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Qiao H, Jiao B, Wang J, Yang Y, Yang F, Geng Z, Zhao G, Liu Y, Dong F, Wang Y, Zhou S. Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat. Genes (Basel) 2023; 14:1586. [PMID: 37628637 PMCID: PMC10454085 DOI: 10.3390/genes14081586] [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: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high-throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real-time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt-treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance.
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Affiliation(s)
- Hualiang Qiao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Bo Jiao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Jiao Wang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Yang Yang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Fan Yang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Yongwei Liu
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Fushuang Dong
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Shuo Zhou
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
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Han M, Yang H, Yu G, Jiang P, You S, Zhang L, Lin H, Liu J, Shu Y. Application of Non-invasive Micro-test Technology (NMT) in environmental fields: A comprehensive review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 240:113706. [PMID: 35659702 DOI: 10.1016/j.ecoenv.2022.113706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Non-invasive Micro-test Technology (NMT) is a selective microelectrode technique which can detect the flux rates and three-dimensional motion directions of ions or molecules into and out of living organisms in situ without damaging the sample. It has the advantages of maintaining sample integrity, high temporal and spatial resolution, and being able to measure multiple sites simultaneously. In this paper we provide a comprehensive review on the development of NMT in recent years. Its principles, characteristics, and the differences with other microelectrode techniques are introduced. We discuss the applications of NMT in the field of phytoremediation, plant resistance, water quality monitoring, and toxicity mechanisms of heavy metals on organisms. Furthermore, the challenges and future prospects of NMT in the environmental field are presented.
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Affiliation(s)
- Mengxuan Han
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, China
| | - Huan Yang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, China
| | - Guo Yu
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, China.
| | - Pingping Jiang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, China
| | - Shaohong You
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, China; Technical Innovation Center of Mine Geological Environmental Restoration Engineering in Southern Karst Area, MNR, Guilin, China.
| | - Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Hua Lin
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, China
| | - Jie Liu
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, China; Technical Innovation Center of Mine Geological Environmental Restoration Engineering in Southern Karst Area, MNR, Guilin, China
| | - Yi Shu
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, China
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Kiseleva AA, Leonova IN, Pshenichnikova TA, Salina EA. Dissection of novel candidate genes for grain texture in Russian wheat varieties. PLANT MOLECULAR BIOLOGY 2020; 104:219-233. [PMID: 32617826 DOI: 10.1007/s11103-020-01025-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Antonina A Kiseleva
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090.
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090.
| | - Irina N Leonova
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
| | - Tatyana A Pshenichnikova
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
| | - Elena A Salina
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
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Singh AK, Chaurasia S, Kumar S, Singh R, Kumari J, Yadav MC, Singh N, Gaba S, Jacob SR. Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat. BMC PLANT BIOLOGY 2018; 18:249. [PMID: 30342465 PMCID: PMC6195990 DOI: 10.1186/s12870-018-1476-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/09/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Salinity severely limits wheat production in many parts of the world. Development of salt tolerant varieties represents the most practical option for enhancing wheat production from these areas. Application of marker assisted selection may assist in fast tracking development of salt tolerant wheat varieties. However, SSR markers available in the public domain are not specifically targeted to functional regions of wheat genome, therefore large numbers of these need to be analysed for identification of markers associated with traits of interest. With the availability of a fully annotated wheat genome assembly, it is possible to develop SSR markers specifically targeted to genic regions. We performed extensive analysis to identify candidate gene based SSRs and assessed their utility in characterizing molecular diversity in a panel of wheat genotypes. RESULTS Our analysis revealed, 161 SSR motifs in 94 salt tolerance candidate genes of wheat. These SSR motifs were nearly equally distributed on the three wheat sub-genomes; 29.8% in A, 35.7% in B and 34.4% in D sub-genome. The maximum number of SSR motifs was present in exons (31.1%) followed by promoters (29.8%), 5'UTRs (21.1%), introns (14.3%) and 3'UTRs (3.7%). Out of the 65 candidate gene based SSR markers selected for validation, 30 were found polymorphic based on initial screening and employed for characterizing genetic diversity in a panel of wheat genotypes including salt tolerant and susceptible lines. These markers generated an average of 2.83 alleles/locus. Phylogenetic analysis revealed four clusters. Salt susceptible genotypes were mainly represented in clusters I and III, whereas high and moderate salt tolerant genotypes were distributed in the remaining two clusters. Population structure analysis revealed two sub-populations, sub-population 1 contained the majority of salt tolerant whereas sub-population 2 contained majority of susceptible genotypes. Moreover, we observed reasonably higher transferability of SSR markers to related wheat species. CONCLUSION We have developed salt responsive gene based SSRs in wheat for the first time. These were highly useful in unravelling functional diversity among wheat genotypes with varying responses to salt stress. The identified gene based SSR markers will be valuable genomic resources for genetic/association mapping of salinity tolerance in wheat.
