response. As a result, variation in the expression levels of studied miRNAs in the presence of target genes provides a plausible explanation for miRNA-based abiotic stress regulation. A regulatory network of miRNA and their targets revealed that fourteen miRNA interact with 55 GRAS targets from various subfamilies that contribute in the plant growth and development. CONCLUSIONS These findings provide evidence for temporal and variety-specific differential regulation of miRNAs and their targets in wheat in response to osmotic shock, and they may aid in determining the potential.
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Affiliation(s)
- Shefali Mishra
- ICAR-Indian Institute of Wheat and Barley Research, Karnal Agrasain Marg, Karnal, Haryana, 132 001, India
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal, India
| | - Reeti Chaudhary
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal Agrasain Marg, Karnal, Haryana, 132 001, India.
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29
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Pradhan UK, Meher PK, Naha S, Rao AR, Kumar U, Pal S, Gupta A. ASmiR: a machine learning framework for prediction of abiotic stress-specific miRNAs in plants. Funct Integr Genomics 2023; 23:92. [PMID: 36939943 DOI: 10.1007/s10142-023-01014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 03/21/2023]
Abstract
Abiotic stresses have become a major challenge in recent years due to their pervasive nature and shocking impacts on plant growth, development, and quality. MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of specific abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational model for prediction of miRNAs associated with four specific abiotic stresses such as cold, drought, heat and salt. The pseudo K-tuple nucleotide compositional features of Kmer size 1 to 5 were used to represent miRNAs in numeric form. Feature selection strategy was employed to select important features. With the selected feature sets, support vector machine (SVM) achieved the highest cross-validation accuracy in all four abiotic stress conditions. The highest cross-validated prediction accuracies in terms of area under precision-recall curve were found to be 90.15, 90.09, 87.71, and 89.25% for cold, drought, heat and salt respectively. Overall prediction accuracies for the independent dataset were respectively observed 84.57, 80.62, 80.38 and 82.78%, for the abiotic stresses. The SVM was also seen to outperform different deep learning models for prediction of abiotic stress-responsive miRNAs. To implement our method with ease, an online prediction server "ASmiR" has been established at https://iasri-sg.icar.gov.in/asmir/ . The proposed computational model and the developed prediction tool are believed to supplement the existing effort for identification of specific abiotic stress-responsive miRNAs in plants.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India.
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | | | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Soumen Pal
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
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Li Y, Liu Y, Gao Z, Wang F, Xu T, Qi M, Liu Y, Li T. MicroRNA162 regulates stomatal conductance in response to low night temperature stress via abscisic acid signaling pathway in tomato. FRONTIERS IN PLANT SCIENCE 2023; 14:1045112. [PMID: 36938045 PMCID: PMC10019595 DOI: 10.3389/fpls.2023.1045112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
MicroRNAs (miRNAs) mediate the degradation of target mRNA and inhibit mRNA translation to regulate gene expression at the transcriptional and post-transcriptional levels in response to environmental stress in plants. We characterized the post-transcriptional mechanism by deep sequencing small RNA (sRNA) to examine how miRNAs were involved in low night temperature (LNT) stress in tomato and whether the molecular mechanism depended on the abscisic acid (ABA) signaling pathway. We annotated conserved miRNAs and novel miRNAs with four sRNA libraries composed of wild-type (WT) tomato plants and ABA-deficient mutant (sit) plants under normal growth and LNT stress conditions. Reverse genetics analysis suggested that miR162 participated in LNT resistance and the ABA-dependent signaling pathway in tomato. miR162-overexpressing (pRI-miR162) and miR162-silenced (pRNAi-miR162) transgenic tomato plants were generated to evaluate miR162 functions in response to LNT stress. miR162 deficiency exhibited high photosynthetic capacity and regulated stomatal opening, suggesting negative regulation of miR162 in the ABA-dependent signaling pathway in response to LNT stress. As feedback regulation, miR162 positively regulated ABA to maintain homeostasis of tomato under diverse abiotic stresses. The mRNA of DICER-LIKE1 (DCL1) was targeted by miR162, and miR162 inhibited DCL1 cleavage in LNT response, including the regulation of miRNA160/164/171a and their targets. The DCL1-deficient mutants (dcl1) with CRISPR/Cas9 prevented stomatal opening to influence photosynthesis in the ABA signaling pathway under LNT stress. Finally, we established the regulatory mechanism of ABA-miR162-DCL1, which systematically mediated cold tolerance in tomato. This study suggests that post-transcriptional modulators acted as systemic signal responders via the stress hormone signaling pathway, and the model at the post-transcriptional level presents a new direction for research in plant abiotic stress resistance.
