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Zhang Z, Yang T, Li N, Tang G, Tang J. MicroRNA166: Old Players and New Insights into Crop Agronomic Traits Improvement. Genes (Basel) 2024; 15:944. [PMID: 39062723 PMCID: PMC11276106 DOI: 10.3390/genes15070944] [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: 06/21/2024] [Revised: 07/14/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
MicroRNA (miRNA), a type of non-coding RNA, is crucial for controlling gene expression. Among the various miRNA families, miR166 stands out as a highly conserved group found in both model and crop plants. It plays a key role in regulating a wide range of developmental and environmental responses. In this review, we explore the diverse sequences of MIR166s in major crops and discuss the important regulatory functions of miR166 in plant growth and stress responses. Additionally, we summarize how miR166 interacts with other miRNAs and highlight the potential for enhancing agronomic traits by manipulating the expression of miR166 and its targeted HD-ZIP III genes.
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Affiliation(s)
- Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China;
| | - Tianxiao Yang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA;
| | - Na Li
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China;
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA;
| | - Jihua Tang
- The Shennong Laboratory, Zhengzhou 450002, China
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Bhat A, Mishra S, Kaul S, Dhar MK. Comparative analysis of miRNA expression profiles in flowering and non-flowering tissue of Crocus sativus L. PROTOPLASMA 2024; 261:749-769. [PMID: 38340171 DOI: 10.1007/s00709-024-01931-4] [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: 10/24/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
Crocus sativus is a valuable plant due to the presence of apocarotenoids in its stigma. Considerable work has been done in the past to understand the apocarotenoid biosynthetic pathway in saffron. However, the reports on understanding the regulation of flowering at the post-transcriptional level are meagre. The study aimed to discover the candidate miRNAs, target genes, transcription factors (TFs), and apocarotenoid biosynthetic pathway genes associated with the regulation and transition of flowering in C. sativus. In the present investigation, miRNA profiling was performed in flowering and non-flowering corms of saffron, along with expression analysis of apocarotenoid genes and transcription factors involved in the synthesis of secondary metabolites. Significant modulation in the expression of miR156, miR159, miR166, miR172, miR395, miR396, miR399, and miR408 gene families was observed. We obtained 36 known miRNAs (26 in flowering and 10 in non-flowering) and 64 novel miRNAs (40 in flowering and 24 in non-flowering) unique to specific tissues in our analysis. TFs, including CsMADS and CsMYb, showed significant modulation in expression in flowering tissue, followed by CsHB. Additionally, the miRNAs were predicted to be involved in carbohydrate metabolism, phytohormone signalling, regulation of flower development, and response to stress, cold, and defence. The comprehensive study has enhanced our understanding of the regulatory machinery comprising factors like phytohormones, abiotic stress, apocarotenoid genes, transcription factors, and miRNAs responsible for the synthesis of apocarotenoids and developmental processes during and after flowering.
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Affiliation(s)
- Archana Bhat
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
| | - Sonal Mishra
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
| | - Manoj Kumar Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India.
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Meng J, Li W, Qi F, Yang T, Li N, Wan J, Li X, Jiang Y, Wang C, Huang M, Zhang Y, Chen Y, Teotia S, Tang G, Zhang Z, Tang J. Knockdown of microRNA390 Enhances Maize Brace Root Growth. Int J Mol Sci 2024; 25:6791. [PMID: 38928499 PMCID: PMC11203754 DOI: 10.3390/ijms25126791] [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: 04/09/2024] [Revised: 05/13/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Brace root architecture is a critical determinant of maize's stalk anchorage and nutrition uptake, influencing root lodging resistance, stress tolerance, and plant growth. To identify the key microRNAs (miRNAs) in control of maize brace root growth, we performed small RNA sequencing using brace root samples at emergence and growth stages. We focused on the genetic modulation of brace root development in maize through manipulation of miR390 and its downstream regulated auxin response factors (ARFs). In the present study, miR167, miR166, miR172, and miR390 were identified to be involved in maize brace root growth in inbred line B73. Utilizing short tandem target mimic (STTM) technology, we further developed maize lines with reduced miR390 expression and analyzed their root architecture compared to wild-type controls. Our findings show that STTM390 maize lines exhibit enhanced brace root length and increased whorl numbers. Gene expression analyses revealed that the suppression of miR390 leads to upregulation of its downstream regulated ARF genes, specifically ZmARF11 and ZmARF26, which may significantly alter root architecture. Additionally, loss-of-function mutants for ZmARF11 and ZmARF26 were characterized to further confirm the role of these genes in brace root growth. These results demonstrate that miR390, ZmARF11, and ZmARF26 play crucial roles in regulating maize brace root growth; the involved complicated molecular mechanisms need to be further explored. This study provides a genetic basis for breeding maize varieties with improved lodging resistance and adaptability to diverse agricultural environments.
