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Liu G, Li H, Fu D. Applications of virus-induced gene silencing for identification of gene function in fruit. FOOD QUALITY AND SAFETY 2021. [DOI: 10.1093/fqsafe/fyab018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Abstract
With the development of bioinformatics, it is easy to obtain information and data about thousands of genes, but the determination of the functions of these genes depends on methods for rapid and effective functional identification. Virus-induced gene silencing (VIGS) is a mature method of gene functional identification developed over the last 20 years, which has been widely used in many research fields involving many species. Fruit quality formation is a complex biological process, which is closely related to ripening. Here, we review the progress and contribution of VIGS to our understanding of fruit biology and its advantages and disadvantages in determining gene function.
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2
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Shu P, Min D, Zhou J, Ai W, Li J, Li Z, Zhang X, Shi Z, Sun Y, Li F, Li X, Guo Y. The Synergism of 1-Methylcyclopropene and Ethephon Preserves Quality of "Laiyang" Pears With Recovery of Aroma Formation After Long-Term Cold Storage. FRONTIERS IN PLANT SCIENCE 2020; 11:490. [PMID: 32523587 PMCID: PMC7261920 DOI: 10.3389/fpls.2020.00490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
A "Laiyang" pear is a climacteric fruit with a special taste and nutritional value but is prone to a post-harvest aroma compound loss and a loss in fruit quality. In this study, pears were pretreated with 0.5 μl L-1 1-methylcyclopropene (1-MCP) at 20°C for 12 h and then stored at 0 ± 1°C for 150 days to evaluate the influence of 1-MCP on fruit quality and the changes in components of volatile aromas. In addition, pears were further treated with 2 mmol L-1 ethephon. The effects of ethephon on the recovery of aroma production were investigated during the 150 day storage at 0 ± 1°C and the subsequent 7 day shelf life at 20 ± 1°C. Treatment with 1-MCP inhibited firmness loss, increased electrical conductivity, reduced respiration and ethylene production rates as well as the contents of soluble solids, and maintained the storage quality of the fruits. However, 1-MCP treatment inhibited the emission of volatile aromas in pear fruits by decreasing the activities of various enzymes, such as lipoxygenase (LOX), hydroperoxide lyase (HPL), alcohol dehydrogenase (ADH), pyruvate carboxylase (PDC), and alcohol acetyltransferase (AAT). During the shelf-life, activities of the above mentioned enzymes were significantly enhanced, and a higher content of volatile aromas were found in fruits treated with 1-MCP + ethephon, while other qualities were not compromised. These results showed that 1-MCP treatment could effectively maintain the quality of the "Laiyang" pear during cold storage, and the additional application of ethephon on fruits during shelf-life may be a promising way to restore volatile aromas in pear fruits after long-term storage.
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Affiliation(s)
| | | | | | | | | | | | - Xinhua Zhang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | | | | | - Fujun Li
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
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Zhao X, Yuan X, Chen S, Fu DQ, Jiang CZ. Metabolomic and Transcriptomic Analyses Reveal That a MADS-Box Transcription Factor TDR4 Regulates Tomato Fruit Quality. FRONTIERS IN PLANT SCIENCE 2019; 10:792. [PMID: 31275340 PMCID: PMC6593160 DOI: 10.3389/fpls.2019.00792] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/31/2019] [Indexed: 05/18/2023]
Abstract
Tomato fruit ripening is a complex process, which determines the formation of fruit quality. Many factors affect fruit ripening, including environmental conditions and genetic factors. Transcription factors (TFs) play key roles in regulating fruit ripening and quality formation. Current studies have found that the TDR4 gene is an important TF for tomato fruit ripening, but its effects on fruit metabolism and quality are less well studied. In this study, suppression of TDR4 gene expression obtained through virus-induced gene silencing (VIGS) technology resulted in an orange pericarp phenotype. Transcriptomic analysis of TDR4-silenced fruit showed changes in the expression of genes involved in various metabolic pathways, including amino acid and flavonoid biosynthesis pathways. Metabolomic analysis showed that levels of several amino acids including phenylalanine and tyrosine, and organic acids were reduced in TDR4-silenced fruit, while α-tomatine accumulated in TDR4-silenced fruit. Taken together, our RNA-seq and metabolomics analyses of TDR4-silenced fruit showed that TDR4 is involved in ripening and nutrient synthesis in tomato fruit, and is therefore an important regulator of fruit quality.
