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Zaman F, Khattak WA, Ihtisham M, Ilyas M, Ali A, Ali A, Khan H, Khan KA, Ni D, Zhao H, Chen FS. Assessing the health risks of heavy metals and seasonal minerals fluctuations in Camellia sinensis cultivars during their growth seasons. Food Chem Toxicol 2024; 187:114586. [PMID: 38493978 DOI: 10.1016/j.fct.2024.114586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
The risk assessment of heavy metals in tea is extremely imperative for the health of tea consumers. However, the effects of varietal variations and seasonal fluctuations on heavy metals and minerals in tea plants remain unclear. Inductively coupled plasma optical emission spectrometry (ICP-OES) was used to evaluate the contents of aluminum (Al), manganese (Mn), magnesium (Mg), boron (B), calcium (Ca), copper (Cu), cobalt (Co), iron (Fe), sodium (Na), zinc (Zn), arsenic (As), cadmium (Cd), chromium (Cr), nickel (Ni), and antimony (Sb) in the two categories of young leaves (YL) and mature leaves (ML) of tea (Camellia sinensis) cultivars throughout the growing seasons. The results showed significant variations in the contents of the investigated nutrients both among the different cultivars and growing seasons as well. Furthermore, the average concentrations of Al, Mn, Mg, B, Ca, Cu, Co, Fe, Na, Zn, As, Cd, Cr, Ni, and Sb in YL ranged, from 671.58-2209.12, 1260.58-1902.21, 2290.56-2995.36, 91.18-164.68, 821.95-5708.20, 2.55-3.80, 3.96-25.22, 37.95-202.84, 81.79-205.05, 27.10-69.67, 0.028-0.053, 0.065-0.127, 2.40-3.73, 10.57-12.64, 0.11-0.14 mg kg-1, respectively. In ML, the concentrations were 2626.41-7834.60, 3980.82-6473.64, 3335.38-4537.48, 327.33-501.70, 9619.89-13153.68, 4.23-8.18, 17.23-34.20, 329.39-567.19, 145.36-248.69, 40.50-81.42, 0.089-0.169, 0.23-0.27, 5.24-7.89, 18.51-23.97, 0.15-0.19 mg kg-1, respectively. The contents of all analyzed nutrients were found to be higher in ML than in YL. Target hazard quotients (THQ) of As, Cd, Cr, Ni, and Sb, as well as the hazard index (HI), were all less than one, suggesting no risk to human health via tea consumption. This research might provide the groundwork for essential minerals recommendations, as well as a better understanding and management of heavy metal risks in tea.
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Affiliation(s)
- Fawad Zaman
- Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China; National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wajid Ali Khattak
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Muhammad Ihtisham
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, 644000, China
| | - Muhammad Ilyas
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Abbas Ali
- Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haroon Khan
- Department of Weed Science and Botany, The University of Agriculture, Peshawar, Pakistan
| | - Khalid Ali Khan
- Applied College, Center of Bee Research and Its Products, Unit of Bee Research and Honey Production, Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Dejiang Ni
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hua Zhao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Fu-Sheng Chen
- Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
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Yao X, Chen H, Zhang B, Lu L. Transcriptome Analysis Reveals Differentially Expressed Genes Involved in Aluminum, Copper and Cadmium Accumulation in Tea 'Qianmei 419' and 'Qianfu 4'. PLANTS (BASEL, SWITZERLAND) 2023; 12:2580. [PMID: 37447140 DOI: 10.3390/plants12132580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
Tea, as a global nonalcoholic beverage, is widely consumed due to its economic, health and cultural importance. Polyploids have the ability to solve the problems of low yield, cold resistance and insect resistance in tea tree varieties. However, the response mechanism to aluminum and heavy metal remains unclear. In this study, the content of Al, Cu and Cd were measured in the leaves and roots of 'Qianmei 419' and 'Qianfu 4', respectively. The content of Al, Cd and Cu in the roots of the 'Qianmei 419' tea variety were significantly higher than in 'Qianfu 4' roots. Only the content of Cu in the leaves of the 'Qianmei 419' tea variety was significantly higher than that in the roots of the 'Qianfu 4' tea variety. Moreover, we found that the content of Al, Cu and Cd in the soil around the root of 'Qianfu 4' were higher than in the soil around the root of 'Qianmei 419'. RNA-seq was performed to identify the DEGs involved in the accumulation of Al, Cu and Cd between 'Qianmei 419' and 'Qianfu 4'. A total of 23,813 DEGs were identified in the triploid tea variety, including 16,459 upregulated DEGs and 7354 downregulated DEGs. Among them, by analyzing the expression levels of some metal transporter genes, it was found that most of the metal transporter genes were downregulated in the triploid tea plants. In short, through the analysis of transcriptome data and metal content, it was found that changes in metal transporter gene expression affect the accumulation of metals in tea plants. These results provide candidate genes to enhance multi-metal tolerance through genetic engineering technology.
