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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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2
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Asadi M, Millar AA. Review: Plant microRNAs in pathogen defense: A panacea or a piece of the puzzle? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111993. [PMID: 38266718 DOI: 10.1016/j.plantsci.2024.111993] [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: 10/30/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Plant microRNAs (miRNAs) control key agronomic traits that are associated with their conserved role(s) in development. However, despite a multitude of studies, the utility of miRNAs in plant-pathogen resistance remains less certain. Reviewing the literature identifies three general classes of miRNAs regarding plant pathogen defense. Firstly, a number of evolutionary dynamic 22 nucleotide miRNA families that repress large numbers of plant immunity genes, either directly, or through triggering the biogenesis of secondary siRNAs. However, understanding of their role in defense and of their manipulation to enhance pathogen resistance are still lacking. Secondly, highly conserved miRNAs that indirectly impact disease resistance through their targets that are primarily regulating development or hormone signaling. Any alteration of these miRNAs usually results in pleiotropic impacts, which may alter disease resistance in some plant species, and against some pathogens. Thirdly, are the comparatively diverse and evolutionary dynamic set of non-conserved miRNAs, some of which contribute to pathogen resistance, but whose narrow evolutionary presence will likely restrict their utility. Therefore, reflecting the diverse and evolving nature of plant-pathogen interactions, a complex interplay of plant miRNAs with pathogen responses exists. Any miRNA-based solution for pathogen resistance will likely be highly specific, rather than a general panacea.
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Affiliation(s)
- Mohsen Asadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran; Department of Agricultural Science, Technical and Vocational University (TVU), Tehran, Iran
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australia; ARC Training Centre for Accelerated Future Crop development, ANU, Canberra, Australia.
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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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4
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Li Y, Wang N, Guo J, Zhou X, Bai X, Azeem M, Zhu L, Chen L, Chu M, Wang H, Cheng W. Integrative Transcriptome Analysis of mRNA and miRNA in Pepper's Response to Phytophthora capsici Infection. BIOLOGY 2024; 13:186. [PMID: 38534455 DOI: 10.3390/biology13030186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Phytophthora blight of pepper is a notorious disease caused by the oomycete pathogen Phytophthora capsici, which poses a great threat to global pepper production. MicroRNA (miRNA) is a class of non-coding small RNAs that regulate gene expressions by altering the translation efficiency or stability of targeted mRNAs, which play important roles in the regulation of a plant's response to pathogens. Herein, time-series mRNA-seq libraries and small RNA-seq libraries were constructed using pepper roots from the resistant line CM334 and the susceptible line EC01 inoculated with P. capsici at 0, 6, 24, and 48 h post-inoculation, respectively. For mRNA-seq analysis, a total of 2159 and 2971 differentially expressed genes (DEGs) were identified in CM334 and EC01, respectively. For miRNA-seq analysis, 491 pepper miRNAs were identified, including 330 known miRNAs and 161 novel miRNAs. Among them, 69 and 88 differentially expressed miRNAs (DEMs) were identified in CM334 and EC01, respectively. Examination of DEMs and their targets revealed 22 regulatory networks, predominantly featuring up-regulated miRNAs corresponding to down-regulated target genes. Notably, these DEM-DEG regulatory networks exhibited significant overlap between CM334 and EC01, suggesting that they might contribute to pepper's basal defense against P. capsici. Furthermore, five selected DEMs (miR166, miR1171, miR395, miR530 and miRN2) and their target genes underwent qRT-PCR validation, confirming a consistent negative correlation in the expression patterns of miRNAs and their targets. This comprehensive analysis provides novel insights into the regulatory networks of miRNAs and their targets, offering valuable contributions to our understanding of pepper's defense mechanisms against P. capsici.
