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Zheng L, Assane Hamidou A, Zhao X, Ouyang Z, Lin H, Li J, Zhang X, Luo K, Chen Y. Superoxide dismutase gene family in cassava revealed their involvement in environmental stress via genome-wide analysis. iScience 2023; 26:107801. [PMID: 37954140 PMCID: PMC10638475 DOI: 10.1016/j.isci.2023.107801] [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: 12/27/2022] [Revised: 07/29/2023] [Accepted: 08/29/2023] [Indexed: 11/14/2023] Open
Abstract
Superoxide dismutase (SOD) is a crucial metal-containing enzyme that plays a vital role in catalyzing the dismutation of superoxide anions, converting them into molecular oxygen and hydrogen peroxide, essential for enhancing plant stress tolerance. We identified 8 SOD genes (4 CSODs, 2 FSODs, and 2 MSODs) in cassava. Bioinformatics analyses provided insights into chromosomal location, phylogenetic relationships, gene structure, conserved motifs, and gene ontology annotations. MeSOD genes were classified into two groups through phylogenetic analysis, revealing evolutionary connections. Promoters of these genes harbored stress-related cis-elements. Duplication analysis indicated the functional significance of MeCSOD2/MeCSOD4 and MeMSOD1/MeMSOD2. Through qRT-PCR, MeCSOD2 responded to salt stress, MeMSOD2 to drought, and cassava bacterial blight. Silencing MeMSOD2 increased XpmCHN11 virulence, indicating MeMSOD2 is essential for cassava's defense against XpmCHN11 infection. These findings enhance our understanding of the SOD gene family's role in cassava and contribute to strategies for stress tolerance improvement.
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Affiliation(s)
- Linling Zheng
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Abdoulaye Assane Hamidou
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xuerui Zhao
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Zhiwei Ouyang
- HNU-ASU Joint International Tourism College, Hainan University, Haikou 570228, China
| | - Hongxin Lin
- Soil Fertilizer and Resources Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Junyi Li
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xiaofei Zhang
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Kai Luo
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
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Renganathan VG, Renuka R, Vanniarajan C, Raveendran M, Elangovan A. Selection and validation of reliable reference genes for quantitative real-time PCR in Barnyard millet (Echinochloa spp.) under varied abiotic stress conditions. Sci Rep 2023; 13:15573. [PMID: 37731036 PMCID: PMC10511452 DOI: 10.1038/s41598-023-40526-6] [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: 12/16/2022] [Accepted: 08/11/2023] [Indexed: 09/22/2023] Open
Abstract
Quantitative real-time polymerase chain reaction (RT-qPCR) using a stable reference gene is widely used for gene expression research. Barnyard millet (Echinochloa spp.) is an ancient crop in Asia and Africa that is widely cultivated for food and fodder. It thrives well under drought, salinity, cold, and heat environmental conditions, besides adapting to any soil type. To date, there are no gene expression studies performed to identify the potential candidate gene responsible for stress response in barnyard millet, due to lack of reference gene. Here, 10 candidate reference genes, Actin (ACT), α-tubulin (α-TUB), β-tubulin (β-TUB), RNA pol II (RP II), elongation factor-1 alpha (EF-1α), adenine phosphoribosyltransferase (APRT), TATA-binding protein-like factor (TLF), ubiquitin-conjugating enzyme 2 (UBC2), ubiquitin-conjugating enzyme E2L5 (UBC5) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were selected from mRNA sequences of E. crus-galli and E. colona var frumentacea. Five statistical algorithms (geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder) were applied to determine the expression stabilities of these genes in barnyard millet grown under four different abiotic stress (drought, salinity, cold and heat) exposed at different time points. The UBC5 and ɑ-TUB in drought, GAPDH in salinity, GAPDH and APRT in cold, and EF-1α and RP II in heat were the most stable reference genes, whereas ß-TUB was the least stable irrespective of stress conditions applied. Further Vn/Vn + 1 analysis revealed two reference genes were sufficient to normalize gene expression across all sample sets. The suitability of identified reference genes was validated with Cu-ZnSOD (SOD1) in the plants exposed to different abiotic stress conditions. The results revealed that the relative quantification of the SOD1 gene varied according to reference genes and the number of reference genes used, thus highlighting the importance of the choice of a reference gene in such experiments. This study provides a foundational framework for standardizing RT-qPCR analyses, enabling accurate gene expression profiling in barnyard millet.
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Affiliation(s)
- Vellaichamy Gandhimeyyan Renganathan
- Department of Biotechnology, Centre of Excellence for Innovations, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Raman Renuka
- Department of Biotechnology, Centre of Excellence for Innovations, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India.
| | - Chockalingam Vanniarajan
- Anbil Dharmalingam Agricultural College & Research Institute, Tamil Nadu Agricultural University, Tiruchirappalli, India
| | - Muthurajan Raveendran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Allimuthu Elangovan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
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Riyazuddin R, Singh K, Iqbal N, Labhane N, Ramteke P, Singh VP, Gupta R. Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107978. [PMID: 37660607 DOI: 10.1016/j.plaphy.2023.107978] [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: 04/04/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.
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Affiliation(s)
- Riyazuddin Riyazuddin
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary.
| | - Kalpita Singh
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary; Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, H-2462, Martonvásár, Hungary.
| | - Nadeem Iqbal
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, 6726, Szeged, Hungary; Doctoral School of Environmental Sciences, University of Szeged, Szeged, Hungary.
| | - Nitin Labhane
- Department of Botany, Bhavan's College Andheri West, Mumbai, 400058, India.
| | - Pramod Ramteke
- Department of Biotechnology, Dr. Ambedkar College, Nagpur, India.
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Ravi Gupta
- College of General Education, Kookmin University, 02707, Seoul, Republic of Korea.
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Waite JM, Kelly EA, Zhang H, Hargarten HL, Waliullah S, Altman NS, dePamphilis CW, Honaas LA, Kalcsits L. Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit. G3 (BETHESDA, MD.) 2023; 13:jkad120. [PMID: 37259608 PMCID: PMC10411604 DOI: 10.1093/g3journal/jkad120] [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: 12/20/2022] [Revised: 12/20/2022] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
Abstract
Apples grown in high heat, high light, and low humidity environments are at risk for sun injury disorders like sunburn and associated crop losses. Understanding the physiological and molecular mechanisms underlying sunburn will support improvement of mitigation strategies and breeding for more resilient varieties. Numerous studies have highlighted key biochemical processes involved in sun injury, such as the phenylpropanoid and reactive oxygen species (ROS) pathways, demonstrating both enzyme activities and expression of related genes in response to sunburn conditions. Most previous studies have focused on at-harvest activity of a small number of genes in response to heat stress. Thus, it remains unclear how stress events earlier in the season affect physiology and gene expression. Here, we applied heat stress to mid-season apples in the field and collected tissue along a time course-24, 48, and 72 h following a heat stimulus-to investigate dynamic gene expression changes using a transcriptomic lens. We found a relatively small number of differentially expressed genes (DEGs) and enriched functional terms in response to heat treatments. Only a few of these belonged to pathways previously described to be involved in sunburn, such as the AsA-GSH pathway, while most DEGs had not yet been implicated in sunburn or heat stress in pome fruit.
