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Involvement of miRNAs-mediated senescence and salicylic acid defense in postharvest litchi downy blight. Food Chem 2023; 404:134662. [DOI: 10.1016/j.foodchem.2022.134662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 09/19/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022]
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2
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Jain N, Shiv A, Sinha N, Singh PK, Prasad P, Balyan HS, Gupta PK. Leaf rust responsive miRNA and their target genes in wheat. Funct Integr Genomics 2022; 23:14. [PMID: 36550370 DOI: 10.1007/s10142-022-00928-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation-reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.
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Affiliation(s)
- Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Aalok Shiv
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - P K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Pramod Prasad
- Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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Niekerk LA, Carelse MF, Bakare OO, Mavumengwana V, Keyster M, Gokul A. The Relationship between Cadmium Toxicity and the Modulation of Epigenetic Traits in Plants. Int J Mol Sci 2021; 22:ijms22137046. [PMID: 34209014 PMCID: PMC8268939 DOI: 10.3390/ijms22137046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 01/17/2023] Open
Abstract
Elevated concentrations of heavy metals such as cadmium (Cd) have a negative impact on staple crop production due to their ability to elicit cytotoxic and genotoxic effects on plants. In order to understand the relationship between Cd stress and plants in an effort to improve Cd tolerance, studies have identified genetic mechanisms which could be important for conferring stress tolerance. In recent years epigenetic studies have garnered much attention and hold great potential in both improving the understanding of Cd stress in plants as well as revealing candidate mechanisms for future work. This review describes some of the main epigenetic mechanisms involved in Cd stress responses. We summarize recent literature and data pertaining to chromatin remodeling, DNA methylation, histone acetylation and miRNAs in order to understand the role these epigenetic traits play in cadmium tolerance. The review aims to provide the framework for future studies where these epigenetic traits may be used in plant breeding and molecular studies in order to improve Cd tolerance.
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Affiliation(s)
- Lee-Ann Niekerk
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
| | - Mogamat Fahiem Carelse
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
| | - Olalekan Olanrewaju Bakare
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
| | - Vuyo Mavumengwana
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Tygerberg Campus, Stellenbosch University, Cape Town 7505, South Africa;
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
- Correspondence: (M.K.); (A.G.); Tel.: +27-587185392 (M.K. & A.G.)
| | - Arun Gokul
- Department of Plant Sciences, Qwaqwa Campus, University of the Free State, Phuthadithjaba 9866, South Africa
- Correspondence: (M.K.); (A.G.); Tel.: +27-587185392 (M.K. & A.G.)
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Gao X, Zhang Q, Zhao Y, Yang J, He H, Jia G. The lre-miR159a-LrGAMYB pathway mediates resistance to grey mould infection in Lilium regale. MOLECULAR PLANT PATHOLOGY 2020; 21:749-760. [PMID: 32319186 PMCID: PMC7214475 DOI: 10.1111/mpp.12923] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 05/04/2023]
Abstract
Grey mould is one of the most determinative factors of lily growth and plays a major role in limiting lily productivity. MicroRNA159 (miR159) is a highly conserved microRNA in plants, and participates in the regulation of plant development and stress responses. Our previous studies revealed that lre-miR159a participates in the response of Lilium regale to Botrytis elliptica according to deep sequencing analyses; however, the response mechanism remains unknown. Here, lre-miR159a and its target LrGAMYB gene were isolated from L. regale. Transgenic Arabidopsis overexpressing lre-MIR159a exhibited larger leaves and smaller necrotic spots on inoculation with Botrytis than those of wild-type and overexpressing LrGAMYB plants. The lre-MIR159a overexpression also led to repressed expression of two targets of miR159, AtMYB33 and AtMYB65, and enhanced accumulation of hormone-related genes, including AtPR1, AtPR2, AtNPR1, AtPDF1.2, and AtLOX for both the jasmonic acid and salicylic acid pathways. Moreover, lower levels of H2 O2 and O2- were observed in lre-MIR159a transgenic Arabidopsis, which reduced the damage from reactive oxygen species accumulation. Taken together, these results indicate that lre-miR159a positively regulates resistance to grey mould by repressing the expression of its target LrGAMYB gene and activating a defence response.