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Affiliation(s)
- Juan Meng
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Weiya Li
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Feiyan Qi
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Tianxiao Yang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA;
| | - Na Li
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Xiaoqi Li
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Yajuan Jiang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Chenhui Wang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Meilian Huang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Yuanyuan Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Yongqiang Chen
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Sachin Teotia
- Department of Biotechnology, Sharda University, Greater Noida 201306, India;
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA;
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
- The Shennong Laboratory, Zhengzhou 450002, China
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Fedorin DN, Eprintsev AT, Chuykova VO, Igamberdiev AU. Participation of miR165a in the Phytochrome Signal Transduction in Maize ( Zea mays L.) Leaves under Changing Light Conditions. Int J Mol Sci 2024; 25:5733. [PMID: 38891921 PMCID: PMC11171563 DOI: 10.3390/ijms25115733] [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: 03/27/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
The involvement of the microRNA miR165a in the light-dependent mechanisms of regulation of target genes in maize (Zea mays) has been studied. The light-induced change in the content of free miR165a was associated with its binding by the AGO10 protein and not with a change in the rate of its synthesis from the precursor. The use of knockout Arabidopsis plants for the phytochrome A and B genes demonstrated that the presence of an active form of phytochrome B causes an increase in the level of the RNA-induced silencing miR165a complex, which triggers the degradation of target mRNAs. The two fractions of vesicles from maize leaves, P40 and P100 that bind miR165a, were isolated by ultracentrifugation. The P40 fraction consisted of larger vesicles of the size >0.170 µm, while the P100 fraction vesicles were <0.147 µm. Based on the quantitative PCR data, the predominant location of miR165a on the surface of extracellular vesicles of both fractions was established. The formation of the active form of phytochrome upon the irradiation of maize plants with red light led to a redistribution of miR165a, resulting in an increase in its proportion inside P40 vesicles and a decrease in P100 vesicles.
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Affiliation(s)
- Dmitry N. Fedorin
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia; (D.N.F.); (A.T.E.); (V.O.C.)
| | - Alexander T. Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia; (D.N.F.); (A.T.E.); (V.O.C.)
| | - Victoria O. Chuykova
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia; (D.N.F.); (A.T.E.); (V.O.C.)
| | - Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
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Gandham P, Rajasekaran K, Sickler C, Mohan H, Gilbert M, Baisakh N. MicroRNA (miRNA) profiling of maize genotypes with differential response to Aspergillus flavus implies zma-miR156-squamosa promoter binding protein (SBP) and zma-miR398/zma-miR394-F -box combinations involved in resistance mechanisms. STRESS BIOLOGY 2024; 4:26. [PMID: 38727957 PMCID: PMC11087424 DOI: 10.1007/s44154-024-00158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/05/2024] [Indexed: 05/13/2024]
Abstract
Maize (Zea mays), a major food crop worldwide, is susceptible to infection by the saprophytic fungus Aspergillus flavus that can produce the carcinogenic metabolite aflatoxin (AF) especially under climate change induced abiotic stressors that favor mold growth. Several studies have used "-omics" approaches to identify genetic elements with potential roles in AF resistance, but there is a lack of research identifying the involvement of small RNAs such as microRNAs (miRNAs) in maize-A. flavus interaction. In this study, we compared the miRNA profiles of three maize lines (resistant TZAR102, moderately resistant MI82, and susceptible Va35) at 8 h, 3 d, and 7 d after A. flavus infection to investigate possible regulatory antifungal role of miRNAs. A total of 316 miRNAs (275 known and 41 putative novel) belonging to 115 miRNA families were identified in response to the fungal infection across all three maize lines. Eighty-two unique miRNAs were significantly differentially expressed with 39 miRNAs exhibiting temporal differential regulation irrespective of the maize genotype, which targeted 544 genes (mRNAs) involved in diverse molecular functions. The two most notable biological processes involved in plant immunity, namely cellular responses to oxidative stress (GO:00345990) and reactive oxygen species (GO:0034614) were significantly enriched in the resistant line TZAR102. Coexpression network analysis identified 34 hubs of miRNA-mRNA pairs where nine hubs had a node in the module connected to their target gene with potentially important roles in resistance/susceptible response of maize to A. flavus. The miRNA hubs in resistance modules (TZAR102 and MI82) were mostly connected to transcription factors and protein kinases. Specifically, the module of miRNA zma-miR156b-nb - squamosa promoter binding protein (SBP), zma-miR398a-3p - SKIP5, and zma-miR394a-5p - F-box protein 6 combinations in the resistance-associated modules were considered important candidates for future functional studies.
