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Luo D, Usman M, Pang F, Zhang W, Qin Y, Li Q, Li Y, Xing Y, Dong D. Comparative transcriptomic and physiological analyses unravel wheat source root adaptation to phosphorous deficiency. Sci Rep 2024; 14:11050. [PMID: 38745054 PMCID: PMC11094128 DOI: 10.1038/s41598-024-61767-z] [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: 01/19/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
Phosphorus (P) is a crucial macronutrient for plant growth and development. Basic metabolic processes regulate growth; however, the molecular detail of these pathways under low phosphorous (LP) in wheat is still unclear. This study aims to elucidate the varied regulatory pathways responses to LP stress in wheat genotypes. Phenotypic, physiological, and transcriptome analyses were conducted on Fielder (P efficient) and Ardito (P inefficient) wheat genotypes after four days of normal phosphorous (NP) and LP stress. In response to LP, Fielder outperformed Ardito, displaying higher chlorophyll content-SPAD values (13%), plant height (45%), stem diameter (12%), shoot dry weight (42%), and root biomass (75%). Root structure analysis revealed that Fielder had greater total root length (50%), surface area (56%), volume (15%), and diameter (4%) than Ardito under LP. These findings highlight Fielder's superior performance and adaptation to LP stress. Transcriptome analysis of wheat genotype roots identified 3029 differentially expressed genes (DEGs) in Fielder and 1430 in Ardito, highlighting LP-induced changes. Key DEGs include acid phosphatases (PAPs), phosphate transporters (PHT1 and PHO1), SPX, and transcription factors (MYB, bHLH, and WRKY). KEGG enrichment analysis revealed key pathways like plant hormones signal transduction, biosynthesis of secondary metabolites, and carbohydrate biosynthesis metabolism. This study unveils crucial genes and the intricate regulatory process in wheat's response to LP stress, offering genetic insights for enhancing plant P utilization efficiency.
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Affiliation(s)
- Daozhen Luo
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Muhammad Usman
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Fei Pang
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Wenjie Zhang
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Ying Qin
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Qing Li
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Yangrui Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yongxiu Xing
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, 530004, China.
| | - Dengfeng Dong
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, 530004, China.
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Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
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Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
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Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
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Pei LL, Zhang LL, Liu X, Jiang J. Role of microRNA miR171 in plant development. PeerJ 2023; 11:e15632. [PMID: 37456878 PMCID: PMC10340099 DOI: 10.7717/peerj.15632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNA with 19-24 nucleotides (nts) in length, which play an essential role in regulating gene expression at the post-transcriptional level. As one of the first miRNAs found in plants, miR171 is a typical class of conserved miRNAs. The miR171 sequences among different species are highly similar, and the vast majority of them have both "GAGCCG" and "CAAUAU" fragments. In addition to being involved in plant growth and development, hormone signaling and stress response, miR171 also plays multiple and important roles in plants through interactions with microbe and other small-RNAs. The miRNA functions by regulating the expression of target genes. Most of miR171's target genes are in the GRAS gene family, but also include some NSP, miRNAs, lncRNAs, and other genes. This review is intended to summarize recent updates on miR171 regarding its function in plant life and hopefully provide new ideas for understanding miR171 function and regulatory mechanisms.
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Affiliation(s)
- Ling Ling Pei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Ling Ling Zhang
- College of Horticulture, Shenyang Agriculture University, Shenyang, Shenhe District, China
| | - Xin Liu
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Jing Jiang
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
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Begum Y. Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants. Gene 2022; 821:146283. [PMID: 35143944 DOI: 10.1016/j.gene.2022.146283] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/12/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, West Bengal, India; Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, JD-2, Sector III, Salt Lake, Kolkata 700106, West Bengal, India.