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Affiliation(s)
- Xiaodan Zhao
- School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, China
- *Correspondence: Xiaodan Zhao,
| | - Xinyu Yuan
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Sha Chen
- Institute of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Da-Qi Fu
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, United States
- Cai-Zhong Jiang,
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Clark S, Yu F, Gu L, Min XJ. Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato. FRONTIERS IN PLANT SCIENCE 2019; 10:689. [PMID: 31191588 PMCID: PMC6546887 DOI: 10.3389/fpls.2019.00689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/08/2019] [Indexed: 05/17/2023]
Abstract
Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice).
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Affiliation(s)
- Sarah Clark
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, United States
| | - Feng Yu
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiang Jia Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, United States
- *Correspondence: Xiang Jia Min,
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Mata CI, Fabre B, Parsons HT, Hertog MLATM, Van Raemdonck G, Baggerman G, Van de Poel B, Lilley KS, Nicolaï BM. Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2018; 9:1626. [PMID: 30467512 PMCID: PMC6235968 DOI: 10.3389/fpls.2018.01626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/18/2018] [Indexed: 05/18/2023]
Abstract
Ethylene, the plant ripening hormone of climacteric fruit, is perceived by ethylene receptors which is the first step in the complex ethylene signal transduction pathway. Much progress has been made in elucidating the mechanism of this pathway, but there is still a lot to be done in the proteomic quantification of the main proteins involved, particularly during fruit ripening. This work focuses on the mass spectrometry based identification and quantification of the ethylene receptors (ETRs) and the downstream components of the pathway, CTR-like proteins (CTRs) and ETHYLENE INSENSITIVE 2 (EIN2). We used tomato as a model fruit to study changes in protein abundance involved in the ethylene signal transduction during fruit ripening. In order to detect and quantify these low abundant proteins located in the membrane of the endoplasmic reticulum, we developed a workflow comprising sample fractionation and MS analysis using parallel reaction monitoring. This work shows the feasibility of the identification and absolute quantification of all seven ethylene receptors, three out of four CTRs and EIN2 in four ripening stages of tomato. In parallel, gene expression was analyzed through real-time qPCR. Correlation between transcriptomic and proteomic profiles during ripening was only observed for three of the studied proteins, suggesting that the other signaling proteins are likely post-transcriptionally regulated. Based on our quantification results we were able to show that the protein levels of SlETR3 and SlETR4 increased during ripening, probably to control ethylene sensitivity. The other receptors and CTRs showed either stable levels that could sustain, or decreasing levels that could promote fruit ripening.
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Affiliation(s)
- Clara I. Mata
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Bertrand Fabre
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Harriet T. Parsons
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Maarten L. A. T. M. Hertog
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Geert Van Raemdonck
- Centre for Proteomics and Mass Spectrometry, University of Antwerp, Antwerp, Belgium
| | - Geert Baggerman
- Centre for Proteomics and Mass Spectrometry, University of Antwerp, Antwerp, Belgium
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Bram Van de Poel
- Molecular Plant Hormone Physiology, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Bart M. Nicolaï
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
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Zhan Y, Qu Y, Zhu L, Shen C, Feng X, Yu C. Transcriptome analysis of tomato (Solanum lycopersicum L.) shoots reveals a crosstalk between auxin and strigolactone. PLoS One 2018; 13:e0201124. [PMID: 30044859 PMCID: PMC6059464 DOI: 10.1371/journal.pone.0201124] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 07/09/2018] [Indexed: 11/22/2022] Open
Abstract
Auxin and strigolactone (SL) are two important phytohormones involved in shoot branching and morphology. Tomato (Solanum lycopersicum L.), a member of the Solanaceae family, is one of the most popular food crops with high economic value in the world. To seek a better understanding of the responses to exogenous hormones, transcriptome analyses of the tomato shoots treated with exogenous auxin and SL, separately or together, were performed. A total of 2326, 260 and 1379 differential expressed genes (DEGs) were identified under the IAA, GR24 and IAA+GR24 treatments, respectively. Network analysis pointed out two enriched interaction clusters, including “ethylene biosynthesis” and “photosynthesis”. Several ethylene biosynthesis and metabolism-related genes were up-regulated under both IAA and IAA+GR24 treatments, suggesting their involvement in the regulation of ethylene biosynthesis. Besides, auxin-SLs-triggered the expression of several CAB genes may lead to systemic increases in the induction of photosynthesis. Several auxin-activated metabolic pathways could be reduced by the GR24 treatment, indicated that the crosstalk between auxin and SLs may be involved in the metabolic regulation of tomato. Further analysis showed that SLs affect the responses of tomato shoots to auxin by inducing the expression of a series of auxin downstream genes. On the other hand, auxin regulated the biosynthesis of SLs by affecting the genes in the “Carotenoid biosynthesis” pathway. Our data will give us an opportunity to reveal the crosstalk between auxin and SLs in the shoots of tomato.