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Affiliation(s)
- Xinzhuan Yao
- Institute of Plant Health & Medicine, College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Hufang Chen
- Institute of Plant Health & Medicine, College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Baohui Zhang
- Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Litang Lu
- Institute of Plant Health & Medicine, College of Tea Sciences, Guizhou University, Guiyang 550025, China
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Aluminum and Fluoride Stresses Altered Organic Acid and Secondary Metabolism in Tea ( Camellia sinensis) Plants: Influences on Plant Tolerance, Tea Quality and Safety. Int J Mol Sci 2023; 24:ijms24054640. [PMID: 36902071 PMCID: PMC10003434 DOI: 10.3390/ijms24054640] [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: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Tea plants have adapted to grow in tropical acidic soils containing high concentrations of aluminum (Al) and fluoride (F) (as Al/F hyperaccumulators) and use secret organic acids (OAs) to acidify the rhizosphere for acquiring phosphorous and element nutrients. The self-enhanced rhizosphere acidification under Al/F stress and acid rain also render tea plants prone to accumulate more heavy metals and F, which raises significant food safety and health concerns. However, the mechanism behind this is not fully understood. Here, we report that tea plants responded to Al and F stresses by synthesizing and secreting OAs and altering profiles of amino acids, catechins, and caffeine in their roots. These organic compounds could form tea-plant mechanisms to tolerate lower pH and higher Al and F concentrations. Furthermore, high concentrations of Al and F stresses negatively affected the accumulation of tea secondary metabolites in young leaves, and thereby tea nutrient value. The young leaves of tea seedlings under Al and F stresses also tended to increase Al and F accumulation in young leaves but lower essential tea secondary metabolites, which challenged tea quality and safety. Comparisons of transcriptome data combined with metabolite profiling revealed that the corresponding metabolic gene expression supported and explained the metabolism changes in tea roots and young leaves via stresses from high concentrations of Al and F. The study provides new insight into Al- and F-stressed tea plants with regard to responsive metabolism changes and tolerance strategy establishment in tea plants and the impacts of Al/F stresses on metabolite compositions in young leaves used for making teas, which could influence tea nutritional value and food safety.
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Garcia K, Cloghessy K, Cooney DR, Shelley B, Chakraborty S, Kafle A, Busidan A, Sonawala U, Collier R, Jayaraman D, Ané JM, Pilot G. The putative transporter MtUMAMIT14 participates in nodule formation in Medicago truncatula. Sci Rep 2023; 13:804. [PMID: 36646812 PMCID: PMC9842706 DOI: 10.1038/s41598-023-28160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/13/2023] [Indexed: 01/17/2023] Open
Abstract
Transport systems are crucial in many plant processes, including plant-microbe interactions. Nodule formation and function in legumes involve the expression and regulation of multiple transport proteins, and many are still uncharacterized, particularly for nitrogen transport. Amino acids originating from the nitrogen-fixing process are an essential form of nitrogen for legumes. This work evaluates the role of MtN21 (henceforth MtUMAMIT14), a putative transport system from the MtN21/EamA-like/UMAMIT family, in nodule formation and nitrogen fixation in Medicago truncatula. To dissect this transporter's role, we assessed the expression of MtUMAMIT14 using GUS staining, localized the corresponding protein in M. truncatula root and tobacco leaf cells, and investigated two independent MtUMAMIT14 mutant lines. Our results indicate that MtUMAMIT14 is localized in endosomal structures and is expressed in both the infection zone and interzone of nodules. Comparison of mutant and wild-type M. truncatula indicates MtUMAMIT14, the expression of which is dependent on the presence of NIN, DNF1, and DNF2, plays a role in nodule formation and nitrogen-fixation. While the function of the transporter is still unclear, our results connect root nodule nitrogen fixation in legumes with the UMAMIT family.