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Affiliation(s)
- Xue Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Qian Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Yu‐Qian Zhao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Jie Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Heng‐Bin He
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Gui‐Xia Jia
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
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One Small RNA of Fusarium graminearum Targets and Silences CEBiP Gene in Common Wheat. Microorganisms 2019; 7:microorganisms7100425. [PMID: 31600909 PMCID: PMC6843203 DOI: 10.3390/microorganisms7100425] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/04/2019] [Accepted: 10/06/2019] [Indexed: 12/24/2022] Open
Abstract
The pathogenic fungus Fusarium graminearum (F. graminearum), causing Fusarium head blight (FHB) or scab, is one of the most important cereal killers worldwide, exerting great economic and agronomic losses on global grain production. To repress pathogen invasion, plants have evolved a sophisticated innate immunity system for pathogen recognition and defense activation. Simultaneously, pathogens continue to evolve more effective means of invasion to conquer plant resistance systems. In the process of co-evolution of plants and pathogens, several small RNAs (sRNAs) have been proved in regulating plant immune response and plant-microbial interaction. In this study, we report that a F. graminearum sRNA (Fg-sRNA1) can suppress wheat defense response by targeting and silencing a resistance-related gene, which codes a Chitin Elicitor Binding Protein (TaCEBiP). Transcriptional level evidence indicates that Fg-sRNA1 can target TaCEBiP mRNA and trigger silencing of TaCEBiP in vivo, and in Nicotiana benthamiana (N. benthamiana) plants, Western blotting experiments and YFP Fluorescence observation proofs show that Fg-sRNA1 can suppress the accumulation of protein coding by TaCEBiP gene in vitro. F. graminearum PH-1 strain displays a weakening ability to invasion when Barley stripe mosaic virus (BSMV) vector induces effective silencing Fg-sRNA1 in PH-1 infected wheat plants. Taken together, our results suggest that a small RNA from F. graminearum can target and silence the wheat TaCEBiP gene to enhance invasion of F. graminearum.
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Comparative profiling of roots small RNA expression and corresponding gene ontology and pathway analyses for low- and high-cadmium-accumulating genotypes of wheat in response to cadmium stress. Funct Integr Genomics 2019; 20:177-190. [PMID: 31435847 DOI: 10.1007/s10142-019-00710-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
MicroRNAs (miRNAs) participate in multiple biological processes in plant. Cd accumulation ability differs among varieties in wheat, but little is known about miRNAs and their function in Cd accumulation of wheat under Cd stress. Therefore, the present study detected small RNAs responsible for differential Cd accumulation between two contrasting wheat genotypes (low-Cd accumulation one L17 and high-Cd accumulation one H17) to identify novel targets to further study Cd stress in wheat. Under normal conditions, 139 miRNAs were differentially expressed between L17 and H17, while this value reached 142 after Cd exposure. For Cd-induced DEMs, total 25 miRNAs were differentially expressed in L17 after Cd treatment, while, 70 Cd-induced DEMs were found in H17. Moreover, GO analysis revealed that target genes of DEMs related to lipid biosynthetic process and chlorophyll binding are uniquely enriched in L17, target genes of DEMs related to ribosome biogenesis and sucrose alpha-glucosidase activity are uniquely enriched in H17. By pathway analysis, target genes of DEMs related to PI3K-Akt signaling pathway was specifically enriched in L17, target genes of DEMs related to carbohydrate digestion and absorption pathway was uniquely enriched in H17. In addition, miRNA-gene co-expression showed that tae-miR9774 was uniquely expressed between L17Cd and L17CK, while tae-miR398 was specially expressed between H17Cd and H17CK. Our results suggested that Cd-accumulating ability of L17 and H17 varied from the expression of induced unique miRNA, such as expression of tae-miR-9774 and tae-miR-398. Our study not only provide the foundation for further exploring the miRNAs-induced molecular mechanisms of Cd accumulation in wheat but also supply novel strategies for improving phytoremediation ability of food plants through genetic engineering.