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Chen J, Han X, Ye S, Liu L, Yang B, Cao Y, Zhuo R, Yao X. Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera. FRONTIERS IN PLANT SCIENCE 2022; 13:932926. [PMID: 35979079 PMCID: PMC9377520 DOI: 10.3389/fpls.2022.932926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/11/2022] [Indexed: 05/02/2023]
Abstract
Phosphorus (P) is an indispensable macronutrient for plant growth and development, and it is involved in various cellular biological activities in plants. Camellia oleifera is a unique high-quality woody oil plant that grows in the hills and mountains of southern China. However, the available P content is deficient in southern woodland soil. Until now, few studies focused on the regulatory functions of microRNAs (miRNAs) and their target genes under low inorganic phosphate (Pi) stress. In this study, we integrated small RNA, degradome, and transcriptome sequencing data to investigate the mechanism of low Pi adaptation in C. oleifera. We identified 40,689 unigenes and 386 miRNAs by the deep sequencing technology and divided the miRNAs into four different groups. We found 32 miRNAs which were differentially expressed under low Pi treatment. A total of 414 target genes of 108 miRNAs were verified by degradome sequencing. Gene ontology (GO) functional analysis of target genes found that they were related to the signal response to the stimulus and transporter activity, indicating that they may respond to low Pi stress. The integrated analysis revealed that 31 miRNA-target pairs had negatively correlated expression patterns. A co-expression regulatory network was established based on the profiles of differentially expressed genes. In total, three hub genes (ARF22, WRKY53, and SCL6), which were the targets of differentially expressed miRNAs, were discovered. Our results showed that integrated analyses of the small RNA, degradome, and transcriptome sequencing data provided a valuable basis for investigating low Pi in C. oleifera and offer new perspectives on the mechanism of low Pi tolerance in woody oil plants.
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Affiliation(s)
- Juanjuan Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Forestry Faculty, Nanjing Forestry University, Nanjing, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Sicheng Ye
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Linxiu Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Bingbing Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yongqing Cao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- *Correspondence: Renying Zhuo,
| | - Xiaohua Yao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Xiaohua Yao,
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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Hajiahmadi Z, Abedi A, Wei H, Sun W, Ruan H, Zhuge Q, Movahedi A. Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.). BMC Genomics 2020; 21:778. [PMID: 33167859 PMCID: PMC7653692 DOI: 10.1186/s12864-020-07199-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/27/2020] [Indexed: 12/28/2022] Open
Abstract
Backgrounds Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheat FAD gene family (TaFADs). Results 68 FAD genes were identified from the wheat genome. Based on the phylogenetic analysis, wheat FADs clustered into five subfamilies, including FAB2, FAD2/FAD6, FAD4, DES/SLD, and FAD3/FAD7/FAD8. The TaFADs were distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in the TaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47 TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related to TaFAB2.5, TaFAB2.12, TaFAB2.15, TaFAB2.17, TaFAB2.20, TaFAD2.1, TaFAD2.6, and TaFAD2.8 genes while the highest expression in response to temperature stress was related to TaFAD2.6, TaFAD2.8, TaFAB2.15, TaFAB2.17, and TaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses. Conclusions This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07199-1.
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Affiliation(s)
- Zahra Hajiahmadi
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, 4199613776, Iran
| | - Amin Abedi
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, 4199613776, Iran
| | - Hui Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Honghua Ruan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China.
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Technologies to Address Plant microRNA Functions. CONCEPTS AND STRATEGIES IN PLANT SCIENCES 2020. [DOI: 10.1007/978-3-030-35772-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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MicroRNAs and their targeted genes associated with phase changes of stem explants during tissue culture of tea plant. Sci Rep 2019; 9:20239. [PMID: 31882926 PMCID: PMC6934718 DOI: 10.1038/s41598-019-56686-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 12/13/2019] [Indexed: 11/08/2022] Open
Abstract
Elucidation of the molecular mechanism related to the dedifferentiation and redifferentiation during tissue culture will be useful for optimizing regeneration system of tea plant. In this study, an integrated sRNAome and transcriptome analyses were carried out during phase changes of the stem explant culture. Among 198 miRNAs and 8001 predicted target genes, 178 differentially expressed miRNAs and 4264 potential targets were screened out from explants, primary calli, as well as regenerated roots and shoots. According to KEGG analysis of the potential targets, pathway of "aminoacyl-tRNA biosynthesis", "proteasome" and "glutathione metabolism" was of great significance during the dedifferentiation, and pathway of "porphyrin and chlorophyll metabolism", "mRNA surveillance pathway", "nucleotide excision repair" was indispensable for redifferentiation of the calli. Expression pattern of 12 miRNAs, including csn-micR390e, csn-miR156b-5p, csn-miR157d-5p, csn-miR156, csn-miR166a-3p, csn-miR166e, csn-miR167d, csn-miR393c-3p, csn-miR394, csn-miR396a-3p, csn-miR396 and csn-miR396e-3p, was validated by qRT-PCR among 57 differentially expressed phase-specific miRNAs. Validation also confirmed that regulatory module of csn-miR167d/ERF3, csn-miR156/SPB1, csn-miR166a-3p/ATHB15, csn-miR396/AIP15A, csn-miR157d-5p/GST and csn-miR393c-3p/ATG18b might play important roles in regulating the phase changes during tissue culture of stem explants.
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