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Affiliation(s)
- Yangyang Li
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, China
- Collaborative Innovation Center of Protected Vegetable Surrounds Bohai Gulf Region, Shenyang, China
| | - Yang Liu
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
- Tongliao Agricultural Technology Extension Center, Tongliao, China
| | - Zhenhua Gao
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, China
- Collaborative Innovation Center of Protected Vegetable Surrounds Bohai Gulf Region, Shenyang, China
| | - Feng Wang
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, China
- Collaborative Innovation Center of Protected Vegetable Surrounds Bohai Gulf Region, Shenyang, China
| | - Tao Xu
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, China
- Collaborative Innovation Center of Protected Vegetable Surrounds Bohai Gulf Region, Shenyang, China
| | - Mingfang Qi
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, China
- Collaborative Innovation Center of Protected Vegetable Surrounds Bohai Gulf Region, Shenyang, China
| | - Yufeng Liu
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, China
- Collaborative Innovation Center of Protected Vegetable Surrounds Bohai Gulf Region, Shenyang, China
| | - Tianlai Li
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, China
- Collaborative Innovation Center of Protected Vegetable Surrounds Bohai Gulf Region, Shenyang, China
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Genome-wide identification of drought-responsive microRNAs and their target genes in Chinese jujube by deep sequencing. Genes Genomics 2023; 45:231-245. [PMID: 35819623 DOI: 10.1007/s13258-022-01274-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/22/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are about 21 snucleotide (nt) long, non-coding RNAs that play an important role in plant abiotic stress responses. Chinese jujube is a native fruit tree in China, which is also an admittedly drought-resistant plant. But the drought-related miRNAs have little been reported in jujube. OBJECTIVE To identify possibly drought-responsive microRNAs and their target genes in Chinese Jujube. METHODS Twelve small RNA libraries were constructed from two jujube genotypes both drought treated and control samples with three replicates to identify known and novel miRNAs in Chinese Jujube, DESeq2 was used to identify expression pattern of miRNAs between drought treatment and control samples, TargetFinder program was used to predict potential target genes of conserved and novel miRNAs, RT-qPCR were used to analysis the expression levels of drought-related miRNAs and their potential targets. The RNA ligase-mediated RLM-5' RACE experiments were performed to validate predicted target genes of drought-related miRNAs. RESULTS 43 known miRNAs and 431 novel miRNAs were identified in Chinese jujube. Expression analysis showed that 28 miRNAs were differential expressed under drought stress in jujube variety "Dongzao", including 21 up-regulated miRNAs and 7 down-regulated miRNAs, 61 miRNAs were differential expressed under drought stress in Chinese jujube variety "Zanhuangdazao", including 23 up-regulated miRNAs and 37 down-regulated miRNAs. Depend on miRNAs target prediction, functional annotation and expression analysis, we identified 9 drought-related miRNAs, and 7 target genes of 6 miRNAs were confirmed using the modified 5'-RACE method. Also, RT-qPCR analyses revealed that relative expression of those miRNAs and their targets have negative tendency. CONCLUSION We identified 6 drought-related miRNAs by high-throughout sequencing and target gene annotation from Chinese jujube, and targets of those miRNAs were confirmed by the modified 5'-RACE method. These findings provide molecular evidence for enhancing drought tolerance in Chinese jujube and other plants.
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Chirivì D, Betti C. Molecular Links between Flowering and Abiotic Stress Response: A Focus on Poaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:331. [PMID: 36679044 PMCID: PMC9866591 DOI: 10.3390/plants12020331] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Extreme temperatures, drought, salinity and soil pollution are the most common types of abiotic stresses crops can encounter in fields; these variations represent a general warning to plant productivity and survival, being more harmful when in combination. Plant response to such conditions involves the activation of several molecular mechanisms, starting from perception to signaling, transcriptional reprogramming and protein modifications. This can influence the plant's life cycle and development to different extents. Flowering developmental transition is very sensitive to environmental stresses, being critical to reproduction and to agricultural profitability for crops. The Poacee family contains some of the most widespread domesticated plants, such as wheat, barley and rice, which are commonly referred to as cereals and represent a primary food source. In cultivated Poaceae, stress-induced modifications of flowering time and development cause important yield losses by directly affecting seed production. At the molecular level, this reflects important changes in gene expression and protein activity. Here, we present a comprehensive overview on the latest research investigating the molecular pathways linking flowering control to osmotic and temperature extreme conditions in agronomically relevant monocotyledons. This aims to provide hints for biotechnological strategies that can ensure agricultural stability in ever-changing climatic conditions.