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Affiliation(s)
- Jessica M Waite
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, 1100 N. Western Ave., Wenatchee, WA, 98801, USA
| | - Elizabeth A Kelly
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, 101 Huck Life Sciences Building, University Park, PA, 16802, USA
| | - Huiting Zhang
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
- Department of Horticulture, Washington State University, 251 Clark Hall, Pullman, WA, 99164, USA
| | - Heidi L Hargarten
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
| | - Sumyya Waliullah
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, 1100 N. Western Ave., Wenatchee, WA, 98801, USA
- Department of Plant Pathology, University of Georgia, 2360 Rainwater Rd, Tifton, GA, 31798, USA
| | - Naomi S Altman
- Department of Statistics, The Huck Institutes of the Life Sciences, Pennsylvania State University, 312 Thomas Building, University Park, PA, 16802, USA
| | - Claude W dePamphilis
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, 101 Huck Life Sciences Building, University Park, PA, 16802, USA
| | - Loren A Honaas
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
| | - Lee Kalcsits
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, 1100 N. Western Ave., Wenatchee, WA, 98801, USA
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Zhang X, Liu K, Tang Q, Zeng L, Wu Z. Light Intensity Regulates Low-Temperature Adaptability of Tea Plant through ROS Stress and Developmental Programs. Int J Mol Sci 2023; 24:9852. [PMID: 37373002 DOI: 10.3390/ijms24129852] [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: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Low-temperature stress limits global tea planting areas and production efficiency. Light is another essential ecological factor that acts in conjunction with temperature in the plant life cycle. However, it is unclear whether the differential light environment affects the low temperature adaptability of tea plant (Camellia sect. Thea). In this study, tea plant materials in three groups of light intensity treatments showed differentiated characteristics for low-temperature adaptability. Strong light (ST, 240 μmol·m-2·s-1) caused the degradation of chlorophyll and a decrease in peroxidase (POD), superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and polyphenol oxidase (PPO) activities, as well as an increase in soluble sugar, soluble protein, malondialdehyde (MDA), and relative conductivity in tea leaves. In contrast, antioxidant enzyme activities, chlorophyll content, and relative conductivity were highest in weak light (WT, 15 μmol·m-2·s-1). Damage was observed in both ST and WT materials relative to moderate light intensity (MT, 160 μmol·m-2·s-1) in a frost resistance test. Chlorophyll degradation in strong light was a behavior that prevented photodamage, and the maximum photosynthetic quantum yield of PS II (Fv/Fm) decreased with increasing light intensity. This suggests that the browning that occurs on the leaf surface of ST materials through frost may have been stressed by the previous increase in reactive oxygen species (ROS). Frost intolerance of WT materials is mainly related to delayed tissue development and tenderness holding. Interestingly, transcriptome sequencing revealed that stronger light favors starch biosynthesis, while cellulose biosynthesis is enhanced in weaker light. It showed that light intensity mediated the form of carbon fixation in tea plant, and this was associated with low-temperature adaptability.
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Affiliation(s)
- Xin Zhang
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing 400715, China
- Integrative Science Center of Germplasm Creation, Southwest University, Chongqing 401329, China
- Tea Research Institute, Southwest University, Chongqing 400715, China
| | - Keyi Liu
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing 400715, China
- Integrative Science Center of Germplasm Creation, Southwest University, Chongqing 401329, China
- Tea Research Institute, Southwest University, Chongqing 400715, China
| | - Qianhui Tang
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing 400715, China
- Integrative Science Center of Germplasm Creation, Southwest University, Chongqing 401329, China
- Tea Research Institute, Southwest University, Chongqing 400715, China
| | - Liang Zeng
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing 400715, China
- Integrative Science Center of Germplasm Creation, Southwest University, Chongqing 401329, China
- Tea Research Institute, Southwest University, Chongqing 400715, China
| | - Zhijun Wu
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing 400715, China
- Integrative Science Center of Germplasm Creation, Southwest University, Chongqing 401329, China
- Tea Research Institute, Southwest University, Chongqing 400715, China
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6
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Miao X, Zhu W, Jin Q, Song Z, Li L. ZmHOX32 is related to photosynthesis and likely functions in plant architecture of maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1119678. [PMID: 37035059 PMCID: PMC10073575 DOI: 10.3389/fpls.2023.1119678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
HOX32, a member of the HD-ZIP III family, functions in the leaf morphogenesis and plant photosynthesis. However, the regulatory mechanism of HOX32 in maize has not been studied and the regulatory relationship in photosynthesis is unclear. We conducted a comprehensive study, including phylogenetic analysis, expression profiling at both transcriptome and translatome levels, subcellular localization, tsCUT&Tag, co-expression analysis, and association analysis with agronomic traits on HOX32 for the dissection of the functional roles of HOX32. ZmHOX32 shows conservation in plants. As expected, maize HOX32 protein is specifically expressed in the nucleus. ZmHOX32 showed constitutively expression at both transcriptome and translatome levels. We uncovered the downstream target genes of ZmHOX32 by tsCUT&Tag and constructed a cascaded regulatory network combining the co-expression networks. Both direct and indirect targets of ZmHOX32 showed significant gene ontology enrichment in terms of photosynthesis in maize. The association study suggested that ZmHOX32 plays an important role in regulation of plant architecture. Our results illustrate a complex regulatory network of HOX32 involving in photosynthesis and plant architecture, which deepens our understanding of the phenotypic variation in plants.
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Affiliation(s)
- Xinxin Miao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hongshan Laboratory, Wuhan, China
| | - Wanchao Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hongshan Laboratory, Wuhan, China
| | - Qixiao Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hongshan Laboratory, Wuhan, China
| | - Zemeng Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hongshan Laboratory, Wuhan, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hongshan Laboratory, Wuhan, China
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Molina G, Laino A, Arrighetti F, Lacava M, Romero S, Mijailovsky S, Garcia CF. Effect of the Insecticide Chlorpyrifos on Behavioral and Metabolic Aspects of the Spider Polybetes pythagoricus. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1293-1308. [PMID: 36919993 DOI: 10.1002/etc.5607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/09/2023] [Accepted: 03/13/2023] [Indexed: 05/09/2023]
Abstract
The toxicity of pesticides to organisms depends on the total amount of chemical exposure. Toxicity can be minimized if the organism recognizes the pesticide and alters its behavior. Furthermore, the physical barrier of cuticular hydrocarbons can prevent the entrance of the pesticide into the organism. Finally, if the pesticide enters the body, the organism experiences physiological changes favoring detoxification and the maintenance of homeostasis. We analyzed the behavioral and metabolic response of the spider Polybetes pythagoricus at different times of exposure to the organophosphate pesticide chlorpyrifos. First we observed that the individuals are capable of recognizing and avoiding surfaces treated with pesticides based on a behavioral analysis. Subsequently, we characterized cuticular hydrocarbons as a possible barrier against pesticides. Then we observed that the pesticide provoked histological damage, mainly at the level of the midgut diverticula. Finally, we analyzed the activity of several of the spider's enzymes linked to oxidative stress after exposure to chlorpyrifos for different lengths of time (6, 24, and 48 h). We observed that catalase activity was high at the start, whereas the activity of superoxide dismutase and glutathione S-transferase changed significantly at 48 h. Lipid peroxidation became high at 6 h, but decreased at 48 h. In conclusion, although P. pythagoricus can avoid contact with chlorpyrifos, this pesticide causes activation of the antioxidant system when it enters the body. Our results make a significant contribution to the ecotoxicology of spiders. Environ Toxicol Chem 2023;00:1-16. © 2023 SETAC.