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Affiliation(s)
- Yuan Li
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Nan Wang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Jianwen Guo
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xianjun Zhou
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Xueyi Bai
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Muhammad Azeem
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Liyun Zhu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Lin Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Moli Chu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Hui Wang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Wei Cheng
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
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Song H, Gao X, Song L, Jiao Y, Shen L, Yang J, Li C, Shang J, Wang H, Zhang S, Li Y. Unraveling the regulatory network of miRNA expression in Potato Y virus-infected of Nicotiana benthamiana using integrated small RNA and transcriptome sequencing. Front Genet 2024; 14:1290466. [PMID: 38259624 PMCID: PMC10800900 DOI: 10.3389/fgene.2023.1290466] [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: 09/07/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Potato virus Y (PVY) disease is a global problem that causes significant damage to crop quality and yield. As traditional chemical control methods are ineffective against PVY, it is crucial to explore new control strategies. MicroRNAs (miRNAs) play a crucial role in plant and animal defense responses to biotic and abiotic stresses. These endogenous miRNAs act as a link between antiviral gene pathways and host immunity. Several miRNAs target plant immune genes and are involved in the virus infection process. In this study, we conducted small RNA sequencing and transcriptome sequencing on healthy and PVY-infected N. benthamiana tissues (roots, stems, and leaves). Through bioinformatics analysis, we predicted potential targets of differentially expressed miRNAs using the N. benthamiana reference genome and the PVY genome. We then compared the identified differentially expressed mRNAs with the predicted target genes to uncover the complex relationships between miRNAs and their targets. This study successfully constructed a miRNA-mRNA network through the joint analysis of Small RNA sequencing and transcriptome sequencing, which unveiled potential miRNA targets and identified potential binding sites of miRNAs on the PVY genome. This miRNA-mRNA regulatory network suggests the involvement of miRNAs in the virus infection process.
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Affiliation(s)
- Hongping Song
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, Hubei, China
| | - Xinwen Gao
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Liyun Song
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yubing Jiao
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lili Shen
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Changquan Li
- Liupanshui City Company of Guizhou Tobacco Company, Guizhou, Guizhou, China
| | - Jun Shang
- Liupanshui City Company of Guizhou Tobacco Company, Guizhou, Guizhou, China
| | - Hui Wang
- Luoyang City Company of Henan Tobacco Company, Luoyang, Henan, China
| | - Songbai Zhang
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, Hubei, China
| | - Ying Li
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Romero-Rodríguez B, Petek M, Jiao C, Križnik M, Zagorščak M, Fei Z, Bejarano ER, Gruden K, Castillo AG. Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomato. BMC PLANT BIOLOGY 2023; 23:651. [PMID: 38110861 PMCID: PMC10726652 DOI: 10.1186/s12870-023-04534-y] [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: 08/10/2023] [Accepted: 10/17/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies allow the simultaneous analysis of multiple aspects of viral infection at a large scale, generating new insights into the molecular mechanisms underlying plant-virus interactions. However, an integrative study of the changes in the host transcriptome, small RNA profile and methylome during a geminivirus infection has not been performed yet. Using a time-scale approach, we aim to decipher the gene regulation in tomato in response to the infection with the geminivirus, tomato yellow leaf curl virus (TYLCV). RESULTS We showed that tomato undergoes substantial transcriptional and post-transcriptional changes upon TYLCV infection and identified the main altered regulatory pathways. Interestingly, although the principal plant defense-related processes, gene silencing and the immune response were induced, this cannot prevent the establishment of the infection. Moreover, we identified extra- and intracellular immune receptors as targets for the deregulated microRNAs (miRNAs) and established a network for those that also produced phased secondary small interfering RNAs (phasiRNAs). On the other hand, there were no significant genome-wide changes in tomato methylome at 14 days post infection, the time point at which the symptoms were general, and the amount of viral DNA had reached its maximum level, but we were able to identify differentially methylated regions that could be involved in the transcriptional regulation of some of the differentially expressed genes. CONCLUSION We have conducted a comprehensive and reliable study on the changes at transcriptional, post-transcriptional and epigenetic levels in tomato throughout TYLCV infection. The generated genomic information is substantial for understanding the genetic, molecular and physiological changes caused by TYLCV infection in tomato.
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Affiliation(s)
- Beatriz Romero-Rodríguez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- The Key Lab of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Araceli G Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain.
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Sharma S, Sett S, Das T, Prasad A, Prasad M. Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107852. [PMID: 37356385 DOI: 10.1016/j.plaphy.2023.107852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/06/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.