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Affiliation(s)
- Prasad Gandham
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70726, USA.
| | - Christine Sickler
- Food and Feed Safety Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70726, USA
| | - Harikrishnan Mohan
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Matthew Gilbert
- Food and Feed Safety Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70726, USA
| | - Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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Zhou C, Yang N, Tian C, Wen S, Zhang C, Zheng A, Hu X, Fang J, Zhang Z, Lai Z, Lin Y, Guo Y. The miR166 targets CsHDZ3 genes to negatively regulate drought tolerance in tea plant (Camellia sinensis). Int J Biol Macromol 2024; 264:130735. [PMID: 38471611 DOI: 10.1016/j.ijbiomac.2024.130735] [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: 11/29/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/14/2024]
Abstract
Drought is the stressor with a significant adverse impact on the yield stability of tea plants. HD-ZIP III transcription factors (TFs) play important regulatory roles in plant growth, development, and stress responses. However, whether and how HD-ZIP III TFs are involved in drought response and tolerance in tea plants remains unclear. Here, we identified seven HD-ZIP III genes (CsHDZ3-1 to CsHDZ3-7) in tea plant genome. The evolutionary analysis demonstrated that CsHDZ3 members were subjected to purify selection. Subcellular localization analysis revealed that all seven CsHDZ3s located in the nucleus. Yeast self-activation and dual-luciferase reporter assays demonstrated that CsHDZ3-1 to CsHDZ3-4 have trans-activation ability whereas CsHDZ3-5 to CsHDZ3-7 served as transcriptional inhibitors. The qRT-PCR assay showed that all seven CsHDZ3 genes could respond to simulated natural drought stress and polyethylene glycol treatment. Further assays verified that all CsHDZ3 genes can be cleaved by csn-miR166. Overexpression of csn-miR166 inhibited the expression of seven CsHDZ3 genes and weakened drought tolerance of tea leaves. In contrast, suppression of csn-miR166 promoted the expression of seven CsHDZ3 genes and enhanced drought tolerance of tea leaves. These findings established the foundation for further understanding the mechanism of CsHDZ3-miR166 modules' participation in drought responses and tolerance.
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Affiliation(s)
- Chengzhe Zhou
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Niannian Yang
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Caiyun Tian
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shengjing Wen
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cheng Zhang
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Anru Zheng
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaowen Hu
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiaxin Fang
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhendong Zhang
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuling Lin
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqiong Guo
- Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Wei B, Wang Y, Ruan Q, Zhu X, Wang X, Wang T, Zhao Y, Wei X. Mechanism of action of microRNA166 on nitric oxide in alfalfa (Medicago sativa L.) under drought stress. BMC Genomics 2024; 25:316. [PMID: 38549050 PMCID: PMC10976769 DOI: 10.1186/s12864-024-10095-7] [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: 09/08/2023] [Accepted: 02/07/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Alfalfa is a perennial forage crop of high importance, but its cultivation is often affected by drought stress. Currently, the investigation of drought-related small RNAs is a popular research topic to uncover plant drought resistance mechanisms. Among these small RNAs, microRNA166 (miR166) is associated with drought in numerous plant species. Initial small RNA sequencing studies have shown that miR166 is highly responsive to exogenous nitric oxide (NO) and drought. Therefore, analyzing the expression of Msa-miR166 under nitric oxide and drought treatment is significant. RESULT Bioinformatics analysis revealed that the miR166 family is widely distributed among plants, ranging from mosses to eudicots, with significant distribution differences between species. The evolutionary degree of Msa-miR166s is highly similar to that of Barrel medic (Medicago truncatula) and Soybean (Glycine max), but significantly different from the model plant Arabidopsis (Arabidopsis thaliana). It is suggested that there are no significant differences in miR166s within the species, and members of Msa-miR166s can form a typical stem-loop. The lowest level of exogenous nitric oxide was observed in Msa-miR166s under drought stress, followed by individual drought, and the highest level was observed after removing endogenous nitric oxide. CONCLUSION In response to short-term drought, Msa-miR166s down-regulate expression in alfalfa (Medicago sativa L.). Exogenous nitric oxide can reduce the expression of Msa-miR166s in response to short-term drought. These findings suggest that Msa-miR166e-5p is responsive to environmental changes. The expression levels of target genes showed an opposite trend to Msa-miR166s, verifying the accuracy of Degradome sequencing in the early stage. This suggests that alfalfa experiences drought stress when regulated by exogenous nitric oxide, targeting HD ZIP-III, FRI, and CoA ligase genes. Additionally, the expression of Msa-miR166s in response to drought stress varies between leaves and roots, indicating spatiotemporal specificity.