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Affiliation(s)
- Gabriel Molina
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner,", La Plata, Argentina
| | - Aldana Laino
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner,", La Plata, Argentina
| | - Florencia Arrighetti
- Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Consejo National de Investigaciones Cientificas y Téchnicas, Buenos Aires, Argentina
| | - Mariangeles Lacava
- Centro Universitario de Rivera, Universidad de La República, Rivera, Uruguay
| | - Sofia Romero
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner,", La Plata, Argentina
| | - Sergio Mijailovsky
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner,", La Plata, Argentina
| | - Carlos Fernando Garcia
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner,", La Plata, Argentina
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Genome-Wide Identification of Superoxide Dismutase and Expression in Response to Fruit Development and Biological Stress in Akebia trifoliata: A Bioinformatics Study. Antioxidants (Basel) 2023; 12:antiox12030726. [PMID: 36978974 PMCID: PMC10045841 DOI: 10.3390/antiox12030726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Akebia trifoliata is a newly domesticated perennial fruit tree, and the lack of molecular research on stress resistance seriously affects its genetic improvement and commercial value development. Superoxide dismutase (SOD) can effectively eliminate the accumulation of reactive oxygen species (ROS) during the rapid growth of plant organs under biotic and abiotic stresses, maintaining a steady state of physiological metabolism. In this study, 13 SODs consisting of two FeSODs (FSDs), four MnSODs (MSDs) and seven Cu/ZnSODs (CSDs) were identified in the A. trifoliata genome. Structurally, the phylogeny, intron–exon pattern and motif sequences within these three subfamilies show high conservation. Evolutionarily, segmental/wide genome duplication (WGD) and dispersed duplication form the current SOD profile of A. trifoliata. Weighted gene coexpression network analysis (WGCNA) revealed the metabolic pathways of nine (69.2%) SODs involved in fruit development, among which AktMSD4 regulates fruit development and AktCSD4 participates in the stress response. In addition, under the stress of multiple pathogens, six (46.6%) SODs were continuously upregulated in the rinds of resistant lines; of these, three SODs (AktMSD1, AktMSD2 and AktMSD3) were weakly or not expressed in susceptible lines. The results pave the way for theoretical research on SODs and afford the opportunity for genetic improvement of A. trifoliata.
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Biosynthesized Ag nanoparticles on urea-based periodic mesoporous organosilica enhance galegine content in Galega. Appl Microbiol Biotechnol 2023; 107:1589-1608. [PMID: 36738339 DOI: 10.1007/s00253-023-12414-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 02/05/2023]
Abstract
The biological approach for synthesizing nanoparticles (NPs) using plant extracts is an efficient alternative to conventional physicochemical methods. Galegine, isolated from Galega (Galega officinalis L.), has anti-diabetic properties. In the present study, silver nanoparticles (AgNPs) loaded onto urea-based periodic mesoporous organosilica (AgNPs/Ur-PMO) were bio-synthesized using G. officinalis leaf extract. The synthesized NPs were characterized and confirmed via analysis methods. Different concentrations of biosynthesized AgNPs/Ur-PMO nanoparticles (0, 1, 5, 10, and 20 mg L-1) were used as elicitors in cell suspension culture (CSC) of G. officinalis. The callus cells from hypocotyl explants were treated at their logarithmic growth phase (8th d) and were collected at time intervals of 24, 72, 120, and 168 h. The viability and growth of cells were reduced (by 17% and 35%, respectively) at higher concentrations and longer treatments of AgNPs/Ur-PMO; however, the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA) were increased (1.23 and 3.01 fold, respectively in comparison with the control average). The highest total phenolic (2.43 mg g-1 dry weight) and flavonoid (2.22 mg g-1 dry weight) contents were obtained 168 h after treatment with 10 mg L-1 AgNPs/Ur-PMO. An increasing tendency in the antioxidant enzyme activities was also observed in all the elicitor concentrations. Treatment with AgNPs/Ur-PMO (in particular 5 mg L-1 for 120 h) significantly enhanced the galegine content (up to 17.42 mg g-1) about 1.80 fold compared with the control. The results suggest that AgNPs/Ur-PMO can be used as an effective elicitor for enhancing galegine production in the CSC of G. officinalis. KEY POINTS: • The green biosynthesis of AgNPs/Ur-PMO was done using G. officinalis leaf extract • Its toxicity as an elicitor increased with increasing concentration and treatment time • AgNPs/Ur-PMO significantly increased the antioxidant capacity and galegine content.
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Li L, Guo B, Feng C, Liu H, Lin D. Growth, physiological, and temperature characteristics in chinese cabbage pakchoi as affected by Cd- stressed conditions and identifying its main controlling factors using PLS model. BMC PLANT BIOLOGY 2022; 22:571. [PMID: 36476235 PMCID: PMC9727860 DOI: 10.1186/s12870-022-03966-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Although hormesis induced by heavy metals is a well-known phenomenon, the involved biological mechanisms are not fully understood. Cadmium (Cd) is a prevalent heavy metal in the environment. Exposure of Cd, via intake or consumption of Cd-contaminated air or food, poses a huge threat to human health. Chinese cabbage pakchoi (Brassica chinensis L.) is widely planted and consumed as a popular vegetable in China. Therefore, studying the response of Chinese cabbage pakchoi to Cd- stressed conditions is critical to assess whether cabbage can accumulate Cd and serve as an important Cd exposure pathway to human beings. In this study, we investigated the influence of Cd stress on growth, photosynthetic physiology, antioxidant enzyme activities, nutritional quality, anatomical structure, and canopy temperature in Chinese cabbage pakchoi. A partial least squares (PLS) model was used to quantify the relationship between physical and chemical indicators with Cd accumulation in cabbage, and identify the main controlling factors. RESULTS Results showed that Cd stress significantly inhibited cabbage's growth and development. When Cd stress was increased, the phenotypic indicators were significantly reduced. Meanwhile, Cd stress significantly enhanced the oxidative stress response of cabbage, such as the activities of catalase (CAT), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), and the content of malondialdehyde (MDA) in leaves. Such a change tended to increase fenestrated tissues' thickness but decrease the thickness of leaf and spongy tissues. Moreover, Cd stress significantly increased soluble sugar, protein, and vitamin C contents in leaves as well as the temperature in the plant canopy. The PLS model analysis showed that the studied phenotypic and physicochemical indicators had good relationships with Cd accumulation in roots, shoots, and the whole plant of cabbage, with high coefficient of determination (R2) values of 0.891, 0.811, and 0.845, and low relative percent deviation (RPD) values of 3.052, 2.317, and 2.557, respectively. Furthermore, through analyzing each parameter's variable importance for projection (VIP) value, the SOD activity was identified as a key factor for indicating Cd accumulation in cabbage. Meanwhile, the effects of CAT on Cd accumulation in cabbage and the canopy mean temperature were also high. CONCLUSION Cd stress has significant inhibitory effects and can cause damage cabbage's growth and development, and the SOD activity may serve as a key factor to indicate Cd uptake and accumulation in cabbage.
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Affiliation(s)
- Lantao Li
- College of Resources and Environment, Henan Agricultural University, 450002, Zhengzhou, China
| | - Binglin Guo
- College of Forestry, Henan Agricultural University, No. 63 Nongye Road., Jinshui District, 450002, Zhengzhou, China
| | - Chenchen Feng
- College of Forestry, Henan Agricultural University, No. 63 Nongye Road., Jinshui District, 450002, Zhengzhou, China
| | - Haitao Liu
- College of Resources and Environment, Henan Agricultural University, 450002, Zhengzhou, China
| | - Di Lin
- College of Forestry, Henan Agricultural University, No. 63 Nongye Road., Jinshui District, 450002, Zhengzhou, China.