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7
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Zhou M, Zheng S, Liu R, Lu L, Zhang C, Zhang L, Yant L, Wu Y. The genome-wide impact of cadmium on microRNA and mRNA expression in contrasting Cd responsive wheat genotypes. BMC Genomics 2019; 20:615. [PMID: 31357934 PMCID: PMC6664702 DOI: 10.1186/s12864-019-5939-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 06/26/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Heavy metal ATPases (HMAs) are responsible for Cd translocation and play a primary role in Cd detoxification in various plant species. However, the characteristics of HMAs and the regulatory mechanisms between HMAs and microRNAs in wheat (Triticum aestivum L) remain unknown. RESULTS By comparative microRNA and transcriptome analysis, a total three known and 19 novel differentially expressed microRNAs (DEMs) and 1561 differentially expressed genes (DEGs) were found in L17 after Cd treatment. In H17, by contrast, 12 known and 57 novel DEMs, and only 297 Cd-induced DEGs were found. Functional enrichments of DEMs and DEGs indicate how genotype-specific biological processes responded to Cd stress. Processes found to be involved in microRNAs-associated Cd response include: ubiquitin mediated proteolysis, tyrosine metabolism, and carbon fixation pathways and thiamine metabolism. For the mRNA response, categories including terpenoid backbone biosynthesis and phenylalanine metabolism, and photosynthesis - antenna proteins and ABC transporters were enriched. Moreover, we identified 32 TaHMA genes in wheat. Phylogenetic trees, chromosomal locations, conserved motifs and expression levels in different tissues and roots under Cd stress are presented. Finally, we infer a microRNA-TaHMAs expression network, indicating that miRNAs can regulate TaHMAs. CONCLUSION Our findings suggest that microRNAs play important role in wheat under Cd stress through regulation of targets such as TaHMA2;1. Identification of these targets will be useful for screening and breeding low-Cd accumulation wheat lines.
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Affiliation(s)
- Min Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Shigang Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Rong Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lu Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Chihong Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Lei Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
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Kuan T, Zhai Y, Ma W. Small RNAs regulate plant responses to filamentous pathogens. Semin Cell Dev Biol 2016; 56:190-200. [PMID: 27208726 DOI: 10.1016/j.semcdb.2016.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/10/2016] [Accepted: 05/17/2016] [Indexed: 01/04/2023]
Abstract
Small RNAs are central players of RNA silencing in eukaryotes. These short RNA molecules (20-25 nucleotides in length) repress target gene expression based on sequence complementarity. While small RNAs are well-known for their essential function in regulating growth and development, recent research has revealed that they also influence plant immunity. Extensive changes in small RNA accumulation have been observed during infection. This review focuses on specific small RNA changes that are involved in plant responses to filamentous eukaryotic pathogens including fungi and oomycetes. We describe how changes in small RNA accumulation influence plant immunity and summarize the cellular processes affected by these small RNAs. In particular, we discuss secondary small interfering RNAs that directly modulate the expression of defense-related genes.
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Affiliation(s)
- Tung Kuan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA; Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
| | - Yi Zhai
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA; Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA; Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA.
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Budak H, Kantar M, Bulut R, Akpinar BA. Stress responsive miRNAs and isomiRs in cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:1-13. [PMID: 25900561 DOI: 10.1016/j.plantsci.2015.02.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.
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Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey.
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Reyyan Bulut
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Bala Ani Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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Jiao J, Wang Y, Selvaraj JN, Xing F, Liu Y. Barley Stripe Mosaic Virus (BSMV) Induced MicroRNA Silencing in Common Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0126621. [PMID: 25955840 PMCID: PMC4425524 DOI: 10.1371/journal.pone.0126621] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/03/2015] [Indexed: 01/14/2023] Open
Abstract
MicroRNAs (miRNAs) play important roles in growth, development, and response to environmental changes in plants. Based on the whole-genome shotgun sequencing strategy, more and more wheat miRNAs have been annotated. Now, there is a need for an effective technology to analyse endogenous miRNAs function in wheat. We report here that the modified barley stripe mosaic virus (BSMV)-induced miRNAs silencing system can be utilized to silence miRNAs in wheat. BSMV-based miRNA silencing system is performed through BSMV-based expression of miRNA target mimics to suppress miR159a and miR3134a. The relative expression levels of mature miR159a and miR3134a decrease with increasing transcript levels of their target genes in wheat plants. In summary, the developed approach is effective in silencing endogenous miRNAs, thereby providing a powerful tool for biological function analyses of miRNA molecules in common wheat.