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Identification of microRNA and analysis of target genes in Panax ginseng. CHINESE HERBAL MEDICINES 2023; 15:69-75. [PMID: 36875435 PMCID: PMC9975625 DOI: 10.1016/j.chmed.2022.08.006] [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: 05/05/2022] [Revised: 07/05/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Objective Ginsenosides, polysaccharides and phenols, the main active ingredients in Panax ginseng, are not different significantly in content between 3 and 5 years old of ginsengs called Yuan ginseng and more than ten years old ones called Shizhu ginseng. The responsible chemical compounds cannot fully explain difference in efficacy between them. According to reports in Lonicerae Japonicae Flos (Jinyinhua in Chinese) and Glycyrrhizae Radix et Rhizoma (Gancao in Chinese), microRNA may play a role in efficacy, so we identified microRNAs in P. ginseng at the different growth years and analyzed their target genes. Methods Using high-throughput sequencing, the RNA-Seq, small RNA-Seq and degradome databases of P. ginseng were constructed. The differentially expressed microRNAs was identified by qRT-PCR. Results A total of 63,875 unigenes and 24,154,579 small RNA clean reads were obtained from the roots of P. ginseng. From these small RNAs, 71 miRNA families were identified by bioinformatics target prediction software, including 34 conserved miRNAs, 37 non-conserved miRNA families, as well as 179 target genes of 17 known miRNAs. Through degradome sequencing and computation, we finally verified 13 targets of eight miRNAs involved in transcription, energy metabolism, biological stress and disease resistance, suggesting the significance of miRNAs in the development of P. ginseng. Consistently, major miRNA targets exhibited tissue specificity and complexity in expression patterns. Conclusion Differential expression microRNAs were found in different growth years of ginsengs (Shizhu ginseng and Yuan ginseng), and the regulatory roles and functional annotations of miRNA targets in P. ginseng need further investigation.
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Sarwar R, Li L, Yu J, Zhang Y, Geng R, Meng Q, Zhu K, Tan XL. Functional Characterization of the Cystine-Rich-Receptor-like Kinases ( CRKs) and Their Expression Response to Sclerotinia sclerotiorum and Abiotic Stresses in Brassica napus. Int J Mol Sci 2022; 24:ijms24010511. [PMID: 36613954 PMCID: PMC9820174 DOI: 10.3390/ijms24010511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/24/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins that bind to the calcium ion to regulate stress-signaling and plant development-related pathways, as indicated by several pieces of evidence. However, the CRK gene family hasn’t been inadequately examined in Brassica napus. In our study, 27 members of the CRK gene family were identified in Brassica napus, which are categorized into three phylogenetic groups and display synteny relationship to the Arabidopsis thaliana orthologs. All the CRK genes contain highly conserved N-terminal PKINASE domain; however, the distribution of motifs and gene structure were variable conserved. The functional divergence analysis between BnaCRK groups indicates a shift in evolutionary rate after duplication events, demonstrating that BnaCRKs might direct a specific function. RNA-Seq datasets and quantitative real-time PCR (qRT-PCR) exhibit the complex expression profile of the BnaCRKs in plant tissues under multiple stresses. Nevertheless, BnaA06CRK6-1 and BnaA08CRK8 from group B were perceived to play a predominant role in the Brassica napus stress signaling pathway in response to drought, salinity, and Sclerotinia sclerotiorum infection. Insights gained from this study improve our knowledge about the Brassica napus CRK gene family and provide a basis for enhancing the quality of rapeseed.
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Affiliation(s)
- Rehman Sarwar
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Lei Li
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Jiang Yu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Yijie Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Rui Geng
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Qingfeng Meng
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Keming Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
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Kaur S, Kumar S, Mohapatra T. MicroRNA: noncoding but still coding, another example of self-catalysis. Funct Integr Genomics 2022; 23:4. [PMID: 36527514 DOI: 10.1007/s10142-022-00926-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
MicroRNAs (miRNAs) are known to interact with specific mRNAs to regulate gene expression at the post-transcriptional level by cleaving/repressing the translation process. MiRNA-mediated regulation of gene expression has become an interesting area of research on biological processes like growth, development, and stress responses. Studies suggest that some of the noncoding RNAs possess short open reading frames (ORFs) that code for micropeptides (miPEPs) having a regulatory function. Dual functions of some MIR genes are being deciphered, wherein the gene is transcribed into a longer transcript having a stem-loop structure and a shorter alternatively spliced transcript with no stem-loop. While the longer transcript is processed into miRNA, the shorter one is translated into miPEP. The miPEP enhances the transcription/production of the pri-miRNA from which it originates. Regulatory action of miPEP being species-specific, synthetic miPEP being is tested for exogenous application on crop plant to improve stress tolerance/agronomic performance. Deployment of the miPEP-mediated regulatory function might be a promising strategy to modulated miRNA-facilitated regulation of gene/trait of interest towards developing climate-resilient crops. In this review, we describe the newly identified and verified function of the MIR gene in the coding of miPEPs along with the comparison of the features of miRNA and miPEP in plant. We also discuss about their potential role in crop improvement and some of the yet unanswered question about miPEP.