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11
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Yu W, Kong G, Chao J, Yin T, Tian H, Ya H, He L, Zhang H. Genome-wide identification of the rubber tree superoxide dismutase ( SOD) gene family and analysis of its expression under abiotic stress. PeerJ 2022; 10:e14251. [PMID: 36312747 PMCID: PMC9610661 DOI: 10.7717/peerj.14251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
Background The rubber tree (Hevea brasiliensis) is the only species capable of producing high-quality natural rubber for commercial use, and is often subjected to various abiotic stresses in non-traditional rubber plantation areas. Superoxide dismutase (SOD) is a vital metalloenzyme translated by a SOD gene family member and acts as a first-line of protection in plant cells by catalysing the disproportionation of reactive oxygen species (ROS) to produce H2O2 and O2. However, the SOD gene family is not reported in rubber trees. Methods Here, we used hidden markov model (HMM) and BLASTP methods to identify SOD genes in the H. brasiliensis genome. Phylogenetic tree, conserved motifs, gene structures, cis elements, and gene ontology annotation (GO) analyses were performed using MEGA 6.0, MEME, TBtools, PlantCARE, and eggNOG database, respectively. HbSOD gene expression profiles were analysed using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results We identified nine HbSOD genes in the rubber tree genome, including five HbCSDs, two HbFSDs, and two HbMSDs. Phylogenetic relationship analysis classified the SOD proteins from the rubber tree and other related species into three subfamilies. The results of gene structure and conserved motif analysis illustrated that most HbSOD genes have similar exon-intron numbers and conserved motifs in the same evolutionary branch. Five hormone-related, four stress-related, and light-responsive elements were detected in the HbSODs' promoters. HbSODs were expressed in different tissues, gradually increased with leaf development, and were abundantly expressed in mature leaves. HbCSD2 and HbCSD4 was significantly upregulated under low and high temperatures, and salt stress, except for HbCSD2, by heat. Furthermore, most HbSOD genes were significantly upregulated by drought, except HbMSD2. These findings imply that these genes may play vital roles in rubber tree stress resistance. Our results provide a basis for further studies on the functions of HbSOD genes in rubber trees and stress response mechanisms.
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Affiliation(s)
- Wencai Yu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China,Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Guanghong Kong
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Jinquan Chao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan Province, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China
| | - Hai Tian
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Huajin Ya
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Ligang He
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China
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12
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Niu YF, Li GH, Zheng C, Liu ZY, Liu J. Insights to the superoxide dismutase genes and its roles in Hevea brasiliensis under abiotic stress. 3 Biotech 2022; 12:274. [PMID: 36110566 PMCID: PMC9468202 DOI: 10.1007/s13205-022-03328-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
The superoxide dismutase (SOD) protein significantly influences the development and growth of plants and their reaction to abiotic stresses. However, little is known about the characteristics of rubber tree SOD genes and their expression changes under abiotic stresses. The present study recognized 11 SOD genes in the rubber tree genome, including 7 Cu/ZnSODs, 2 MnSODs, and 2 FeSODs. Except for HbFSD1, SODs were scattered on five chromosomes. The phylogenetic analysis of SOD proteins in rubber trees and a few other plants demonstrated that the SOD proteins contained three major subgroups. Moreover, the genes belonging to the same clade contained similar gene structures, which confirmed their classification further. The extension of the SOD gene family in the rubber tree was mainly induced by the segmental duplication events. The cis-acting components analysis showed that HbSODs were utilized in many biological procedures. The transcriptomics data indicated that the phosphorylation of the C-terminal domain of RNA polymerase II might control the cold response genes through the CBF pathway and activate the SOD system to respond to cold stress. The qRT-PCR results showed that the expression of HbCSD1 was significantly downregulated under drought and salt stresses, which might dominate the adaption capability to different stresses. Additionally, salt promoted the expression levels of HbMSD1 and HbMSD2, exhibiting their indispensable role in the salinity reaction. The study results will provide a theoretical basis for deep research on HbSODs in rubber trees. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03328-7.
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Affiliation(s)
- Ying-Feng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Guo-Hua Li
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Cheng Zheng
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Zi-Yan Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
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13
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Study on the biocontrol effect and physiological mechanism of Hannaella sinensis on the blue mold decay of apples. Int J Food Microbiol 2022; 382:109931. [PMID: 36137461 DOI: 10.1016/j.ijfoodmicro.2022.109931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/26/2022] [Accepted: 09/11/2022] [Indexed: 11/23/2022]
Abstract
Blue mold decay is a major postharvest disease of apples, causing considerable losses to the apple industry. In the early stage of this research, an antagonistic yeast, Hannaella sinensis, with a good control effect on the blue mold of apples, was selected. On this basis, the main purpose of this work was to study the biocontrol effect of H. sinensis on the blue mold of apples and the mechanisms involved. The results showed that H. sinensis could effectively control the blue mold decay of apples, reduce the rot rate and diameter, and the antagonistic effect strengthened with the increase of H. sinensis concentration (1 × 108 cells/mL). Further in vitro experiments proved that H. sinensis could significantly inhibit the spore germination and germ tube length of P. expansum. In addition, stable colonization of H. sinensis on apple wounds and surfaces confirmed the environmental adaptability and the ability to compete with other microbiota for nutrition and space. Moreover, H. sinensis induced the activities of resistance-related enzymes such as polyphenol oxidase (PPO), peroxidase (POD), ascorbate peroxidase (APX), superoxide dismutase (SOD), and phenylalanine ammonia-lyase (PAL) in apples and the content of the coding genes corresponding to these enzymes was also higher than that of the control group. Our results indicate that H. sinensis treatment could induce the disease resistance of apples. In summary, H. sinensis served as a promising antagonistic yeast for the prevention and treatment of postharvest blue mold decay of apples.
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14
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Saud S, Wang L. Mechanism of cotton resistance to abiotic stress, and recent research advances in the osmoregulation related genes. FRONTIERS IN PLANT SCIENCE 2022; 13:972635. [PMID: 36061778 PMCID: PMC9428623 DOI: 10.3389/fpls.2022.972635] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/25/2022] [Indexed: 05/27/2023]
Abstract
Abiotic stress is an important factor affecting the normal growth and development of plants and crop yield. To reduce the impact of abiotic adversity on cotton growth and development, the material basis of cotton resistance and its physiological functions are analyzed at the molecular level. At the same time, the use of genetic engineering methods to recombine resistance genes has become a hot spot in cotton resistance research. This paper provides an overviews of the resistance mechanism of cotton against the threat of non-biological adversity, as well as the research progress of osmoregulation-related genes, protein-acting genes, and transcription regulatory factor genes in recent years, and outlines the explored gene resources in cotton resistance genetic engineering, with the aim to provide ideas and reference bases for future research on cotton resistance.
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15
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Zameer R, Fatima K, Azeem F, ALgwaiz HIM, Sadaqat M, Rasheed A, Batool R, Shah AN, Zaynab M, Shah AA, Attia KA, AlKahtani MDF, Fiaz S. Genome-Wide Characterization of Superoxide Dismutase (SOD) Genes in Daucus carota: Novel Insights Into Structure, Expression, and Binding Interaction With Hydrogen Peroxide (H 2O 2) Under Abiotic Stress Condition. FRONTIERS IN PLANT SCIENCE 2022; 13:870241. [PMID: 35783965 PMCID: PMC9246500 DOI: 10.3389/fpls.2022.870241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/08/2022] [Indexed: 05/27/2023]
Abstract
Superoxide dismutase (SOD) proteins are important antioxidant enzymes that help plants to grow, develop, and respond to a variety of abiotic stressors. SOD gene family has been identified in a number of plant species but not yet in Daucus carota. A total of 9 DcSOD genes, comprising 2 FeSODs, 2 MnSODs, and 5 Cu/ZnSODs, are identified in the complete genome of D. carota, which are dispersed in five out of nine chromosomes. Based on phylogenetic analysis, SOD proteins from D. carota were categorized into two main classes (Cu/ZnSODs and MnFeSODs). It was predicted that members of the same subgroups have the same subcellular location. The phylogenetic analysis was further validated by sequence motifs, exon-intron structure, and 3D protein structures, with each subgroup having a similar gene and protein structure. Cis-regulatory elements responsive to abiotic stresses were identified in the promoter region, which may contribute to their differential expression. Based on RNA-seq data, tissue-specific expression revealed that DcCSD2 had higher expression in both xylem and phloem. Moreover, DcCSD2 was differentially expressed in dark stress. All SOD genes were subjected to qPCR analysis after cold, heat, salt, or drought stress imposition. SODs are antioxidants and play a critical role in removing reactive oxygen species (ROS), including hydrogen peroxide (H2O2). DcSODs were docked with H2O2 to evaluate their binding. The findings of this study will serve as a basis for further functional insights into the DcSOD gene family.