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Affiliation(s)
| | - Susmita Sett
- National Institute of Plant Genome Research, New Delhi, India.
| | - Tuhin Das
- National Institute of Plant Genome Research, New Delhi, India.
| | - Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
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Lei X, Chen M, Xu K, Sun R, Zhao S, Wu N, Zhang S, Yang X, Xiao K, Zhao Y. The miR166d/ TaCPK7-D Signaling Module Is a Critical Mediator of Wheat ( Triticum aestivum L.) Tolerance to K + Deficiency. Int J Mol Sci 2023; 24:ijms24097926. [PMID: 37175632 PMCID: PMC10178733 DOI: 10.3390/ijms24097926] [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: 03/28/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
It is well established that potassium (K+) is an essential nutrient for wheat (Triticum aestivum L.) growth and development. Several microRNAs (miRNAs), including miR166, are reportedly vital roles related to plant growth and stress responses. In this study, a K+ starvation-responsive miRNA (miR166d) was identified, which showed increased expression in the roots of wheat seedlings exposed to low-K+ stress. The overexpression of miR166d considerably increased the tolerance of transgenic Arabidopsis plants to K+ deprivation treatment. Furthermore, disrupting miR166d expression via virus-induced gene silencing (VIGS) adversely affected wheat adaptation to low-K+ stress. Additionally, miR166d directly targeted the calcium-dependent protein kinase 7-D gene (TaCPK7-D) in wheat. The TaCPK7-D gene expression was decreased in wheat seedling roots following K+ starvation treatment. Silencing TaCPK7-D in wheat increased K+ uptake under K+ starvation. Moreover, we observed that the miR166d/TaCPK7-D module could affect wheat tolerance to K+ starvation stress by regulating TaAKT1 and TaHAK1 expression. Taken together, our results indicate that miR166d is vital for K+ uptake and K+ starvation tolerance of wheat via regulation of TaCPK7-D.
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Affiliation(s)
- Xiaotong Lei
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
| | - Miaomiao Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
| | - Ke Xu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
| | - Ruoxi Sun
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
| | - Sihang Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
| | - Ningjing Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
| | - Shuhua Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
| | - Xueju Yang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
| | - Kai Xiao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
| | - Yong Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding 071000, China
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9
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Lu Y, Zhang J, Han Z, Han Z, Li S, Zhang J, Ma H, Han Y. Screening of differentially expressed microRNAs and target genes in two potato varieties under nitrogen stress. BMC PLANT BIOLOGY 2022; 22:478. [PMID: 36207676 PMCID: PMC9547441 DOI: 10.1186/s12870-022-03866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND A reasonable supply of nitrogen (N) fertilizer is essential for obtaining high-quality, high-level, and stable potato yields, and an improvement in the N utilization efficiency can effectively reduce N fertilizer use. It is important to use accurate, straightforward, and efficient transgenic breeding techniques for the identification of genes that can improve nitrogen use efficiency, thus enabling us to achieve the ultimate goal of breeding N-efficient potato varieties. In recent years, some of the mechanisms of miRNAs have been elucidated via the analysis of the correlation between the expression levels of potato miRNA target genes and regulated genes under conditions of stress, but the role of miRNAs in the inhibition/expression of key genes regulating N metabolism under N stress is still unclear. Our study aimed to identify the role played by specific enzymes and miRNAs in the responses of plants to N stress. RESULTS The roots and leaves of the N-efficient potato variety, Yanshu4 ("Y"), and N-inefficient potato variety, Atlantic ("D"), were collected at the seedling and budding stages after they were exposed to different N fertilizer treatments. The miRNAs expressed differentially under the two types of N stress and their corresponding target genes were first predicted using miRNA and degradome analysis. Then, quantitative polymerase chain reaction (qRT-PCR) was performed to verify the expression of differential miRNAs that were closely related to N metabolism. Finally, the shearing relationship between stu-miR396-5p and its target gene StNiR was determined by analyzing luciferase activity levels. The results showed that NiR activity increased significantly with an increase in the applied N levels from the seedling stage to the budding stage, and NiR responded significantly to different N treatments. miRNA sequencing enabled us to predict 48 families with conserved miRNAs that were mainly involved in N