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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, USA
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Wan J, Meng S, Wang Q, Zhao J, Qiu X, Wang L, Li J, Lin Y, Mu L, Dang K, Xie Q, Tang J, Ding D, Zhang Z. Suppression of microRNA168 enhances salt tolerance in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2022; 22:563. [PMID: 36460977 PMCID: PMC9719116 DOI: 10.1186/s12870-022-03959-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Rice is a salt-sensitive crop. Complex gene regulatory cascades are likely involved in salinity stress in rice roots. microRNA168 (miR168) is a conserved miRNA among different plant species. It in-directly regulates the expression of all miRNAs by targeting gene ARGONAUTE1(AGO1). Short Tandem Target Mimic (STTM) technology is an ideal approach to study miRNA functions by in-activating mature miRNA in plants. RESULTS In this study, rice miR168 was inactivated by STTM. The T3 generation seedlings of STTM168 exhibited significantly enhanced salt resistance. Direct target genes of rice miR168 were obtained by in silico prediction and further confirmed by degradome-sequencing. PINHEAD (OsAGO1), which was previously suggested to be a plant abiotic stress response regulator. RNA-Seq was performed in root samples of 150mM salt-treated STTM168 and control seedlings. Among these screened 481 differentially expressed genes within STTM168 and the control, 44 abiotic stress response related genes showed significant difference, including four known salt-responsive genes. CONCLUSION Based on sequencing and qRT-PCR, a "miR168-AGO1-downstream" gene regulation model was proposed to be responsible for rice salt stress response. The present study proved miR168-AGO1 cascade to play important role in rice salinity stress responding, as well as to be applied in agronomic improvement in further.
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Affiliation(s)
- Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Jiawen Zhao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Liangfa Wang
- Hebi Academy of Agricultural Sciences, 458030, Hebi, China
| | - Juan Li
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, 550006, Guiyang, China
| | - Yuan Lin
- Hebi Academy of Agricultural Sciences, 458030, Hebi, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Kuntai Dang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Qiankun Xie
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
- The Shennong laboratory, 450002, Zhengzhou, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China.
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China.
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Islam W, Idrees A, Waheed A, Zeng F. Plant responses to drought stress: microRNAs in action. ENVIRONMENTAL RESEARCH 2022; 215:114282. [PMID: 36122702 DOI: 10.1016/j.envres.2022.114282] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Drought is common in most regions of the world, and it has a significant impact on plant growth and development. Plants, on the other hand, have evolved their own defense systems to deal with the extreme weather. The reprogramming of gene expression by microRNAs (miRNAs) is one of these defense mechanisms. miRNAs are short noncoding RNAs that have emerged as key post-transcriptional gene regulators in a variety of species. Drought stress modulates the expression of certain miRNAs that are functionally conserved across plant species. These characteristics imply that miRNA-based genetic changes might improve drought resistance in plants. This study highlights current knowledge of plant miRNA biogenesis, regulatory mechanisms and their role in drought stress responses. miRNAs functions and their adaptations by plants during drought stress has also been explained that can be exploited to promote drought-resistance among economically important crops.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Atif Idrees
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Abdul Waheed
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Maqsood H, Munir F, Amir R, Gul A. Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 13:1031679. [PMID: 36507398 PMCID: PMC9731513 DOI: 10.3389/fpls.2022.1031679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/25/2022] [Indexed: 06/12/2023]
Abstract
Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.
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Affiliation(s)
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Feng Y, Qi N, Lei P, Wang Y, Xuan Y, Liu X, Fan H, Chen L, Duan Y, Zhu X. Gma-miR408 Enhances Soybean Cyst Nematode Susceptibility by Suppressing Reactive Oxygen Species Accumulation. Int J Mol Sci 2022; 23:ijms232214022. [PMID: 36430501 PMCID: PMC9695887 DOI: 10.3390/ijms232214022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycine) is a serious damaging disease in soybean worldwide, thus resulting in severe yield losses. MicroRNA408 (miR408) is an ancient and highly conserved miRNA involved in regulating plant growth, development, biotic and abiotic stress response. Here, we analyzed the evolution of miR408 in plants and verified four miR408 members in Glycine max. In the current research, highly upregulated gma-miR408 expressing was detected during nematode migration and syncytium formation response to soybean cyst nematode infection. Overexpressing and silencing miR408 vectors were transformed to soybean to confirm its potential role in plant and nematode interaction. Significant variations were observed in the MAPK signaling pathway with low OXI1, PR1, and wounding of the overexpressing lines. Overexpressing miR408 could negatively regulate soybean resistance to SCN by suppressing reactive oxygen species accumulation. Conversely, silencing miR408 positively regulates soybean resistance to SCN. Overall, gma-miR408 enhances soybean cyst nematode susceptibility by suppressing reactive oxygen species accumulation.