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Affiliation(s)
- Roshan Zameer
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Kinza Fatima
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Hussah I. M. ALgwaiz
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Muhammad Sadaqat
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Asima Rasheed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Riffat Batool
- Department of Botany, GC Women University, Faisalabad, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Anis Ali Shah
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Kotb A. Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Muneera D. F. AlKahtani
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
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16
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Huo C, He L, Yu T, Ji X, Li R, Zhu S, Zhang F, Xie H, Liu W. The Superoxide Dismutase Gene Family in Nicotiana tabacum: Genome-Wide Identification, Characterization, Expression Profiling and Functional Analysis in Response to Heavy Metal Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:904105. [PMID: 35599861 PMCID: PMC9121019 DOI: 10.3389/fpls.2022.904105] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/11/2022] [Indexed: 05/27/2023]
Abstract
Superoxide dismutases (SODs) play an important role in protecting plants against ROS toxicity induced by biotic and abiotic stress. Recent studies have shown that the SOD gene family is involved in plant growth and development; however, knowledge of the SOD gene family in tobacco is still limited. In the present study, the SOD gene family was systematically characterized in the tobacco genome. Based on the conserved motif and phylogenetic tree, 15 NtSOD genes were identified and classified into three subgroups, including 5 NtCSDs, 7 NtFSDs and 3 NtMSDs. The predicted results of the transport peptide or signal peptide were consistent with their subcellular localization. Most NtSOD genes showed relatively well-maintained exon-intron and motif structures in the same subgroup. An analysis of cis-acting elements in SOD gene promoters showed that NtSOD expression was regulated by plant hormones, defense and stress responses, and light. In addition, multiple transcription factors and miRNAs are predicted to be involved in the regulation of NtSOD gene expression. The qPCR results indicated specific spatial and temporal expression patterns of the NtSOD gene family in different tissues and developmental stages, and this gene family played an important role in protecting against heavy metal stress. The results of functional complementation tests in the yeast mutant suggested that NtCSD1a, NtFSD1e and NtMSD1b scavenge ROS produced by heavy metal stress. This study represents the first genome-wide analysis of the NtSOD gene family, which lays a foundation for a better understanding of the function of the NtSOD gene family and improving the tolerance of plants to heavy metal toxicity.
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Affiliation(s)
- Chunsong Huo
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, China
| | - Linshen He
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, China
| | - Ting Yu
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, China
| | - Xue Ji
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, China
| | - Rui Li
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, China
| | - Shunqin Zhu
- School of Life Sciences, Southwest University, Chongqing, China
| | - Fangyuan Zhang
- School of Life Sciences, Southwest University, Chongqing, China
| | - He Xie
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Wanhong Liu
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, China
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Genome-Wide Investigation of the MiR166 Family Provides New Insights into Its Involvement in the Drought Stress Responses of Tea Plants (Camellia sinensis (L.) O. Kuntze). FORESTS 2022. [DOI: 10.3390/f13040628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
MicroRNA166 (miR166) is a highly conserved plant miRNA that plays a crucial role in plant growth and the resistance to various abiotic stresses. However, the miR166s in tea (Camellia sinensis (L.) O. Kuntze) have not been comprehensively identified and analyzed. This study identified 30 mature miR166s and twelve pre-miR166s in tea plants. An evolutionary analysis revealed that csn-miR166s originating from the 3′ arm of their precursors were more conserved than the csn-miR166s derived from the 5′ arm of their precursors. The twelve pre-miR166s in tea were divided into two groups, with csn-MIR166 Scaffold364-2 separated from the other precursors. The Mfold-based predictions indicated that the twelve csn-MIR166s formed typical and stable structures comprising a stem-loop hairpin, with minimum free energy ranging from −110.90 to −71.80 kcal/mol. An analysis of the CsMIR166 promoters detected diverse cis-acting elements, including those related to light responses, biosynthesis and metabolism, abiotic stress defenses, and hormone responses. There was no one-to-one relationship between the csn-miR166s and their targets, but most csn-miR166s targeted HD-Zip III genes. Physiological characterization of tea plants under drought stress showed that leaf water content proportionally decreased with the aggravation of drought stress. In contrast, tea leaves’ malondialdehyde (MDA) content proportionally increased. Moreover, the cleavage site of the ATHB-15-like transcript was identified according to a modified 5′ RNA ligase-mediated rapid amplification of cDNA ends. The RT-qPCR data indicated that the transcription of nine csn-miR166s was negatively correlated with their target gene.
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18
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Aleem M, Aleem S, Sharif I, Wu Z, Aleem M, Tahir A, Atif RM, Cheema HMN, Shakeel A, Lei S, Yu D, Wang H, Kaushik P, Alyemeni MN, Bhat JA, Ahmad P. Characterization of SOD and GPX Gene Families in the Soybeans in Response to Drought and Salinity Stresses. Antioxidants (Basel) 2022; 11:antiox11030460. [PMID: 35326109 PMCID: PMC8944523 DOI: 10.3390/antiox11030460] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 12/31/2022] Open
Abstract
Plant stresses causing accumulation of reactive oxidative species (ROS) are scavenged by effective antioxidant defense systems. Therefore, the present study performed genome-wide identification of superoxide dismutase (SOD) and glutathione peroxidase (GPX) gene families in cultivated and wild soybeans, and 11 other legume species. We identified a total of 101 and 95 genes of SOD and GPX, respectively, across thirteen legume species. The highest numbers of SODs and GPXs were identified in cultivated (Glycine max) and wild (Glycine soja). A comparative phylogenetic study revealed highest homology among the SODs and GPXs of cultivated and wild soybeans relative to other legumes. The exon/intron structure, motif and synteny blocks were conserved in both soybean species. According to Ka/Ks, purifying the selection played the major evolutionary role in these gene families, and segmental duplication are major driving force for SODs and GPXs expansion. In addition, the qRT-PCR analysis of the G. max and G. soja SOD and GPX genes revealed significant differential expression of these genes in response to oxidative, drought and salinity stresses in root tissue. In conclusion, our study provides new insights for the evolution of SOD and GPX gene families in legumes, and provides resources for further functional characterization of these genes for multiple stresses.
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Affiliation(s)
- Muqadas Aleem
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad 38040, Pakistan;
| | - Saba Aleem
- Barani Agricultural Research Station, Fatehjang 43350, Pakistan;
| | - Iram Sharif
- Cotton Research Station, Ayub Agricultural Research Institute, Faisalabad 38040, Pakistan;
| | - Zhiyi Wu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
| | - Maida Aleem
- Department of Botany, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Ammara Tahir
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
| | - Rana Muhammad Atif
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad 38040, Pakistan;
| | - Hafiza Masooma Naseer Cheema
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38040, Pakistan; (H.M.N.C.); (A.S.)
| | - Amir Shakeel
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38040, Pakistan; (H.M.N.C.); (A.S.)
| | - Sun Lei
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
- Correspondence: (D.Y.); (H.W.); (J.A.B.); (P.A.)
| | - Hui Wang
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
- Correspondence: (D.Y.); (H.W.); (J.A.B.); (P.A.)
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Mohammed Nasser Alyemeni
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 12546, Saudi Arabia;
| | - Javaid Akhter Bhat
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
- Correspondence: (D.Y.); (H.W.); (J.A.B.); (P.A.)
| | - Parvaiz Ahmad
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 12546, Saudi Arabia;
- Correspondence: (D.Y.); (H.W.); (J.A.B.); (P.A.)