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Affiliation(s)
- Bochuang Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yizhen Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Qian Ruan
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaolin Zhu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xian Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Tianjie Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ying Zhao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaohong Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
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Kaur G, Jain S, Bhushan S, Das N, Sharma M, Sharma D. Role of microRNAs and their putative mechanism in regulating potato (Solanum tuberosum L.) life cycle and response to various environmental stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108334. [PMID: 38219424 DOI: 10.1016/j.plaphy.2024.108334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 10/31/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
The exponentially increasing population and the demand for food is inextricably linked. This has shifted global attention to improving crop plant traits to meet global food demands. Potato (Solanum tuberosum L.) is a major non-grain food crop that is grown all over the world. Currently, some of the major global potato research work focuses on the significance of microRNAs (miRNAs) in potato. miRNAs are a type of non-coding RNAs that regulate the gene expression of their target mRNA genes by cleavage and/or their translational inhibition. This suggests an essential role of miRNAs in a multitude of plant biological processes, including maintenance of genome integrity, plant growth, development and maturation, and initiation of responses to various stress conditions. Therefore, engineering miRNAs to generate stress-resistant varieties of potato may result in high yield and improved nutritional qualities. In this review, we discuss the potato miRNAs specifically known to play an essential role in the various stages of the potato life cycle, conferring stress-resistant characteristics, and modifying gene expression. This review highlights the significance of the miRNA machinery in plants, especially potato, encouraging further research into engineering miRNAs to boost crop yields and tolerance towards stress.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Sahil Jain
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu and Kashmir (UT), India
| | - Niranjan Das
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Munish Sharma
- Department of Plant Science, Central University of Himachal Pradesh, Shahpur Parisar, Kangra, Himachal Pradesh, India.
| | - Deepak Sharma
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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Rumyantsev SD, Veselova SV, Burkhanova GF, Alekseev VY, Maksimov IV. Bacillus subtilis 26D Triggers Induced Systemic Resistance against Rhopalosiphum padi L. by Regulating the Expression of Genes AGO, DCL and microRNA in Bread Spring Wheat. Microorganisms 2023; 11:2983. [PMID: 38138127 PMCID: PMC10745712 DOI: 10.3390/microorganisms11122983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Bacillus subtilis 26D is a plant growth-promoting endophytic bacteria capable of inducing systemic resistance through the priming mechanism, which includes plant genome reprogramming and the phenomenon of RNA interference (RNAi) and microRNA (miRNAs). The phloem-feeding insect bird cherry-oat aphid Rhopalosiphum padi L. is a serious pest that causes significant damage to crops throughout the world. However, the function of plant miRNAs in the response to aphid infestation remains unclear. The results of this work showed that B. subtilis 26D stimulated aphid resistance in wheat plants, inducing the expression of genes of hormonal signaling pathways ICS, WRKY13, PR1, ACS, EIN3, PR3, and ABI5. In addition, B. subtilis 26D activated the RNAi mechanism and regulated the expression of nine conserved miRNAs through activation of the ethylene, salicylic acid (SA), and abscisic acid (ABA) signaling pathways, which was demonstrated by using treatments with phytohormones. Treatment of plants with SA, ethylene, and ABA acted in a similar manner to B. subtilis 26D on induction of the expression of the AGO4, AGO5 and DCL2, DCL4 genes, as well as the expression of nine conserved miRNAs. Different patterns of miRNA expression were found in aphid-infested plants and in plants treated with B. subtilis 26D or SA, ethylene, and ABA and infested by aphids, suggesting that miRNAs play multiple roles in the plant response to phloem-feeding insects, associated with effects on hormonal signaling pathways, redox metabolism, and the synthesis of secondary metabolites. Our study provides new data to further elucidate the fine mechanisms of bacterial-induced priming. However, further extensive work is needed to fully unravel these mechanisms.
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Affiliation(s)
| | - Svetlana V. Veselova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 71, 450054 Ufa, Russia; (S.D.R.); (G.F.B.); (V.Y.A.); (I.V.M.)