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Affiliation(s)
- Yaxing Feng
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Nawei Qi
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Piao Lei
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Yuanyuan Wang
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanhu Xuan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyu Liu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiyan Fan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Lijie Chen
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuxi Duan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaofeng Zhu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence:
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Nguyen NH, Vu NT, Cheong JJ. Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants. Int J Mol Sci 2022; 23:12918. [PMID: 36361708 PMCID: PMC9654142 DOI: 10.3390/ijms232112918] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2023] Open
Abstract
Plants respond to drought stress by producing abscisic acid, a chemical messenger that regulates gene expression and thereby expedites various physiological and cellular processes including the stomatal operation to mitigate stress and promote tolerance. To trigger or suppress gene transcription under drought stress conditions, the surrounding chromatin architecture must be converted between a repressive and active state by epigenetic remodeling, which is achieved by the dynamic interplay among DNA methylation, histone modifications, loop formation, and non-coding RNA generation. Plants can memorize chromatin status under drought conditions to enable them to deal with recurrent stress. Furthermore, drought tolerance acquired during plant growth can be transmitted to the next generation. The epigenetically modified chromatin architectures of memory genes under stressful conditions can be transmitted to newly developed cells by mitotic cell division, and to germline cells of offspring by overcoming the restraints on meiosis. In mammalian cells, the acquired memory state is completely erased and reset during meiosis. The mechanism by which plant cells overcome this resetting during meiosis to transmit memory is unclear. In this article, we review recent findings on the mechanism underlying transcriptional stress memory and the transgenerational inheritance of drought tolerance in plants.
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Affiliation(s)
- Nguyen Hoai Nguyen
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City 700000, Vietnam
| | - Nam Tuan Vu
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
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Salgado FF, da Silva TLC, Vieira LR, Silva VNB, Leão AP, Costa MMDC, Togawa RC, de Sousa CAF, Grynberg P, Souza MT. The early response of oil palm ( Elaeis guineensis Jacq.) plants to water deprivation: Expression analysis of miRNAs and their putative target genes, and similarities with the response to salinity stress. FRONTIERS IN PLANT SCIENCE 2022; 13:970113. [PMID: 36212369 PMCID: PMC9539919 DOI: 10.3389/fpls.2022.970113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/25/2022] [Indexed: 06/09/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a oilseed crop of great economic importance drastically affected by abiotic stresses. MicroRNAs (miRNAs) play crucial roles in transcription and post-transcription regulation of gene expression, being essential molecules in the response of plants to abiotic stress. To better understand the molecular mechanisms behind the response of young oil palm plants to drought stress, this study reports on the prediction and characterization of miRNAs and their putative target genes in the apical leaf of plants subjected to 14 days of water deprivation. Then, the data from this study were compared to the data from a similar study that focused on salinity stress. Both, the drought-and salt-responsive miRNAs and their putative target genes underwent correlation analysis to identify similarities and dissimilarities among them. Among the 81 identified miRNAs, 29 are specific for oil palm, including two (egu-miR28ds and egu-miR29ds) new ones - described for the first time. As for the expression profile, 62 miRNAs were significantly differentially expressed under drought stress, being five up-regulated (miR396e, miR159b, miR529b, egu-miR19sds, and egu-miR29ds) and 57 down-regulated. Transcription factors, such as MYBs, HOXs, and NF-Ys, were predicted as putative miRNA-target genes in oil palm under water deprivation; making them the most predominant group of such genes. Finally, the correlation analysis study revealed a group of putative target genes with similar behavior under salt and drought stresses. Those genes that are upregulated by these two abiotic stresses encode lncRNAs and proteins linked to stress tolerance, stress memory, modulation of ROS signaling, and defense response regulation to abiotic and biotic stresses. In summary, this study provides molecular evidence for the possible involvement of miRNAs in the drought stress response in oil palm. Besides, it shows that, at the molecular level, there are many similarities in the response of young oil palm plants to these two abiotic stresses.