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Punia Bangar S, Trif M, Ozogul F, Kumar M, Chaudhary V, Vukic M, Tomar M, Changan S. Recent developments in cold plasma-based enzyme activity (browning, cell wall degradation, and antioxidant) in fruits and vegetables. Compr Rev Food Sci Food Saf 2022; 21:1958-1978. [PMID: 35080794 DOI: 10.1111/1541-4337.12895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 12/24/2022]
Abstract
According to the Food and Agriculture Organization of United Nations reports, approximately half of the total harvested fruits and vegetables vanish before they reach the end consumer due to their perishable nature. Enzymatic browning is one of the most common problems faced by fruit and vegetable processing. The perishability of fruits and vegetables is contributed by the various browning enzymes (polyphenol oxidase, peroxidase, and phenylalanine ammonia-lyase) and ripening or cell wall degrading enzyme (pectin methyl-esterase). In contrast, antioxidant enzymes (superoxide dismutase and catalase) assist in reversing the damage caused by reactive oxygen species or free radicals. The cold plasma technique has emerged as a novel, economic, and environmentally friendly approach that reduces the expression of ripening and browning enzymes while increasing the activity of antioxidant enzymes; microorganisms are significantly inhibited, therefore improving the shelf life of fruits and vegetables. This review narrates the mechanism and principle involved in the use of cold plasma technique as a nonthermal agent and its application in impeding the activity of browning and ripening enzymes and increasing the expression of antioxidant enzymes for improving the shelf life and quality of fresh fruits and vegetables and preventing spoilage and pathogenic germs from growing. An overview of hurdles and sustainability advantages of cold plasma technology is presented.
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Affiliation(s)
- Sneh Punia Bangar
- Department of Food, Nutrition and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
| | - Monica Trif
- Food Research Department, Centre for Innovative Process Engineering (Centiv) GmbH, Stuhr, Germany.,CENCIRA Agrofood Research and Innovation Centre, Cluj-Napoca, Romania
| | - Fatih Ozogul
- Department of Seafood Processing Technology, Faculty of Fisheries, Cukurova University, Adana, Turkey
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, India
| | - Vandana Chaudhary
- Department of Dairy Technology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Milan Vukic
- Faculty of Technology Zvornik, University of East Sarajevo, Zvornik, Bosnia and Herzegovina
| | - Maharishi Tomar
- Seed Technology Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Sushil Changan
- Division of Crop Physiology, Biochemistry and Post-Harvest Technology, ICAR-Central Potato Research Institute, Shimla, India
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20
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Iqbal Qureshi AM, Sofi MU, Dar NA, Khan MH, Mahdi SS, Dar ZA, Bangroo S, El-Serehy HA, Hefft DI, Popescu SM. Insilco identification and characterization of superoxide dismutase gene family in Brassica rapa. Saudi J Biol Sci 2021; 28:5526-5537. [PMID: 34588862 PMCID: PMC8459115 DOI: 10.1016/j.sjbs.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/18/2021] [Accepted: 08/01/2021] [Indexed: 01/17/2023] Open
Abstract
Superoxide Dismutase SODs are defense associated proteins that detoxify ROS and primarily serve as scavengers. They have been described in numerous plant species, but their in-depth characterization in Brassica rapa has not been reported. Therefore, the present investigation on genome wide study of SOD gene family was conducted to identify BrSOD genes, their domain-based organization, gene structure analysis, phylogenetic analysis, intron-exon structure of genes and expression analysis. The sequence characterization of Super oxide dismutase gene family in Brassica rapa, their syntenic associateship of conserved motifs and phylogenetic correlationship, prediction of cis-elements and determing the expression analysis in distinct tissues namely plant callus, root, stem, leaf, flower, and silique under abiotic conditions have been analysed using different software’s. The study on SOD gene family identified 17 BrSOD genes which were grouped into eight BrCu-ZnSODs and nine BrFe-MnSODs domain-based organization. Furthermore, the conserved character of BrSODs were confirmed by intron-exon organisation, motif arrangements and domain architectural investigations. Expression analysis using RNA Sequence data of different developmental stages proclaimed that genes were manifested in all six tissues with an exception of BrCu-ZnSOD3, which was not manifested in roots; however, whose transcript was detected in all other tested tissues. The study has genome wide insight into the occurrence and functional specifications of BrSOD gene family in Brassica rapa that can be potentially utilized in breeding program for resilience to climate change and abiotic stresses tolerance Brassica variety.
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Affiliation(s)
- Asif M Iqbal Qureshi
- ARSSSS, Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Mehraj Uddin Sofi
- HMAARI, Leh, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - N A Dar
- ARSSSS, Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - M H Khan
- ARSSSS, Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - S S Mahdi
- Division of Agronomy, FoA Wadura, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Zahoor A Dar
- DARS, Rangreth, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Shabir Bangroo
- Division of Soil Sciences, FoH, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Hamed A El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyad, 11451, Saudi Arabia
| | - Daniel Ingo Hefft
- University Centre Reaseheath, Reaseheath College, Nantwich CW5 6DF, UK
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, 200585, Romania
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21
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Yan C, Zhang N, Wang Q, Fu Y, Wang F, Su Y, Xue B, Zhou L, Liao H. The Effect of Low Temperature Stress on the Leaves and MicroRNA Expression of Potato Seedlings. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.727081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In recent years, with the wanton destruction of the ecological environment by humans and the frequent occurrence of extreme bad weather, many places that should have been warm and blooming in spring have instead experienced the phenomenon of the “April blizzard,” which has seriously affected China's crops, especially spring potato production in most areas. Potato cultivars, especially potato seedlings, are sensitive to frost, and low temperature frost has become one of the most important abiotic stresses affecting potato production. Potato cold tolerance is regulated by a complex gene network. Although some low temperature resistant microRNAs have been identified, little is known about the role of miRNAs in response to low temperature stress in potato. Therefore, the objective of this study is to clarify the influence of low temperature stress on the miRNA expression of potato by comparing the expression differences of miRNA in potato which was treated with different low temperatures. For the study, 307 known miRNAs belonging to 73 small RNA families and 211 novel miRNAs were obtained. When the temperature decreased, the number of both known and novel miRNA decreased, and the minimum temperature was −2°C. Most of the miRNAs respond to low temperature, drought, and disease stress; some conserved miRNAs were first found to respond to low temperature stress in potato, such as stu-miR530, stu-miR156d, and stu-miR167b. The Gene Ontology, Kyoto Encyclopedia of Genes, and Genomes pathway enrichment analysis of 442 different expression miRNAs target genes indicated that there existed diversified low temperature responsive pathways, but Abscisic Acid was found likely to play a central coordinating role in response to low temperature stress in many metabolism pathways. Quantitative real-time PCR assays indicated that the related targets were negatively regulated by the tested different expression miRNAs during low temperature stress. The results indicated that miRNAs may play an important coordination role in response to low temperature stress in many metabolic pathways by regulating abscisic acid and gibberellin, which provided insight into the roles of miRNAs during low temperature stress and would be helpful for alleviating low temperature stress and promoting low temperature resistant breeding in potatoes.
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22
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Progressive Genomic Approaches to Explore Drought- and Salt-Induced Oxidative Stress Responses in Plants under Changing Climate. PLANTS 2021; 10:plants10091910. [PMID: 34579441 PMCID: PMC8471759 DOI: 10.3390/plants10091910] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 11/17/2022]
Abstract
Drought and salinity are the major environmental abiotic stresses that negatively impact crop development and yield. To improve yields under abiotic stress conditions, drought- and salinity-tolerant crops are key to support world crop production and mitigate the demand of the growing world population. Nevertheless, plant responses to abiotic stresses are highly complex and controlled by networks of genetic and ecological factors that are the main targets of crop breeding programs. Several genomics strategies are employed to improve crop productivity under abiotic stress conditions, but traditional techniques are not sufficient to prevent stress-related losses in productivity. Within the last decade, modern genomics studies have advanced our capabilities of improving crop genetics, especially those traits relevant to abiotic stress management. This review provided updated and comprehensive knowledge concerning all possible combinations of advanced genomics tools and the gene regulatory network of reactive oxygen species homeostasis for the appropriate planning of future breeding programs, which will assist sustainable crop production under salinity and drought conditions.