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10
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Zhao S, Tan M, Zhu Y, Zhang Y, Zhang C, Jiao J, Wu P, Feng K, Li L. Combined analysis of microRNA and mRNA profiles provides insights into the pathogenic resistant mechanisms of the lotus rhizome rot. PHYSIOLOGIA PLANTARUM 2023; 175:e14045. [PMID: 37882296 DOI: 10.1111/ppl.14045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/21/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Lotus rhizome rot caused by Fusarium oxysporum is a common vascular fungal disease in plants that significantly impacts the yield. However, only a few studies have studied the mechanism of Nelumbo nucifera responding to lotus rhizome rot. Here, we investigated the pathogenic genes and miRNAs in lotus rhizome rot to uncover the pathogenic resistant mechanisms by transcriptome and small RNA sequencing of lotus roots after inoculation with Fusarium oxysporum. GO and KEGG functional enrichment analysis showed that differential miRNAs were mostly enriched in starch and sucrose metabolism, biosynthesis of secondary metabolites, glutathione metabolism, brassinosteroid biosynthesis and flavonoid biosynthesis pathways. Twenty-seven upregulated miRNAs, 19 downregulated miRNAs and their target genes were identified. Correlation analysis found that miRNAs negatively regulate target genes, which were also enriched in starch and sucrose metabolism and glutathione metabolism pathways. Their expression was measured by reverse transcription quantitative PCR (qRT-PCR), and the results were consistent with the transcriptome analysis, thus verifying the reliability of transcriptome data. We selected three miRNAs (miRNA858-y, miRNA171-z and a novel miRNA novel-m0005-5p) to test the relationship between miRNAs and their target genes. The activity of the GUS testing assay indicated that miRNA could decrease the GUS activity by inhibiting the expression of their target genes. Collectively, this study provides a comprehensive analysis of transcriptome and small RNA sequencing of lotus root after inoculation with Fusarium oxysporum, and we identified candidate miRNAs and their target genes for breeding strategies of Nelumbo nucifera.
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Affiliation(s)
- Shuping Zhao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Mengying Tan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Yamei Zhu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Yao Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Chuyan Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Jiao Jiao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Peng Wu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Kai Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Liangjun Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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11
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Wei H, Song Z, Xie Y, Cheng H, Yan H, Sun F, Liu H, Shen J, Li L, He X, Wang H, Luo K. High temperature inhibits vascular development via the PIF4-miR166-HB15 module in Arabidopsis. Curr Biol 2023; 33:3203-3214.e4. [PMID: 37442138 DOI: 10.1016/j.cub.2023.06.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/16/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
The plant vascular system is an elaborate network of conducting and supporting tissues that extends throughout the plant body, and its structure and function must be orchestrated with different environmental conditions. Under high temperature, plants display thin and lodging stems that may lead to decreased yield and quality of crops. However, the molecular mechanism underlying high-temperature-mediated regulation of vascular development is not known. Here, we show that Arabidopsis plants overexpressing the basic-helix-loop-helix (bHLH) transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4), a central regulator of high-temperature signaling, display fewer vascular bundles (VBs) and decreased secondary cell wall (SCW) thickening, mimicking the lodging inflorescence stems of high-temperature-grown wild-type plants. Rising temperature and elevated PIF4 expression reduced the expression of MIR166 and, concomitantly, elevated the expression of the downstream class III homeodomain leucine-zipper (HD-ZIP III) family gene HB15. Consistently, knockdown of miR166 and overexpression of HB15 led to inhibition of vascular development and SCW formation, whereas the hb15 mutant displayed the opposite phenotype in response to high temperature. Moreover, in vitro and in vivo assays verified that PIF4 binds to the promoters of several MIR166 genes and represses their expression. Our study establishes a direct functional link between PIF4 and the miR166-HB15 module in modulating vascular development and SCW thickening and consequently stem-lodging susceptibility at elevated temperatures.
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Affiliation(s)
- Hongbin Wei
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zhi Song
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongli Cheng
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Huiting Yan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Fan Sun
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Huajie Liu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Junlong Shen
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xinhua He
- Centre of Excellence for Soil Biology, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China.