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Affiliation(s)
- Kevin Garcia
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695-7619, USA.
| | - Kaylee Cloghessy
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Biological Sciences, The University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Danielle R Cooney
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695-7619, USA
| | - Brett Shelley
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Arjun Kafle
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695-7619, USA
| | - Aymeric Busidan
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Unnati Sonawala
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Ray Collier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Molecular Technologies Department, Wisconsin Crop Innovation Center, University of Wisconsin-Madison, Madison, WI, 53562, USA
| | | | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Guillaume Pilot
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24060, USA
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Brhane H, Haileselassie T, Tesfaye K, Ortiz R, Hammenhag C, Abreha KB, Vetukuri RR, Geleta M. Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources. FRONTIERS IN PLANT SCIENCE 2022; 13:1068383. [PMID: 36570897 PMCID: PMC9780683 DOI: 10.3389/fpls.2022.1068383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/21/2022] [Indexed: 06/01/2023]
Abstract
Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet's genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Al-susceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet. RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.
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Affiliation(s)
- Haftom Brhane
- Biology Department, Aksum University, Aksum, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | | | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kibrom B. Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Niu E, Gao S, Yu X, Soleimani A, Zhu S. Comprehensive evaluation of the response to aluminum stress in olive tree ( Olea europaea L.). FRONTIERS IN PLANT SCIENCE 2022; 13:968499. [PMID: 35968113 PMCID: PMC9366337 DOI: 10.3389/fpls.2022.968499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/05/2022] [Indexed: 06/06/2023]
Abstract
Olive (Olea europaea L.) is an ancient tree species in the Mediterranean, but the lack of knowledge about aluminum-resistant varieties limits its introduction to acidic soil. The objective of this study was to have a comprehensive evaluation of the response to aluminum stress in olive tree at germplasm, metabolome, and transcriptome levels. In this experiment, seedlings of 97 olive germplasm with 1.0-3.0 cm roots and two leaves were treated with 50 μM Al3+ (pH = 5.0). By factor analysis of the traits of defoliation rate, rooting rate, length of extended root, and length of new root, 97 germplasm were classified into five different groups according to their diverse responses to aluminum stress: 5 highly resistant (5.15%), 30 moderately resistant (30.93%), 31 general (31.96%), 23 moderately sensitive (23.71%), and 8 highly sensitive (8.25%) germplasm. The three most sensitive and three most resistant germplasm were further used for metabolome and transcriptome analysis. Exposed to aluminum stress, 96 differentially accumulated metabolites (DAMs)/4,845 differentially expressed genes (DEGs) and 66 DAMs/2,752 DEGs were identified in highly sensitive and resistant germplasm, respectively. Using multi-omics technology, the pathways and related DAMs/DEGs involved in cell wall/cytoplasm receptors, reactive oxygen species balance, hormone induction, synthesis of organic acids, Al3+ transport, and synthesis of metabolites were identified to mainly regulate the response to aluminum stress in olive. This study provides a theoretical guide and prior germplasm and genes for further genetic improvement of aluminum tolerance in the olive tree.
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Affiliation(s)
- Erli Niu
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Song Gao
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaomin Yu
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ali Soleimani
- Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Shenlong Zhu
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Tea (Camellia sinensis): A Review of Nutritional Composition, Potential Applications, and Omics Research. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12125874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tea (Camelliasinensis) is the world’s most widely consumed non-alcoholic beverage with essential economic and health benefits since it is an excellent source of polyphenols, catechins, amino acids, flavonoids, carotenoids, vitamins, and polysaccharides. The aim of this review is to summarize the main secondary metabolites in tea plants, and the content and distribution of these compounds in six different types of tea and different organs of tea plant were further investigated. The application of these secondary metabolites on food processing, cosmetics industry, and pharmaceutical industry was reviewed in this study. With the rapid advancements in biotechnology and sequencing technology, omics analyses, including genome, transcriptome, and metabolome, were widely used to detect the main secondary metabolites and their molecular regulatory mechanisms in tea plants. Numerous functional genes and regulatory factors have been discovered, studied, and applied to improve tea plants. Research advances, including secondary metabolites, applications, omics research, and functional gene mining, are comprehensively reviewed here. Further exploration and application trends are briefly described. This review provides a reference for basic and applied research on tea plants.