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23
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Ji HS, Bang SG, Ahn MA, Kim G, Kim E, Eom SH, Hyun TK. Molecular Cloning and Functional Characterization of Heat Stress-Responsive Superoxide Dismutases in Garlic ( Allium sativum L.). Antioxidants (Basel) 2021; 10:antiox10050815. [PMID: 34065356 PMCID: PMC8161062 DOI: 10.3390/antiox10050815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/26/2022] Open
Abstract
Superoxide dismutases (SODs) are key antioxidant enzymes that can detoxify the superoxide radicals generated by various stresses. Although various plant SODs have been suggested to improve stress tolerance, SODs in garlic, an economically important vegetable grown worldwide, remain relatively unknown. In this study, we found that heat stress strongly induced the activities of Cu/ZnSODs, FeSODs, and MnSODs in garlic leaves. In addition, we cloned four garlic SODs (AsSODs) and suggest that heat stress-increased SOD activity was reflected at least by the induction of these AsSODs. The results of the agro-infiltration assay suggested that the cloned AsSODs encoded functional SOD enzymes belonging to the Cu/ZnSOD and MnSOD families. As a first step toward understanding the enzymatic antioxidant system in garlic plants, our results provide a solid foundation for an in-depth analysis of the physiological functions of the AsSOD family.
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24
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Rajput VD, Harish, Singh RK, Verma KK, Sharma L, Quiroz-Figueroa FR, Meena M, Gour VS, Minkina T, Sushkova S, Mandzhieva S. Recent Developments in Enzymatic Antioxidant Defence Mechanism in Plants with Special Reference to Abiotic Stress. BIOLOGY 2021; 10:267. [PMID: 33810535 PMCID: PMC8066271 DOI: 10.3390/biology10040267] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/12/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022]
Abstract
The stationary life of plants has led to the evolution of a complex gridded antioxidant defence system constituting numerous enzymatic components, playing a crucial role in overcoming various stress conditions. Mainly, these plant enzymes are superoxide dismutase (SOD), catalase (CAT), peroxidase (POX), glutathione peroxidase (GPX), glutathione reductase (GR), glutathione S-transferases (GST), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), and dehydroascorbate reductase (DHAR), which work as part of the antioxidant defence system. These enzymes together form a complex set of mechanisms to minimise, buffer, and scavenge the reactive oxygen species (ROS) efficiently. The present review is aimed at articulating the current understanding of each of these enzymatic components, with special attention on the role of each enzyme in response to the various environmental, especially abiotic stresses, their molecular characterisation, and reaction mechanisms. The role of the enzymatic defence system for plant health and development, their significance, and cross-talk mechanisms are discussed in detail. Additionally, the application of antioxidant enzymes in developing stress-tolerant transgenic plants are also discussed.
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Affiliation(s)
- Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia; (T.M.); (S.S.); (S.M.)
| | - Harish
- Department of Botany, Mohan Lal Sukhadia University, Udaipur, Rajasthan 313001, India;
| | - Rupesh Kumar Singh
- Centro de Química de Vila Real, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China;
| | - Lav Sharma
- Centre for the Research and Technology of Agro-Environment and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal;
| | - Francisco Roberto Quiroz-Figueroa
- Laboratorio de Fitomejoramiento Molecular, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional Unidad Sinaloa (CIIDIR-IPN Unidad Sinaloa), Instituto Politécnico Nacional, Blvd. Juan de Dios Bátiz Paredes no. 250, Col. San Joachín, C.P., 81101 Guasave, Mexico;
| | - Mukesh Meena
- Department of Botany, Mohan Lal Sukhadia University, Udaipur, Rajasthan 313001, India;
| | - Vinod Singh Gour
- Amity Institute of Biotechnology, Amity University Rajasthan, NH 11C, Kant Kalwar, Jaipur 303002, India;
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia; (T.M.); (S.S.); (S.M.)
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia; (T.M.); (S.S.); (S.M.)
| | - Saglara Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia; (T.M.); (S.S.); (S.M.)
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25
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Wang H, Ding Z, Gou M, Hu J, Wang Y, Wang L, Wang Y, Di T, Zhang X, Hao X, Wang X, Yang Y, Qian W. Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress. BMC Genomics 2021; 22:121. [PMID: 33596831 PMCID: PMC7891152 DOI: 10.1186/s12864-021-07419-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/31/2021] [Indexed: 12/12/2022] Open
Abstract
Background Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants. Results In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency. Conclusions We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07419-2.
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Affiliation(s)
- Huan Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhaotang Ding
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Mengjie Gou
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jianhui Hu
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yu Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lu Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Yuchun Wang
- College of Agriculture and Food Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Taimei Di
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Xinfu Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xinyuan Hao
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Xinchao Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Yajun Yang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Wenjun Qian
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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26
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Krishnatreya DB, Agarwala N, Gill SS, Bandyopadhyay T. Understanding the role of miRNAs for improvement of tea quality and stress tolerance. J Biotechnol 2021; 328:34-46. [PMID: 33421509 DOI: 10.1016/j.jbiotec.2020.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/04/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are an emerging class of small non-coding RNAs that exhibit important role in regulation of gene expression, mostly through the mechanism of cleavage and/or inhibition of translation of target mRNAs during or after transcription. Although much has been unravelled about the role of miRNAs in diverse biological processes like maintenance of functional integrity of genes and genome, growth and development, metabolism, and adaptive responses towards biotic and abiotic stresses in plants, not much is known on their specific roles in majority of cash crops - an area of investigation with potentially significant and gainful economic implications. Tea (Camellia sinensis) is globally the second most consumed beverage after water and its cultivation has major agro-economic and social ramifications. In recent years, global tea production has been greatly challenged by many biotic and abiotic stress factors and a deeper understanding of molecular processes regulating stress adaptation in this largely under investigated crop stands to significantly facilitate potential crop improvement strategies towards durable stress tolerance. This review endeavours to highlight recent advances in our understanding of the role of miRNAs in regulating stress tolerance traits in tea plant with additional focus on their role in determining tea quality attributes.
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Affiliation(s)
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam, 781014, India.
| | - Sarvajeet Singh Gill
- Center for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
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27
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Li J, Liu S, Chen P, Cai J, Tang S, Yang W, Cao F, Zheng P, Sun B. Systematic Analysis of the R2R3-MYB Family in Camellia sinensis: Evidence for Galloylated Catechins Biosynthesis Regulation. FRONTIERS IN PLANT SCIENCE 2021; 12:782220. [PMID: 35046974 PMCID: PMC8762170 DOI: 10.3389/fpls.2021.782220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/15/2021] [Indexed: 05/08/2023]
Abstract
The R2R3-MYB transcription factor (TF) family regulates metabolism of phenylpropanoids in various plant lineages. Species-expanded or specific MYB TFs may regulate species-specific metabolite biosynthesis including phenylpropanoid-derived bioactive products. Camellia sinensis produces an abundance of specialized metabolites, which makes it an excellent model for digging into the genetic regulation of plant-specific metabolite biosynthesis. The most abundant health-promoting metabolites in tea are galloylated catechins, and the most bioactive of the galloylated catechins, epigallocatechin gallate (EGCG), is specifically relative abundant in C. sinensis. However, the transcriptional regulation of galloylated catechin biosynthesis remains elusive. This study mined the R2R3-MYB TFs associated with galloylated catechin biosynthesis in C. sinensis. A total of 118 R2R3-MYB proteins, classified into 38 subgroups, were identified. R2R3-MYB subgroups specific to or expanded in C. sinensis were hypothesized to be essential to evolutionary diversification of tea-specialized metabolites. Notably, nine of these R2R3-MYB genes were expressed preferentially in apical buds (ABs) and young leaves, exactly where galloylated catechins accumulate. Three putative R2R3-MYB genes displayed strong correlation with key galloylated catechin biosynthesis genes, suggesting a role in regulating biosynthesis of epicatechin gallate (ECG) and EGCG. Overall, this study paves the way to reveal the transcriptional regulation of galloylated catechins in C. sinensis.