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12
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Zhang M, Chen Y, Xing H, Ke W, Shi Y, Sui Z, Xu R, Gao L, Guo G, Li J, Xing J, Zhang Y. Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:772-790. [PMID: 36354146 DOI: 10.1111/jipb.13408] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Lateral roots play essential roles in drought tolerance in maize (Zea mays L.). However, the genetic basis for the variation in the number of lateral roots in maize remains elusive. Here, we identified a major quantitative trait locus (QTL), qLRT5-1, controlling lateral root number using a recombinant inbred population from a cross between the maize lines Zong3 (with many lateral roots) and 87-1 (with few lateral roots). Fine-mapping and functional analysis determined that the candidate gene for qLRT5-1, ZmLRT, expresses the primary transcript for the microRNA miR166a. ZmLRT was highly expressed in root tips and lateral root primordia, and knockout and overexpression of ZmLRT increased and decreased lateral root number, respectively. Compared with 87-1, the ZmLRT gene model of Zong3 lacked the second and third exons and contained a 14 bp deletion at the junction between the first exon and intron, which altered the splicing site. In addition, ZmLRT expression was significantly lower in Zong3 than in 87-1, which might be attributed to the insertions of a transposon and over large DNA fragments in the Zong3 ZmLRT promoter region. These mutations decreased the abundance of mature miR166a in Zong3, resulting in increased lateral roots at the seedling stage. Furthermore, miR166a post-transcriptionally repressed five development-related class-III homeodomain-leucine zipper genes. Moreover, knockout of ZmLRT enhanced drought tolerance of maize seedlings. Our study furthers our understanding of the genetic basis of lateral root number variation in maize and highlights ZmLRT as a target for improving drought tolerance in maize.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yanhong Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Agronomy College of Shandong Agricultural University, Taian, 271018, China
| | - Hongyan Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yunlu Shi
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Yantai Science and Technology Innovation Promotion Center, Yantai, 264003, China
| | - Ruibin Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lulu Gao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ganggang Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yirong Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
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13
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What Do We Know about Barley miRNAs? Int J Mol Sci 2022; 23:ijms232314755. [PMID: 36499082 PMCID: PMC9740008 DOI: 10.3390/ijms232314755] [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: 09/30/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.
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Ahmad M. Genomics and transcriptomics to protect rice ( Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger. FRONTIERS IN PLANT SCIENCE 2022; 13:1002596. [PMID: 36340401 PMCID: PMC9630331 DOI: 10.3389/fpls.2022.1002596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.
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Affiliation(s)
- Mushtaq Ahmad
- Visiting Scientist Plant Sciences, University of Nebraska, Lincoln, NE, United States
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Zhang Y, Zhou Y, Zhu W, Liu J, Cheng F. Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:965745. [PMID: 36311129 PMCID: PMC9597485 DOI: 10.3389/fpls.2022.965745] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/26/2022] [Indexed: 05/24/2023]
Abstract
To survive in adverse environmental conditions, plants have evolved sophisticated genetic and epigenetic regulatory mechanisms to balance their growth and abiotic stress tolerance. An increasing number of non-coding RNAs (ncRNAs), including small RNAs (sRNAs) and long non-coding RNAs (lncRNAs) have been identified as essential regulators which enable plants to coordinate multiple aspects of growth and responses to environmental stresses through modulating the expression of target genes at both the transcriptional and posttranscriptional levels. In this review, we summarize recent advances in understanding ncRNAs-mediated prioritization towards plant growth or tolerance to abiotic stresses, especially to cold, heat, drought and salt stresses. We highlight the diverse roles of evolutionally conserved microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the underlying phytohormone-based signaling crosstalk in regulating the balance between plant growth and abiotic stress tolerance. We also review current discoveries regarding the potential roles of ncRNAs in stress memory in plants, which offer their descendants the potential for better fitness. Future ncRNAs-based breeding strategies are proposed to optimize the balance between growth and stress tolerance to maximize crop yield under the changing climate.
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Affiliation(s)
- Yingying Zhang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ye Zhou
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Weimin Zhu
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Junzhong Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Fang Cheng
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
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16
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Farooqi MQU, Nawaz G, Wani SH, Choudhary JR, Rana M, Sah RP, Afzal M, Zahra Z, Ganie SA, Razzaq A, Reyes VP, Mahmoud EA, Elansary HO, El-Abedin TKZ, Siddique KHM. Recent developments in multi-omics and breeding strategies for abiotic stress tolerance in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2022; 13:965878. [PMID: 36212378 PMCID: PMC9538355 DOI: 10.3389/fpls.2022.965878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/23/2022] [Indexed: 06/12/2023]
Abstract
High-throughput sequencing technologies (HSTs) have revolutionized crop breeding. The advent of these technologies has enabled the identification of beneficial quantitative trait loci (QTL), genes, and alleles for crop improvement. Climate change have made a significant effect on the global maize yield. To date, the well-known omic approaches such as genomics, transcriptomics, proteomics, and metabolomics are being incorporated in maize breeding studies. These approaches have identified novel biological markers that are being utilized for maize improvement against various abiotic stresses. This review discusses the current information on the morpho-physiological and molecular mechanism of abiotic stress tolerance in maize. The utilization of omics approaches to improve abiotic stress tolerance in maize is highlighted. As compared to single approach, the integration of multi-omics offers a great potential in addressing the challenges of abiotic stresses of maize productivity.