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Affiliation(s)
| | | | - Letícia Rios Vieira
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras, MG, Brazil
| | | | - André Pereira Leão
- The Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, Brazil
| | - Marcos Mota do Carmo Costa
- The Brazilian Agricultural Research Corporation, Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
| | - Roberto Coiti Togawa
- The Brazilian Agricultural Research Corporation, Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
| | | | - Priscila Grynberg
- The Brazilian Agricultural Research Corporation, Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
| | - Manoel Teixeira Souza
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras, MG, Brazil
- The Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, Brazil
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Guo L, Shen J, Zhang C, Guo Q, Liang H, Hou X. Characterization and bioinformatics analysis of ptc-miR396g-5p in response to drought stress of Paeonia ostii. Noncoding RNA Res 2022; 7:150-158. [PMID: 35799773 PMCID: PMC9240715 DOI: 10.1016/j.ncrna.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 10/31/2022] Open
Abstract
Drought is one of the main abiotic stress factors affecting yield of Paeonia ostii. In this study, we conducted bioinformatics and differential expression analyses of P. ostii ‘Feng Dan’ ptc-miR396g-5p in leaf samples under different drought stress. ptc-miR396g-5p belongs to the miR396 family. Among the 271 plant species registered in the miRBase database, at least one miR396 member was found in 48 Angiospermae species, 3 in Gymnospermae species, and 1 in Pteridophy. Mature sequence alignment showed that P. ostii ‘Feng Dan’ ptc-miR396g-5p had high sequence similarity with miR396 from other species. Secondary structure prediction showed that the precursor sequence of ‘Feng Dan’ ptc-miR396g-5p could form a stable stem-loop structure, and the mature sequence was located on the 5′ arm of the secondary structure. Phylogenetic tree analysis showed that ‘Feng Dan’ was closely related to 20 species such as Glycine max, Medicago truncatula, Populus trichocarpa, Citrus sinensis, Vitis vinifera, and Theobroma cacao. The predicted target gene of the ‘Feng Dan’ ptc-miR396g-5p encodes a Signal Transducer and Activator of Transcription (STAT) transcription factor. The negative correlation of expression between the miRNA and its target gene was confirmed by qRT-PCR. Our data indicate that ‘Feng Dan’ ptc-miR396g-5p′s expression decreases under drought, leading to an expression increase of the STAT transcription factor.
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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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44
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Hu Y, Chen X, Shen X. Regulatory network established by transcription factors transmits drought stress signals in plant. STRESS BIOLOGY 2022; 2:26. [PMID: 37676542 PMCID: PMC10442052 DOI: 10.1007/s44154-022-00048-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/20/2022] [Indexed: 09/08/2023]
Abstract
Plants are sessile organisms that evolve with a flexible signal transduction system in order to rapidly respond to environmental changes. Drought, a common abiotic stress, affects multiple plant developmental processes especially growth. In response to drought stress, an intricate hierarchical regulatory network is established in plant to survive from the extreme environment. The transcriptional regulation carried out by transcription factors (TFs) is the most important step for the establishment of the network. In this review, we summarized almost all the TFs that have been reported to participate in drought tolerance (DT) in plant. Totally 466 TFs from 86 plant species that mostly belong to 11 families are collected here. This demonstrates that TFs in these 11 families are the main transcriptional regulators of plant DT. The regulatory network is built by direct protein-protein interaction or mutual regulation of TFs. TFs receive upstream signals possibly via post-transcriptional regulation and output signals to downstream targets via direct binding to their promoters to regulate gene expression.
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Affiliation(s)
- Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, 443002 Hubei China
| | - Xiaoliang Chen
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, 443002 Hubei China
| | - Xiangling Shen
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, 443002 Hubei China
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Li C, Duan C, Zhang H, Zhao Y, Meng Z, Zhao Y, Zhang Q. Adaptative Mechanisms of Halophytic Eutrema salsugineum Encountering Saline Environment. FRONTIERS IN PLANT SCIENCE 2022; 13:909527. [PMID: 35837468 PMCID: PMC9274170 DOI: 10.3389/fpls.2022.909527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Salt cress (Eutrema salsugineum), an Arabidopsis-related halophyte, can naturally adapt to various harsh climates and soil conditions; thus, it is considered a desirable model plant for deciphering mechanisms of salt and other abiotic stresses. Accumulating evidence has revealed that compared with Arabidopsis, salt cress possesses stomata that close more tightly and more succulent leaves during extreme salt stress, a noticeably higher level of proline, inositols, sugars, and organic acids, as well as stress-associated transcripts in unstressed plants, and they are induced rapidly under stress. In this review, we systematically summarize the research on the morphology, physiology, genome, gene expression and regulation, and protein and metabolite profile of salt cress under salt stress. We emphasize the latest advances in research on the genome adaptive evolution encountering saline environments, and epigenetic regulation, and discuss the mechanisms underlying salt tolerance in salt cress. Finally, we discuss the existing questions and opportunities for future research in halophytic Eutrema. Together, the review fosters a better understanding of the mechanism of plant salt tolerance and provides a reference for the research and utilization of Eutrema as a model extremophile in the future. Furthermore, the prospects for salt cress applied to explore the mechanism of salt tolerance provide a theoretical basis to develop new strategies for agricultural biotechnology.