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Affiliation(s)
- Yihua Zhan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yinchao Qu
- Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Longjing Zhu
- Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang, China
| | - Chenjia Shen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Xuping Feng
- College of Life Sciences, China Jiliang University, Hangzhou, People’s Republic of China
- * E-mail: (XF); (CY)
| | - Chenliang Yu
- Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (XF); (CY)
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Zhao X, Yuan X, Chen S, Meng L, Fu D. Role of the tomato TAGL1 gene in regulating fruit metabolites elucidated using RNA sequence and metabolomics analyses. PLoS One 2018; 13:e0199083. [PMID: 29894500 PMCID: PMC5997326 DOI: 10.1371/journal.pone.0199083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/31/2018] [Indexed: 01/08/2023] Open
Abstract
Fruit ripening is a complex biological process affecting fruit quality. In tomato the fruit ripening process is delicately regulated by transcription factors (TFs). Among these, the TOMATO AGAMOUS-LIKE 1 (TAGL1) gene plays an important role in both the development and ripening of fruit. In this study, the TAGL1 gene was successfully silenced by virus-induced gene silencing technology (VIGS), and the global gene expression and metabolites profiles of TAGL1-silenced fruits were analyzed by RNA-sequence analysis (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS/MS). The TAGL1-silenced fruits phenotypically displayed an orange pericarp, which was in accordance with the results expected from the down-regulation of genes associated with carotenoid synthesis. Levels of several amino acids and organic acids were lower in the TAGL1-silenced fruits than in the wild-type fruits, whereas, α-tomatine content was greatly increased (more than 10-fold) in the TAGL1-silenced fruits compared to wild-type fruits. The findings of this study showed that TAGL1 not only regulates the ripening of tomato fruits, but also affects the synthesis and levels of nutrients in the fruit.
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Affiliation(s)
- Xiaodan Zhao
- School of Food and Chemical Engineering, Beijing Technology and Business University, Haidian District, Beijing, China
- * E-mail:
| | - Xinyu Yuan
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Sha Chen
- Institute of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanhuan Meng
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Daqi Fu
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
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Zuo J, Wang Y, Zhu B, Luo Y, Wang Q, Gao L. Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit. Genes (Basel) 2018; 9:genes9050266. [PMID: 29883429 PMCID: PMC5977206 DOI: 10.3390/genes9050266] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an essential feature of epigenetic regulation and plays a role in various physiological and biochemical processes at CG, CHG, and CHH sites in plants. LeERF1 is an ethylene response factor (ERF) found in tomatoes which plays an important role in ethylene signal transduction. To explore the characteristics of DNA methylation in the ethylene pathway, sense-/antisense-LeERF1 transgenic tomato fruit were chosen for deep sequencing and bioinformatics parsing. The methylation type with the greatest distribution was CG, (71.60–72.80%) and CHH was found least frequently (10.70–12.50%). The level of DNA methylation was different among different tomato genomic regions. The differentially methylated regions (DMRs) and the differentially expressed genes (DEGs) were conjointly analyzed and 3030 different expressed genes were found, of which several are involved in ethylene synthesis and signaling transduction (such as ACS, ACO, MADS-Box, ERFs, and F-box). Furthermore, the relationships between DNA methylation and microRNAs (miRNAs) were also deciphered, providing basic information for the further study of DNA methylation and small RNAs involved in the ethylene pathway.
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Affiliation(s)
- Jinhua Zuo
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY 14853, USA.
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China.
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Qing Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Lipu Gao
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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