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Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Shiksha Chaurasia
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Sundeep Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Jyoti Kumari
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Mahesh C. Yadav
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Nidhi Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Sonam Gaba
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, 110012 India
| | - Sherry Rachel Jacob
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
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Liang W, Ma X, Wan P, Liu L. Plant salt-tolerance mechanism: A review. Biochem Biophys Res Commun 2017; 495:286-291. [PMID: 29128358 DOI: 10.1016/j.bbrc.2017.11.043] [Citation(s) in RCA: 323] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 11/07/2017] [Indexed: 12/26/2022]
Abstract
Almost all crops that are important to humans are sensitive to high salt concentration in the soil. The presence of salt in soil is one of the most significant abiotic stresses in farming. Therefore, improving plant salt tolerance and increasing the yield and quality of crops in salty land is vital. Transgenic technology is a fast and effective method to obtain salt-tolerant varieties. At present, many scholars have studied salt damage to plant and plant salt-tolerance mechanism. These scholars have cloned a number of salt-related genes and achieved high salt tolerance for transgenic plants, thereby showing attractive prospects. In this paper, the salt-tolerance mechanism of plants is described from four aspects: plant osmotic stress, ion toxicity, oxidative stress, and salt tolerance genes. This review may help in studies to reveal the mechanism of plant salt tolerance, screen high efficiency and quality salt tolerance crops.
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Affiliation(s)
- Wenji Liang
- North China University of Science and Technology, Tangshan 063000, People's Republic of China.
| | - Xiaoli Ma
- Hebei Seed Administration Station, Shijiazhuang 050031, People's Republic of China
| | - Peng Wan
- Institute of Measurement Test, Tangshan Bureau of Quality and Technical Supervision, Tangshan 063000, People's Republic of China
| | - Lianyin Liu
- North China University of Science and Technology, Tangshan 063000, People's Republic of China
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Ma X, Liang W, Gu P, Huang Z. Salt tolerance function of the novel C2H2-type zinc finger protein TaZNF in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 106:129-40. [PMID: 27156137 DOI: 10.1016/j.plaphy.2016.04.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/13/2016] [Accepted: 04/18/2016] [Indexed: 05/20/2023]
Abstract
The expression profile chip of the wheat salt-tolerant mutant RH8706-49 was investigated under salt stress in our laboratory. Results revealed a novel gene induced by salt stress with unknown functions. The gene was named as TaZNF (Triticum aestivum predicted Dof zinc finger protein) because it contains the zf-Dof superfamily and was deposited in GenBank (accession no. KF307327). Further analysis showed that TaZNF significantly improved the salt-tolerance of transgenic Arabidopsis. Various physiological indices of the transgenic plant were improved compared with those of the control after salt stress. Non-invasive micro-test (NMT) detection showed that the root tip of transgenic Arabidopsis significantly expressed Na(+) excretion. TaZNF is mainly localized in the nucleus and exhibited transcriptional activity. Hence, this protein was considered a transcription factor. The TaZNF upstream promoter was then cloned and was found to contain three salts, one jasmonic acid methyl ester (MeJA), and several ABA-responsive elements. The GUS staining and quantitative results of different tissues in the full-length promoter in the transgenic plants showed that the promoter was not tissue specific. The promoter activity in the root, leaf, and flower was enhanced after induction by salt stress. Moreover, GUS staining and quantitative measurement of GUS activity showed that the promoter sequence contained the positive regulatory element of salt and MeJA after their respective elements were mutated in the full-length promoter. RNA-Seq result showed that 2727 genes were differentially expressed; most of these genes were involved in the metabolic pathway and biosynthesis of secondary metabolite pathway.
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Affiliation(s)
- Xiaoli Ma
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, People's Republic of China.
| | - Wenji Liang
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, People's Republic of China; College of Clinical Medicine, North China University of Science and Technology, Tangshan 063000, People's Republic of China.
| | - Peihan Gu
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, People's Republic of China.
| | - Zhanjing Huang
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, People's Republic of China.
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Ma X, Gu P, Liang W, Zhang Y, Jin X, Wang S, Shen Y, Huang Z. Analysis on the transcriptome information of two different wheat mutants and identification of salt-induced differential genes. Biochem Biophys Res Commun 2016; 473:1197-1204. [PMID: 27074578 DOI: 10.1016/j.bbrc.2016.04.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 10/22/2022]
Abstract
This study established a wheat transcriptome library using RH8706-49 and RH8706-34. Salt-induced differential genes were screened by Illumina RNA sequencing (RNA-Seq). Five differential genes were chosen to study the functions by combining transcript sequencing result and gene chip. The expression changes of these five differential genes were analyzed using real-time quantitative PCR (qRT-PCR) technique to determine the reliability and accuracy of transcriptome sequencing and transplanted into Arabidopsis thaliana to obtain transgenic homozygote plants for the salt tolerance test. The salt tolerance test results show that the transgenic plants grew far better than the wild-type plant.
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Affiliation(s)
- Xiaoli Ma
- College of Life Science, Hebei Normal University, Shijiazhuang 050024 Hebei, PR China.
| | - Peihan Gu
- College of Life Science, Hebei Normal University, Shijiazhuang 050024 Hebei, PR China.
| | - Wenji Liang
- College of Life Science, Hebei Normal University, Shijiazhuang 050024 Hebei, PR China; College of Clinical Medicine, North China University of Science and Technology, Tangshan 063000 Hebei, PR China.
| | - Yuxin Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang 050024 Hebei, PR China.
| | - Xiaoli Jin
- College of Life Science, Hebei Normal University, Shijiazhuang 050024 Hebei, PR China.
| | - Shaoxiong Wang
- College of Life Science, Hebei Normal University, Shijiazhuang 050024 Hebei, PR China.
| | - Yinzhu Shen
- College of Life Science, Hebei Normal University, Shijiazhuang 050024 Hebei, PR China.
| | - Zhanjing Huang
- College of Life Science, Hebei Normal University, Shijiazhuang 050024 Hebei, PR China.
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