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Affiliation(s)
- Jian Jiao
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
| | - Yichun Wang
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
| | - Jonathan Nimal Selvaraj
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
| | - Fuguo Xing
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
| | - Yang Liu
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
- * E-mail:
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11
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Budak H, Hussain B, Khan Z, Ozturk NZ, Ullah N. From Genetics to Functional Genomics: Improvement in Drought Signaling and Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2015; 6:1012. [PMID: 26635838 PMCID: PMC4652017 DOI: 10.3389/fpls.2015.01012] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/02/2015] [Indexed: 05/18/2023]
Abstract
Drought being a yield limiting factor has become a major threat to international food security. It is a complex trait and drought tolerance response is carried out by various genes, transcription factors (TFs), microRNAs (miRNAs), hormones, proteins, co-factors, ions, and metabolites. This complexity has limited the development of wheat cultivars for drought tolerance by classical breeding. However, attempts have been made to fill the lost genetic diversity by crossing wheat with wild wheat relatives. In recent years, several molecular markers including single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs) associated with genes for drought signaling pathways have been reported. Screening of large wheat collections by marker assisted selection (MAS) and transformation of wheat with different genes/TFs has improved drought signaling pathways and tolerance. Several miRNAs also provide drought tolerance to wheat by regulating various TFs/genes. Emergence of OMICS techniques including transcriptomics, proteomics, metabolomics, and ionomics has helped to identify and characterize the genes, proteins, metabolites, and ions involved in drought signaling pathways. Together, all these efforts helped in understanding the complex drought tolerance mechanism. Here, we have reviewed the advances in wide hybridization, MAS, QTL mapping, miRNAs, transgenic technique, genome editing system, and above mentioned functional genomics tools for identification and utility of signaling molecules for improvement in wheat drought tolerance.
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Affiliation(s)
- Hikmet Budak
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
- *Correspondence: Hikmet Budak,
| | - Babar Hussain
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Zaeema Khan
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Neslihan Z. Ozturk
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niǧde UniversityNiǧde, Turkey
| | - Naimat Ullah
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
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12
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Inal B, Türktaş M, Eren H, Ilhan E, Okay S, Atak M, Erayman M, Unver T. Genome-wide fungal stress responsive miRNA expression in wheat. PLANTA 2014; 240:1287-98. [PMID: 25156489 DOI: 10.1007/s00425-014-2153-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/12/2014] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding class of RNAs. They were identified in many plants with their diverse regulatory roles in several cellular and metabolic processes. A number of miRNAs were involved in biotic and abiotic stress responses. Here, fungal stress responsive wheat miRNAs were analyzed by using miRNA-microarray strategy. Two different fungi (Fusarium culmorum and Bipolaris sorokiniana) were inoculated on resistant and sensitive wheat cultivars. A total of 87 differentially regulated miRNAs were detected in the 8 × 15 K array including all of the available plant miRNAs. Using bioinformatics tools, the target transcripts of responsive miRNAs were predicted, and related biological processes and mechanisms were assessed. A number of the miRNAs such as miR2592s, miR869.1, miR169b were highly differentially regulated showing more than 200-fold change upon fungal-inoculation. Some of the miRNAs were identified as fungal-inoculation responsive for the first time. The analyses showed that some of the differentially regulated miRNAs targeted resistance-related genes such as LRR, glucuronosyl transferase, peroxidase and Pto kinase. The comparison of the two miRNA-microarray analyses indicated that fungal-responsive wheat miRNAs were differentially regulated in pathogen- and cultivar-specific manners.
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Affiliation(s)
- Behçet Inal
- Department of Biology, Faculty of Science, Cankiri Karatekin University, 18100, Cankiri, Turkey
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13
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Wang B, Sun YF, Song N, Wei JP, Wang XJ, Feng H, Yin ZY, Kang ZS. MicroRNAs involving in cold, wounding and salt stresses in Triticum aestivum L. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 80:90-6. [PMID: 24735552 DOI: 10.1016/j.plaphy.2014.03.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 03/22/2014] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) play critical roles in post-transcriptional regulation and act as important endogenous regulators to various stresses. Cold, wounding and high-salinity are three common environmental stress stimuli influencing crops growth and development. In this study, we identified 31 known miRNAs and 3 novel miRNAs in wheat. Moreover, 19 stress-regulated miRNAs using RT-qPCR data in which the effects of three stresses were surveyed from the known miRNAs. Among them, 16, 12 and 8 miRNAs were regulated under cold, wounding and high-salinity treatments, respectively. Of which 4 miRNAs were highly responsive to cold stress in wheat by northern blot, and 6 wounding-regulated and 3 high-salinity-regulated miRNAs were detected. Meanwhile, miR159, miR393 and miR398 were responsive to multiple stress stimuli. Besides, 2 novel miRNAs were regulated by cold stress. While, the analyses of targets suggested miR159, miR398 and miR6001 could responses to stress conditions in regulation pathways. Taken together, the results of this study suggest that wheat miRNAs may play important roles in response to abiotic stress.