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Affiliation(s)
- Chuanshun Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Chonghao Duan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Hengyang Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Yaoyao Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Zhe Meng
- Research Team of Plant Pathogen Microbiology and Immunology, College of Life Science, Shandong Normal University, Jinan, China
| | - Yanxiu Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Quan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. Int J Genomics 2022; 2022:1092894. [PMID: 35747076 PMCID: PMC9213152 DOI: 10.1155/2022/1092894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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Gao W, Li M, Yang S, Gao C, Su Y, Zeng X, Jiao Z, Xu W, Zhang M, Xia K. miR2105 and the kinase OsSAPK10 co-regulate OsbZIP86 to mediate drought-induced ABA biosynthesis in rice. PLANT PHYSIOLOGY 2022; 189:889-905. [PMID: 35188194 PMCID: PMC9157147 DOI: 10.1093/plphys/kiac071] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/15/2022] [Indexed: 05/27/2023]
Abstract
Mediating induced abscisic acid (ABA) biosynthesis is important for enhancing plant stress tolerance. Here, we found that rice (Oryza sativa L.) osa-miR2105 (miR2105) and the Stress/ABA-activated protein kinase (OsSAPK10) coordinately regulate the rice basic region-leucine zipper transcription factor (bZIP TF; OsbZIP86) at the posttranscriptional and posttranslational levels to control drought-induced ABA biosynthesis via modulation of rice 9-cis-epoxycarotenoid dioxygenase (OsNCED3) expression. OsbZIP86 expression is regulated by miR2105-directed cleavage of the OsbZIP86 mRNA. OsbZIP86 encodes a nuclear TF that binds to the promoter of the ABA biosynthetic gene OsNCED3. OsSAPK10 can phosphorylate and activate OsbZIP86 to enhance the expression of OsNCED3. Under normal growth conditions, altered expression of miR2105 and OsbZIP86 displayed no substantial effect on rice growth. However, under drought conditions, miR2105 knockdown or OsbZIP86 overexpression transgenic rice plants showed higher ABA content, enhanced tolerance to drought, lower rates of water loss, and more stomatal closure of seedlings, compared with wild-type rice Zhonghua 11; in contrast, miR2105 overexpression, OsbZIP86 downregulation, and OsbZIP86 knockout plants displayed opposite phenotypes. Collectively, our results show that the "miR2105-(OsSAPK10)-OsbZIP86-OsNCED3" module regulates the drought-induced ABA biosynthesis without penalty on rice growth under normal conditions, suggesting candidates for improving drought tolerance in rice.
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Affiliation(s)
- Weiwei Gao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
| | - Mingkang Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
| | - Songguang Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chunzhi Gao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yan Su
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuan Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhengli Jiao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weijuan Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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Numan M, Guo W, Choi S, Wang X, Du B, Jin W, Bhandari RK, Ligaba‐Osena A. Analysis of miRNAs responsive to long-term calcium deficiency in tef ( Eragrostis tef (Zucc.) Trotter). PLANT DIRECT 2022; 6:e400. [PMID: 35582629 PMCID: PMC9090557 DOI: 10.1002/pld3.400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 03/23/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) play an important role in growth, development, stress resilience, and epigenetic modifications of plants. However, the effect of calcium (Ca2+) deficiency on miRNA expression in the orphan crop tef (Eragrostis tef) remains unknown. In this study, we analyzed expression of miRNAs in roots and shoots of tef in response to Ca2+ treatment. miRNA-seq followed by bioinformatic analysis allowed us to identify a large number of small RNAs (sRNAs) ranging from 17 to 35 nt in length. A total of 1380 miRNAs were identified in tef experiencing long-term Ca2+ deficiency while 1495 miRNAs were detected in control plants. Among the miRNAs identified in this study, 161 miRNAs were similar with those previously characterized in other plant species and 348 miRNAs were novel, while the remaining miRNAs were uncharacterized. Putative target genes and their functions were predicted for all the known and novel miRNAs that we identified. Based on gene ontology (GO) analysis, the predicted target genes are known to have various biological and molecular functions including calcium uptake and transport. Pairwise comparison of differentially expressed miRNAs revealed that some miRNAs were specifically enriched in roots or shoots of low Ca2+-treated plants. Further characterization of the miRNAs and their targets identified in this study may help in understanding Ca2+ deficiency responses in tef and related orphan crops.