metabolism, carbon metabolism, and amino acid biosynthesis. The differences in the expression of the following miRNAs were identified via screening (high expression levels and P < 0.05): stu-miR396-5p, stu-miR408b-3p_R-1, stu-miR3627-3p, stu-miR482a-3p, stu-miR8036-3p, stu-miR482a-5p, stu-miR827-5p, stu-miR156a_L-1, stu-miR827-3p, stu-miR172b-5p, stu-miR6022-p3_7, stu-miR398a-5p, and stu-miR166c-5p_L-3. Degradome analysis showed that most miRNAs had many-to-many relationships with target genes. The main target genes involved in N metabolism were NiR, NiR1, NRT2.5, and NRT2.7. qRT-PCR analysis showed that there were significant differences in the expression levels of stu-miR396-5p, stu-miR8036-3p, and stu-miR482a-3p in the leaves and roots of the Yanshu4 and Atlantic varieties at the seedling and budding stages under conditions that involved no N and excessive N application; the expression of these miRNAs was induced in response to N stress. The correlation between the differential expression of stu-miR396-5p and its corresponding target gene NiR was further verified by determining the luciferase activity level and was found to be strongly negative. CONCLUSION The activity of NiR was significantly positively correlated with N application from the seedling to the budding stage. Differential miRNAs and target genes showed a many-to-many relationship with each other. The expression of stu-miR396-5p, stu-miR482a-3p, and stu-miR8036-3p in the roots and leaves of the Yanshu4 and Atlantic varieties at the seedling and budding stages was notably different under two types of N stress. Under two types of N stress, stu-miR396-5p was down-regulated in Yanshu4 in the seedling-stage and shoot-stage roots, and up-regulated in seedling-stage roots and shoot-stage leaves; stu-miR482a-3p was up-regulated in the seedling and shoot stages. The expression of stu-miR8036-3p was up-regulated in the leaves and roots at the seedling and budding stages, and down-regulated in roots under both types of N stress. The gene expressing the key enzyme involved in N metabolism, StNiR, and the stu-miR396-5p luciferase assay reporter gene had a strong regulatory relationship with each other. This study provides candidate miRNAs related to nitrogen metabolism and highlights that differential miRNAs play a key role in nitrogen stress in potato, providing insights for future research on miRNAs and their target genes in nitrogen metabolic pathways and breeding nitrogen-efficient potatoes.
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Affiliation(s)
- Yue Lu
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Jingying Zhang
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
- College of Resources and Environment, Jilin Agricultural University, Changchun City, 130118, P.R. China
| | - Zhijun Han
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Zhongcai Han
- Jilin Provincial Research Institute of Vegetables and Flowers, Changchun City, 130052, People's Republic of China
| | - Shuang Li
- Teaching and Research Base Management Office, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Jiayue Zhang
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Haoran Ma
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Yuzhu Han
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China.
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Hong Y, Zhang Y, Cui J, Meng J, Chen Y, Zhang C, Yang J, Luan Y. The lncRNA39896-miR166b-HDZs module affects tomato resistance to Phytophthora infestans. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1979-1993. [PMID: 35929655 DOI: 10.1111/jipb.13339] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The yield and quality of tomatoes (Solanum lycopersicum) is seriously affected by Phytophthora infestans. The long non-coding RNA (lncRNA) Sl-lncRNA39896 is induced after P. infestans infection and was previously predicted to act as an endogenous target mimic (eTM) for the microRNA Sl-miR166b, which function in stress responses. Here, we further examined the role of Sl-lncRNA39896 and Sl-miR166b in tomato resistance to P. infestans. Sl-miR166b levels were higher in Sl-lncRNA39896-knockout mutants than in wild-type plants, and the mutants displayed enhanced resistance to P. infestans. A six-point mutation in the region of Sl-lncRNA39896 that binds to Sl-miR166b disabled the interaction, suggesting that Sl-lncRNA39896 acts as an eTM for Sl-miR166b. Overexpressing Sl-miR166b yielded a similar phenotype to that produced by Sl-lncRNA39896-knockout, whereas silencing of Sl-miR166b impaired resistance. We verified that Sl-miR166b cleaved transcripts of its target class III homeodomain-leucine zipper genes SlHDZ34 and SlHDZ45. Silencing of SlHDZ34/45 decreased pathogen accumulation in plants infected with P. infestans. Additionally, jasmonic acid and ethylene contents were elevated following infection in the plants with enhanced resistance. Sl-lncRNA39896 is the first known lncRNA to negatively regulate resistance to P. infestans in tomato. We propose a novel mechanism in which the lncRNA39896-miR166b-HDZ module modulates resistance to P. infestans.