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Affiliation(s)
| | - Ghazala Nawaz
- Department of Botanical and Environmental Sciences, Kohat University of Science and Technology, Kohat, Pakistan
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Jeet Ram Choudhary
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Maneet Rana
- Division of Crop Improvement, ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rameswar Prasad Sah
- Division of Crop Improvement, ICAR-National Rice Research Institute, Cuttack, India
| | - Muhammad Afzal
- College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Zahra Zahra
- Department of Civil and Environmental Engineering, University of California, Irvine, Irvine, CA, United States
| | | | - Ali Razzaq
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | | | - Eman A. Mahmoud
- Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta, Egypt
| | - Hosam O. Elansary
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
- Floriculture, Ornamental Horticulture, and Garden Design Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
- Department of Geography, Environmental Management, and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Tarek K. Zin El-Abedin
- Department of Agriculture & Biosystems Engineering, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
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Villalba-Bermell P, Marquez-Molins J, Marques MC, Hernandez-Azurdia AG, Corell-Sierra J, Picó B, Monforte AJ, Elena SF, Gomez GG. Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network. FRONTIERS IN PLANT SCIENCE 2021; 12:769093. [PMID: 34899791 PMCID: PMC8656716 DOI: 10.3389/fpls.2021.769093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/14/2021] [Indexed: 06/14/2023]
Abstract
Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress combinations, most interactions were negative, suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling pieces of evidence that the response to combined stresses cannot be easily predicted from the study individual stresses.
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Affiliation(s)
- Pascual Villalba-Bermell
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - Joan Marquez-Molins
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - María-Carmen Marques
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - Andrea G. Hernandez-Azurdia
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - Julia Corell-Sierra
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - Belén Picó
- Instituto de Conservacióny Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
- The Santa Fe Institute, Santa Fe, NM, United States
| | - Gustavo G. Gomez
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
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18
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Chai W, Song N, Su A, Wang J, Si W, Cheng B, Jiang H. ZmmiR190 and its target regulate plant responses to drought stress through an ABA-dependent pathway. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111034. [PMID: 34620438 DOI: 10.1016/j.plantsci.2021.111034] [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: 06/16/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs) are small, non-coding regulatory RNAs that regulate gene expression by facilitating target mRNA cleavage in plants. They are crucial for responses to diverse stresses. The novel drought-responsive miRNA ZmmiR190 was previously identified during an analysis of the maize transcriptome. In this study, we revealed that transgenic Arabidopsis thaliana overexpressing ZmmiR190 is more sensitive to drought than the wild-type control. The transcript of a nuclear-localized gene, ZmCRP04, was identified as a likely target of ZmmiR190. Moreover, ZmmiR190 and ZmCRP04 had the opposite expression profiles following drought and salt treatments. Additionally, 5' RACE and coexpression analyses in A. thaliana provided evidence of the in vivo targeting of the ZmCRP04 transcript by ZmmiR190. Furthermore, the overexpression of ZmCRP04 in A. thaliana and rice significantly enhanced drought tolerance, with lower malonaldehyde contents and relative electrolyte leakage in the transgenic A. thaliana and rice plants than in the wild-type control. Transgenic plants overexpressing ZmmiR190 or ZmCRP04 were hypersensitive to abscisic acid. These results suggest that the ZmCRP04 transcript is targeted by ZmmiR190 and may encode a protein that positively regulates drought stress tolerance via an abscisic acid-dependent pathway. These findings may be relevant for future molecular breeding aimed at improving crop drought tolerance.
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Affiliation(s)
- Wenbo Chai
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China; Lianyungang Academy of Agricultural Sciences, Lianyungang, Jiangsu, 222000, China
| | - Nannan Song
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Anqi Su
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Jun Wang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, Jiangsu, 222000, China
| | - Weina Si
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Haiyang Jiang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China.
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Yadav A, Kumar S, Verma R, Lata C, Sanyal I, Rai SP. microRNA 166: an evolutionarily conserved stress biomarker in land plants targeting HD-ZIP family. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2471-2485. [PMID: 34924705 PMCID: PMC8639965 DOI: 10.1007/s12298-021-01096-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are significant class of noncoding RNAs having analytical investigating and modulatory roles in various signaling mechanisms in plants related to growth, development and environmental stress. Conserved miRNAs are an affirmation of land plants evolution and adaptation. They are a proof of indispensable roles of endogenous gene modulators that mediate plant survival on land. Out of such conserved miRNA families, is one core miRNA known as miR166 that is highly conserved among land plants. This particular miRNA is known to primarily target HD ZIP-III transcription factors. miR166 has roles in various developmental processes, as well as regulatory roles against biotic and abiotic stresses in major crop plants. Major developmental roles indirectly modulated by miR166 include shoot apical meristem and vascular differentiation, leaf and root development. In terms of abiotic stress, it has decisive regulatory roles under drought, salinity, and temperature along with biotic stress management. miR166 and its target genes are also known for their beneficial synergy with microorganisms in leguminous crops in relation to lateral roots and nodule development. Hence it is important to study the roles of miR166 in different crop plants to understand its defensive roles against environmental stresses and improve plant productivity by reprogramming several gene functions at molecular levels. This review is hence a summary of different regulatory roles of miR166 with its target HD-ZIP III and its modulatory and fine tuning against different environmental stresses in various plants.