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Ranjan A, Sinha R, Sharma TR, Pattanayak A, Singh AK. Alleviating aluminum toxicity in plants: Implications of reactive oxygen species signaling and crosstalk with other signaling pathways. PHYSIOLOGIA PLANTARUM 2021; 173:1765-1784. [PMID: 33665830 DOI: 10.1111/ppl.13382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Aluminum (Al) toxicity is a major limiting factor for plant growth and productivity in acidic soil. At pH lower than 5.0 (pH < 5.0), the soluble and toxic form of Al (Al3+ ions) enters root cells and inhibits root growth and uptake of water and nutrients. The organic acids malate, citrate, and oxalate are secreted by the roots and chelate Al3+ to form a non-toxic Al-OA complex, which decreases the entry of Al3+ into the root cells. When Al3+ enters, it leads to the production of reactive oxygen species (ROS) in cells, which are toxic and cause damage to biomolecules like lipids, carbohydrates, proteins, and nucleic acids. When ROS levels rise beyond the threshold, plants activate an antioxidant defense system that comprises of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione S-transferase (GST), ascorbic acid (ASA), phenolics and alkaloids etc., which protect plant cells from oxidative damage by scavenging and neutralizing ROS. Besides, ROS also play an important role in signal transduction and influence many molecular and cellular process like hormone signaling, gene expression, cell wall modification, cell cycle, programed cell death (PCD), and development. In the present review, the mechanisms of Al-induced ROS generation, ROS signaling, and crosstalk with other signaling pathways helping to combat Al toxicity have been summarized, which will help researchers to understand the intricacies of Al-induced plant response at cellular level and plan research for developing Al-toxicity tolerant crops for sustainable agriculture in acid soil-affected regions of the world.
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Affiliation(s)
- Alok Ranjan
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Ragini Sinha
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Tilak Raj Sharma
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | | | - Anil Kumar Singh
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
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9
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Uncovering the transcriptional response of popcorn (Zea mays L. var. everta) under long-term aluminum toxicity. Sci Rep 2021; 11:19644. [PMID: 34608228 PMCID: PMC8490451 DOI: 10.1038/s41598-021-99097-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022] Open
Abstract
To date, the investigation of genes involved in Al resistance has focused mainly on microarrays and short periods of Al exposure. We investigated genes involved in the global response under Al stress by tracking the expression profile of two inbred popcorn lines with different Al sensitivity during 72 h of Al stress. A total of 1003 differentially expressed genes were identified in the Al-sensitive line, and 1751 were identified in the Al-resistant line, of which 273 were shared in both lines. Genes in the category of “response to abiotic stress” were present in both lines, but there was a higher number in the Al-resistant line. Transcription factors, genes involved in fatty acid biosynthesis, and genes involved in cell wall modifications were also detected. In the Al-resistant line, GST6 was identified as one of the key hub genes by co-expression network analysis, and ABC6 may play a role in the downstream regulation of CASP-like 5. In addition, we suggest a class of SWEET transporters that might be involved in the regulation of vacuolar sugar storage and may serve as mechanisms for Al resistance. The results and conclusions expand our understanding of the complex mechanisms involved in Al toxicity and provide a platform for future functional analyses and genomic studies of Al stress in popcorn.
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10
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Zhu Q, Gao S, Zhang W. Identification of Key Transcription Factors Related to Bacterial Spot Resistance in Pepper through Regulatory Network Analyses. Genes (Basel) 2021; 12:genes12091351. [PMID: 34573336 PMCID: PMC8472308 DOI: 10.3390/genes12091351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 01/03/2023] Open
Abstract
Bacterial spot (BS), caused by Xanthomonas campestris pv. Vesicatoria (Xcv), severely affects the quality and yield of pepper. Thus, breeding new pepper cultivars with enhanced resistance to BS can improve economic benefits for pepper production. Identification of BS resistance genes is an essential step to achieve this goal. However, very few BS resistance genes have been well characterized in pepper so far. In this study, we reanalyzed public multiple time points related to RNA-seq data sets from two pepper cultivars, the Xcv-susceptible cultivar ECW and the Xcv-resistant cultivar VI037601, post Xcv infection. We identified a total of 3568 differentially expressed genes (DEGs) between two cultivars post Xcv infection, which were mainly involved in some biological processes, such as Gene Ontology (GO) terms related to defense response to bacterium, immune system process, and regulation of defense response, etc. Through weighted gene co-expression network analysis (WGCNA), we identified 15 hub (Hub) transcription factor (TF) candidates in response to Xcv infection. We further selected 20 TFs from the gene regulatory network (GRN) potentially involved in Xcv resistance response. Finally, we predicted 4 TFs, C3H (p-coumarate 3-hydroxylase), ERF (ethylene-responsive element binding factor), TALE (three-amino-acid-loop-extension), and HSF (heat shock transcription factor), as key factors responsible for BS disease resistance in pepper. In conclusion, our study provides valuable resources for dissecting the underlying molecular mechanism responsible for Xcv resistance in pepper. Additionally, it also provides valuable references for mining transcriptomic data to identify key candidates for disease resistance in horticulture crops.