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Affiliation(s)
- Muhammad Numan
- Present address:
Laboratory of Plant Molecular Biology and Biotechnology, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
| | - Wanli Guo
- Present address:
Laboratory of Plant Molecular Biology and Biotechnology, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
- Present address:
Department of Biotechnology, College of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Sang‐Chul Choi
- Present address:
Laboratory of Plant Molecular Biology and Biotechnology, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
| | - Xuegeng Wang
- Laboratory of Environmental Epigenetics, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
- Institute of Modern Aquaculture Science and Engineering, College of Life SciencesSouth China Normal UniversityGuangzhouP. R. China
| | - Boxuan Du
- Present address:
Department of Biotechnology, College of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Weibo Jin
- Present address:
Department of Biotechnology, College of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Ramji Kumar Bhandari
- Laboratory of Environmental Epigenetics, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
| | - Ayalew Ligaba‐Osena
- Present address:
Laboratory of Plant Molecular Biology and Biotechnology, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
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49
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Singh A, Jain D, Pandey J, Yadav M, Bansal KC, Singh IK. Deciphering the role of miRNA in reprogramming plant responses to drought stress. Crit Rev Biotechnol 2022; 43:613-627. [PMID: 35469523 DOI: 10.1080/07388551.2022.2047880] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Drought is the most prevalent environmental stress that affects plants' growth, development, and crop productivity. However, plants have evolved adaptive mechanisms to respond to the harmful effects of drought. They reprogram their: transcriptome, proteome, and metabolome that alter their cellular and physiological processes and establish cellular homeostasis. One of the crucial regulatory processes that govern this reprogramming is post-transcriptional regulation by microRNAs (miRNAs). miRNAs are small non-coding RNAs, involved in the downregulation of the target mRNA via translation inhibition/mRNA degradation/miRNA-mediated mRNA decay/ribosome drop off/DNA methylation. Many drought-inducible miRNAs have been identified and characterized in plants. Their main targets are regulatory genes that influence growth, development, osmotic stress tolerance, antioxidant defense, phytohormone-mediated signaling, and delayed senescence during drought stress. Overexpression of drought-responsive miRNAs (Osa-miR535, miR160, miR408, Osa-miR393, Osa-miR319, and Gma-miR394) in certain plants has led to tolerance against drought stress indicating their vital role in stress mitigation. Similarly, knock down (miR166/miR398c) or deletion (miR169 and miR827) of miRNAs has also resulted in tolerance to drought stress. Likewise, engineered Arabidopsis plants with miR165, miR166 using short tandem target mimic strategy, exhibited drought tolerance. Since miRNAs regulate the expression of an array of drought-responsive genes, they can act as prospective targets for genetic manipulations to enhance drought tolerance in crops and achieve sustainable agriculture. Further investigations toward functional characterization of diverse miRNAs, and understanding stress-responses regulated by these miRNAs and their utilization in biotechnological applications is highly recommended.
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Affiliation(s)
- Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Deepti Jain
- Department of Plant Molecular Biology, Interdisciplinary Centre for Plant Genomics, Delhi University South Campus, New Delhi, India
| | - Jyotsna Pandey
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Kailash C Bansal
- The Alliance of Bioversity International and CIAT (CGIAR), New Delhi, India
| | - Indrakant K Singh
- Department of Zoology, Molecular Biology Research Lab, Deshbandhu College, University of Delhi, New Delhi, India.,DBC i4 Center, Deshbandhu College, University of Delhi, New Delhi, India
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50
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Wang D, Gao Y, Sun S, Li L, Wang K. Expression Characteristics in Roots, Phloem, Leaves, Flowers and Fruits of Apple circRNA. Genes (Basel) 2022; 13:genes13040712. [PMID: 35456518 PMCID: PMC9030095 DOI: 10.3390/genes13040712] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 01/25/2023] Open
Abstract
Circular RNAs (circRNAs) are covalently closed non-coding RNAs that play pivotal roles in various biological processes. However, circRNAs' roles in different tissues of apple are currently unknown. A total of 6495 unique circRNAs were identified from roots, phloem, leaves, flowers and fruits; 65.99% of them were intergenic circRNAs. Similar to other plants, tissue-specific expression was also observed for apple circRNAs; only 175 (2.69%) circRNAs were prevalently expressed in all five different tissues, while 1256, 1064, 912, 904 and 1080 circRNAs were expressed only in roots, phloem, leaves, flowers and fruit, respectively. The hosting-genes of circRNAs showed significant differences enriched in COG, GO terms or KEGG pathways in five tissues, suggesting the special functions of circRNAs in different tissues. Potential binding interactions between circRNAs and miRNAs were investigated using TargetFinder; 2989 interactions between 647 circRNAs and 192 miRNA were predicated in the present study. It also predicted that Chr00:18744403|18744580-mdm-miR160 might play an important role in the formation of flowers or in regulating the coloration of flowers, Chr10:6857496|6858910-mdm-miR168 might be involved in response to drought stress in roots, and Chr03:1226434|1277176 may absorb mdm-miR482a-3p and play a major role in disease resistance. Two circRNAs were experimentally analyzed by qRT-PCR with divergent primers, the expression levels were consistent with RNA-seq, which indicates that the RNA-seq datasets were reliable.
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Affiliation(s)
| | | | | | | | - Kun Wang
- Correspondence: ; Tel.: +86-429-3598120
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