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Affiliation(s)
- Ankita Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Sanoj Kumar
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005 India
| | - Rita Verma
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Charu Lata
- CSIR-National Institute of Science Communication and Information Resources, 14 Satsang Vihar Marg, New Delhi, 110067 India
| | - Indraneel Sanyal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shashi Pandey Rai
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
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Wu F, Xu J, Gao T, Huang D, Jin W. Molecular mechanism of modulating miR482b level in tomato with botrytis cinerea infection. BMC PLANT BIOLOGY 2021; 21:496. [PMID: 34706648 PMCID: PMC8555085 DOI: 10.1186/s12870-021-03203-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant miRNAs are involved in the response to biotic and abiotic stresses by altering their expression levels, and they play an important role in the regulation of plant resistance to stress. However, the molecular mechanism that regulates the expression levels of miRNAs in plants with biotic and abiotic stress still needs to be explored. Previously, we found that the expression of the miR482 family was changed in tomato infected by Botrytis cinerea. In this study, we investigated and uncovered the mechanism underlying the response of miR482 to B. cinerea infection in tomato. RESULTS First, RT-qPCR was employed to detect the expression patterns of miR482b in tomato infected by B. cinerea, and results showed that miR482b primary transcripts (pri-miR482b) were up-regulated in B. cinerea-infected leaves, but the mature miR482b was down-regulated. Subsequently, we used rapid amplification cDNA end method to amplify the full-length of pri-miR482b. Result showed that the pri-miR482b had two isoforms, with the longer one (consisting 300 bp) having an extra fragment of 53 bp in the 3'-end compared with the shorter one. In vitro Dicer assay indicated that the longer isoform pri-miR482b-x1 had higher efficiency in the post-transcriptional splicing of miRNA than the shorter isoform pri-miR482b-x2. In addition, the transcription level of mature miR482b was much higher in transgenic Arabidopsis overexpressing pri-miR482b-x1 than that in OE pri-miR482b-x2 Arabidopsis. These results confirmed that this extra 53 bp in pri-miR482b-x1 might play a key role in the miR482b biogenesis of post-transcription processing. CONCLUSIONS Extra 53 bp in pri-miR482b-x1 enhanced miR482b biogenesis, which elevated the transcription level of miR482b. This study clarified the response of miR482 to B. cinerea infection in tomato, thereby helping us further understand the molecular mechanisms that regulate the expression levels of other miRNAs.
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Affiliation(s)
- Fangli Wu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jinfeng Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Tiantian Gao
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Diao Huang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Weibo Jin
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China.
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21
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Identification and expression analysis of miRNAs in germination and seedling growth of Tibetan hulless barley. Genomics 2021; 113:3735-3749. [PMID: 34517091 DOI: 10.1016/j.ygeno.2021.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/30/2023]
Abstract
Germination and seedling growth are crucial for plant development and agricultural production. While, the regulatory mechanisms during these processes in Tibetan hulless barley (Hordeum vulgare L. var. nudum) are not well understood. Given the regulatory roles of microRNAs (miRNAs) in crop plants and the irreplaceability of barley in the highland area of China, we herein presented a genome-wide survey of miRNAs to reveal a potential regulatory network in the early developmental stages of two Tibetan hulless barleys, from which a total of 156 miRNAs was identified including 35 known and 121 novel ones. Six of the identified novel miRNAs were further experimentally validated. According to the evolutionary analysis, miR156, miR166, miR168, and miR171 were conserved across Tibetan hulless barleys and eight other seed plants. Expression profiles of ten known miRNAs showed that they were involved in phytohormone signaling, carbohydrate and lipid metabolism, as well as juvenile-adult transition during barley development. Moreover, a total of 1280 genes targeted by 101 miRNAs were predicted from both barley libraries. Three genes (PLN03212, MATE eukaryotic, and GRAS) were validated via the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5' RACE) to be the targets of hvu-miR159a, hvu-miR166a, and hvu-miR171-3p, respectively. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of putative targets, the most abundant pathways were related to "metabolism". These results revealed that miRNA-target pairs participating in the regulation of multigene expression and the embryonic development of Tibetan hulless barleys were controlled by complex mechanisms involving the concordant expression of different miRNAs and feedback loops among miRNAs as well as their targets. The study provides insight into the regulatory network of barley miRNAs for better understanding of miRNA functions during germination and seedling growth.
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