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Affiliation(s)
- Yuhui Hong
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yuanyuan Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China
| | - Jun Cui
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
- College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yinhua Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Chengwei Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100000, China
| | - Jinxiao Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100000, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
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Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response. PLANTS 2022; 11:plants11192497. [PMID: 36235363 PMCID: PMC9572245 DOI: 10.3390/plants11192497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022]
Abstract
DUF966 genes are widely found in monocotyledons, dicotyledons, mosses, and other species. Current evidence strongly suggests that they are involved in growth regulation and stress tolerance in crops. However, their functions in cucumbers remain unexplored. Here, cucumber CsDUF966 was systemically identified and characterized using bioinformatics. Eight CsDUF966 genes were identified in the cucumber genome. These were phylogenetically separated into three groups. All CsDUF966 proteins were hydrophilic and localized to the nucleus. Moreover, three acidic and five basic proteins were identified. Evolutionary analysis of DUF966 between cucumber and 33 other Cucurbitaceae species/cultivars revealed that most CsDUF966 genes were conserved, whereas CsDUF966_4.c and CsDUF966_7.c were positively selected among the five cucumber cultivars. Expression profiling analysis showed that CsDUF966 had variable expression patterns, and that miRNA164, miRNA166, and Csa-novel-35 were involved in the post-transcriptional regulation of CsDUF966_4.c and CsDUF966_7.c. The expression of CsDUF966_4.c and CsDUF966_7.c, which were under strong neofunctionalization selection, was strictly regulated in fruit and tissues, including seeds, pericarps, peels, and spines, suggesting that these genes are fruit growth regulators and were strongly selected during the cucumber breeding program. In conclusion, the results reveal the roles of CsDUF966s in regulating cucumber fruit development and lay the foundation for further functional studies.
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Tian J, Zhang G, Zhang F, Ma J, Wen C, Li H. Genome-Wide Identification of Powdery Mildew Responsive Long Non-Coding RNAs in Cucurbita pepo. Front Genet 2022; 13:933022. [PMID: 35846119 PMCID: PMC9283782 DOI: 10.3389/fgene.2022.933022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022] Open
Abstract
Cucurbita pepo L. is an essential economic vegetable crop worldwide, and its production is severely affected by powdery mildew (PM). However, our understanding of the molecular mechanism of PM resistance in C. pepo is very limited. Long non-coding RNAs (lncRNAs) play an important role in regulating plant responses to biotic stress. Here, we systematically identified 2,363 reliably expressed lncRNAs from the leaves of PM-susceptible (PS) and PM-resistant (PR) C. pepo. The C. pepo lncRNAs are shorter in length and expressed at a lower level than the protein-coding transcripts. Among the 2,363 lncRNAs, a total of 113 and 146 PM-responsive lncRNAs were identified in PS and PR, respectively. Six PM-responsive lncRNAs were predicted as potential precursors of microRNAs (miRNAs). In addition, 58 PM-responsive lncRNAs were predicted as targets of miRNAs and one PM-responsive lncRNA was predicted as an endogenous target mimic (eTM). Furthermore, a total of 5,200 potential cis target genes and 5,625 potential trans target genes were predicted for PM-responsive lncRNAs. Functional enrichment analysis showed that these potential target genes are involved in different biological processes, such as the plant-pathogen interaction pathway, MAPK signaling pathway, and plant hormone signal transduction pathway. Taken together, this study provides a comprehensive view of C. pepo lncRNAs and explores the putative functions of PM-responsive lncRNAs, thus laying the foundation for further study of the regulatory mechanisms of lncRNAs responding to PM.
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Affiliation(s)
- Jiaxing Tian
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Guoyu Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Fan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Jian Ma
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Haizhen Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
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