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28
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Zhu C, Zhang S, Zhou C, Xie S, Chen G, Tian C, Xu K, Lin Y, Lai Z, Guo Y. Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea ( Camellia sinensis) Leaves During Withering Process. FRONTIERS IN PLANT SCIENCE 2021; 12:702303. [PMID: 34211493 PMCID: PMC8240813 DOI: 10.3389/fpls.2021.702303] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/24/2021] [Indexed: 05/12/2023]
Abstract
N6-methyladenosine (m6A), one of the internal modifications of RNA molecules, can directly influence RNA abundance and function without altering the nucleotide sequence, and plays a pivotal role in response to diverse environmental stresses. The precise m6A regulatory mechanism comprises three types of components, namely, m6A writers, erasers, and readers. To date, the research focusing on m6A regulatory genes in plant kingdom is still in its infancy. Here, a total of 34 m6A regulatory genes were identified from the chromosome-scale genome of tea plants. The expansion of m6A regulatory genes was driven mainly by whole-genome duplication (WGD) and segmental duplication, and the duplicated gene pairs evolved through purifying selection. Gene structure analysis revealed that the sequence variation contributed to the functional diversification of m6A regulatory genes. Expression pattern analysis showed that most m6A regulatory genes were differentially expressed under environmental stresses and tea-withering stage. These observations indicated that m6A regulatory genes play essential roles in response to environmental stresses and tea-withering stage. We also found that RNA methylation and DNA methylation formed a negative feedback by interacting with each other's methylation regulatory genes. This study provided a foundation for understanding the m6A-mediated regulatory mechanism in tea plants under environmental stresses and tea-withering stage.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siyi Xie
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guangwu Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Caiyun Tian
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Zhongxiong Lai,
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
- Yuqiong Guo,
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29
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Silva SAF, Silva FLB, Ribas AF, de Souza SGH, dos Santos TB. Genome-wide in silico analysis of SOD genes in common bean (Phaseolus vulgaris L.). ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s12892-020-00030-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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Zhu C, Zhang S, Zhou C, Chen L, Fu H, Li X, Lin Y, Lai Z, Guo Y. Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant ( Camellia sinensis) under abiotic stress and withering processing. PeerJ 2020; 8:e8432. [PMID: 31976183 PMCID: PMC6968495 DOI: 10.7717/peerj.8432] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. In the plant kingdom, cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes have been identified in some plant species. However, to the best of our knowledge, no investigator has focused on the identification and analysis of C5-MTase and dMTase genes in tea plants (Camellia sinensis) based on genome-wide levels. In this study, eight CsC5-MTases and four dMTases were identified in tea plants. These CsC5-MTase genes were divided into four subfamilies, including CsMET, CsCMT, CsDRM and CsDNMT2. The CsdMTase genes can be classified into CsROS, CsDME and CsDML. Based on conserved domain analysis of these genes, the gene loss and duplication events occurred during the evolution of CsC5-MTase and CsdMTase. Furthermore, multiple cis-acting elements were observed in the CsC5-MTase and CsdMTase, including light responsiveness, phytohormone responsiveness, stress responsiveness, and plant growth and development-related elements. Then, we investigated the transcript abundance of CsC5-MTase and CsdMTase under abiotic stress (cold and drought) and withering processing (white tea and oolong tea). Notably, most CsC5-MTases, except for CsCMT1 and CsCMT2, were significantly downregulated under abiotic stress, while the transcript abundance of all four CsdMTase genes was significantly induced. Similarly, the same transcript abundance of CsC5-MTase and CsdMTase was found during withering processing of white tea and oolong tea, respectively. In total, our findings will provide a basis for the roles of CsC5-MTase and CsdMTase in response to abiotic stress and the potential functions of these two gene families in affecting tea flavor during tea withering processing.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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31
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Xia EH, Tong W, Wu Q, Wei S, Zhao J, Zhang ZZ, Wei CL, Wan XC. Tea plant genomics: achievements, challenges and perspectives. HORTICULTURE RESEARCH 2020; 7:7. [PMID: 31908810 PMCID: PMC6938499 DOI: 10.1038/s41438-019-0225-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 05/18/2023]
Abstract
Tea is among the world's most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.
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Affiliation(s)
- En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
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Zhu C, Zhang S, Fu H, Zhou C, Chen L, Li X, Lin Y, Lai Z, Guo Y. Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea ( Camellia sinensis) in Solar-Withering. FRONTIERS IN PLANT SCIENCE 2019; 10:1638. [PMID: 31929782 PMCID: PMC6941427 DOI: 10.3389/fpls.2019.01638] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/20/2019] [Indexed: 05/08/2023]
Abstract
Oolong tea is a popular and semi-fermented beverage. During the processing of tea leaves, withering is the first indispensable process for improving flavor. However, the roles of long non-coding RNAs (lncRNAs) and the characteristic secondary metabolites during the withering of oolong tea leaves remain unknown. In this study, phytochemical analyses indicated that total polyphenols, flavonoids, catechins, epigallocatechin (EGC), catechin gallate (CG), gallocatechin gallate (GCG), epicatechin gallate (ECG), and epigallocatechin gallate (EGCG) were all less abundant in the solar-withered leaves (SW) than in the fresh leaves (FL) and indoor-withered leaves (IW). In contrast, terpenoid, jasmonic acid (JA), and methyl jasmonate (MeJA) contents were higher in the SW than in the FL and IW. By analyzing the transcriptome data, we detected 32,036 lncRNAs. On the basis of the Kyoto Encyclopedia of Genes and Genomes analysis, the flavonoid metabolic pathway, the terpenoid metabolic pathway, and the JA/MeJA biosynthesis and signal transduction pathway were enriched pathways. Additionally, 63 differentially expressed lncRNAs (DE-lncRNAs) and 23 target genes were identified related to the three pathways. A comparison of the expression profiles of the DE-lncRNAs and their target genes between the SW and IW revealed four up-regulated genes (FLS, CCR, CAD, and HCT), seven up-regulated lncRNAs, four down-regulated genes (4CL, CHI, F3H, and F3'H), and three down-regulated lncRNAs related to flavonoid metabolism; nine up-regulated genes (DXS, CMK, HDS, HDR, AACT, MVK, PMK, GGPPS, and TPS), three up-regulated lncRNAs, and six down-regulated lncRNAs related to terpenoid metabolism; as well as six up-regulated genes (LOX, AOS, AOC, OPR, ACX, and MFP2), four up-regulated lncRNAs, and three down-regulated lncRNAs related to JA/MeJA biosynthesis and signal transduction. These results suggested that the expression of DE-lncRNAs and their targets involved in the three pathways may be related to the low abundance of the total polyphenols, flavonoids, and catechins (EGC, CG, GCG, ECG, and EGCG) and the high abundance of terpenoids in the SW. Moreover, solar irradiation, high JA and MeJA contents, and the endogenous target mimic (eTM)-related regulatory mechanism in the SW were also crucial for increasing the terpenoid levels. These findings provide new insights into the greater contribution of solar-withering to the high-quality flavor of oolong tea compared with the effects of indoor-withering.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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