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Affiliation(s)
- Bing Wang
- College of Plant Protection and State Key Laboratory of Crop Stress Biology on Drought Regions, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Yan-Fei Sun
- College of Plant Protection and State Key Laboratory of Crop Stress Biology on Drought Regions, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Na Song
- College of Plant Protection and State Key Laboratory of Crop Stress Biology on Drought Regions, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Jin-Ping Wei
- College of Plant Protection and State Key Laboratory of Crop Stress Biology on Drought Regions, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Xiao-Jie Wang
- College of Plant Protection and State Key Laboratory of Crop Stress Biology on Drought Regions, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Hao Feng
- College of Plant Protection and State Key Laboratory of Crop Stress Biology on Drought Regions, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Zhi-Yuan Yin
- College of Plant Protection and State Key Laboratory of Crop Stress Biology on Drought Regions, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Zhen-Sheng Kang
- College of Plant Protection and State Key Laboratory of Crop Stress Biology on Drought Regions, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
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14
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Budak H, Khan Z, Kantar M. History and current status of wheat miRNAs using next-generation sequencing and their roles in development and stress. Brief Funct Genomics 2014; 14:189-98. [PMID: 24962995 DOI: 10.1093/bfgp/elu021] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As small molecules that aid in posttranscriptional silencing, microRNA (miRNA) discovery and characterization have vastly benefited from the recent development and widespread application of next-generation sequencing (NGS) technologies. Several miRNAs were identified through sequencing of constructed small RNA libraries, whereas others were predicted by in silico methods using the recently accumulating sequence data. NGS was a major breakthrough in efforts to sequence and dissect the genomes of plants, including bread wheat and its progenitors, which have large, repetitive and complex genomes. Availability of survey sequences of wheat whole genome and its individual chromosomes enabled researchers to predict and assess wheat miRNAs both in the subgenomic and whole genome levels. Moreover, small RNA construction and sequencing-based studies identified several putative development- and stress-related wheat miRNAs, revealing their differential expression patterns in specific developmental stages and/or in response to stress conditions. With the vast amount of wheat miRNAs identified in recent years, we are approaching to an overall knowledge on the wheat miRNA repertoire. In the following years, more comprehensive research in relation to miRNA conservation or divergence across wheat and its close relatives or progenitors should be performed. Results may serve valuable in understanding both the significant roles of species-specific miRNAs and also provide us information in relation to the dynamics between miRNAs and evolution in wheat. Furthermore, putative development- or stress-related miRNAs identified should be subjected to further functional analysis, which may be valuable in efforts to develop wheat with better resistance and/or yield.
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15
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Xu W, Meng Y, Wise RP. Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus. THE NEW PHYTOLOGIST 2014; 201:1396-1412. [PMID: 24246006 DOI: 10.1111/nph.12598] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/08/2013] [Indexed: 05/07/2023]
Abstract
• Barley (Hordeum vulgare L.) Mildew resistance locus a (Mla) confers allele-specific interactions with natural variants of the ascomycete fungus Blumeria graminis f. sp. hordei (Bgh), the causal agent of powdery mildew disease. Significant reprogramming of Mla-mediated gene expression occurs upon infection by this obligate biotrophic pathogen. • We utilized a proteomics-based approach, combined with barley mla, required for Mla12 resistance1 (rar1), and restoration of Mla resistance1 (rom1) mutants, to identify components of Mla-directed signaling. • Loss-of-function mutations in Mla and Rar1 both resulted in the reduced accumulation of chloroplast copper/zinc superoxide dismutase 1 (HvSOD1), whereas loss of function in Rom1 re-established HvSOD1 levels. In addition, both Mla and Rom1 negatively regulated hvu-microRNA398 (hvu-miR398), and up-regulation of miR398 was coupled to reduced HvSOD1 expression. Barley stripe mosaic virus (BSMV)-mediated over-expression of both barley and Arabidopsis miR398 repressed accumulation of HvSOD1, and BSMV-induced gene silencing of HvSod1 impeded Mla-triggered H₂O₂ and hypersensitive reaction (HR) at barley-Bgh interaction sites. • These data indicate that Mla- and Rom1-regulated hvu-miR398 represses HvSOD1 accumulation, influencing effector-induced HR in response to the powdery mildew fungus.
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Affiliation(s)
- Weihui Xu
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA, 50011-1020, USA
| | - Yan Meng
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA, 50011-1020, USA
| | - Roger P Wise
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA, 50011-1020, USA
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Iowa State University, Ames, IA, 50011-1020, USA
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