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Affiliation(s)
- Qingquan Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China;
| | - Shenghua Gao
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China;
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China;
- Correspondence: ; Tel.: +86-25-84396610; Fax: +86-25-84396302
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11
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Szurman-Zubrzycka M, Chwiałkowska K, Niemira M, Kwaśniewski M, Nawrot M, Gajecka M, Larsen PB, Szarejko I. Aluminum or Low pH - Which Is the Bigger Enemy of Barley? Transcriptome Analysis of Barley Root Meristem Under Al and Low pH Stress. Front Genet 2021; 12:675260. [PMID: 34220949 PMCID: PMC8244595 DOI: 10.3389/fgene.2021.675260] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
Aluminum (Al) toxicity is considered to be the most harmful abiotic stress in acidic soils that today comprise more than 50% of the world’s arable lands. Barley belongs to a group of crops that are most sensitive to Al in low pH soils. We present the RNA-seq analysis of root meristems of barley seedlings grown in hydroponics at optimal pH (6.0), low pH (4.0), and low pH with Al (10 μM of bioavailable Al3+ ions). Two independent experiments were conducted: with short-term (24 h) and long-term (7 days) Al treatment. In the short-term experiment, more genes were differentially expressed (DEGs) between root meristems grown at pH = 6.0 and pH = 4.0, than between those grown at pH = 4.0 with and without Al treatment. The genes upregulated by low pH were associated mainly with response to oxidative stress, cell wall organization, and iron ion binding. Among genes upregulated by Al, overrepresented were those related to response to stress condition and calcium ion binding. In the long-term experiment, the number of DEGs between hydroponics at pH = 4.0 and 6.0 were lower than in the short-term experiment, which suggests that plants partially adapted to the low pH. Interestingly, 7 days Al treatment caused massive changes in the transcriptome profile. Over 4,000 genes were upregulated and almost 2,000 genes were downregulated by long-term Al stress. These DEGs were related to stress response, cell wall development and metal ion transport. Based on our results we can assume that both, Al3+ ions and low pH are harmful to barley plants. Additionally, we phenotyped the root system of barley seedlings grown in the same hydroponic conditions for 7 days at pH = 6.0, pH = 4.0, and pH = 4.0 with Al. The results correspond to transcriptomic data and show that low pH itself is a stress factor that causes a significant reduction of root growth and the addition of aluminum further increases this reduction. It should be noted that in acidic arable lands, plants are exposed simultaneously to both of these stresses. The presented transcriptome analysis may help to find potential targets for breeding barley plants that are more tolerant to such conditions.
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Affiliation(s)
- Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Mirosław Kwaśniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Małgorzata Nawrot
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Monika Gajecka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paul B Larsen
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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12
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Ding ZJ, Shi YZ, Li GX, Harberd NP, Zheng SJ. Tease out the future: How tea research might enable crop breeding for acid soil tolerance. PLANT COMMUNICATIONS 2021; 2:100182. [PMID: 34027395 PMCID: PMC8132122 DOI: 10.1016/j.xplc.2021.100182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/28/2021] [Accepted: 03/23/2021] [Indexed: 05/15/2023]
Abstract
Unlike most crops, in which soil acidity severely limits productivity, tea (Camellia sinensis) actually prefers acid soils (pH 4.0-5.5). Specifically, tea is very tolerant of acidity-promoted aluminum (Al) toxicity, a major factor that limits the yield of most other crops, and it even requires Al for optimum growth. Understanding tea Al tolerance and Al-stimulatory mechanisms could therefore be fundamental for the future development of crops adapted to acid soils. Here, we summarize the Al-tolerance mechanisms of tea plants, propose possible mechanistic explanations for the stimulation of tea growth by Al based on recent research, and put forward ideas for future crop breeding for acid soils.
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Affiliation(s)
- Zhong Jie Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuan Zhi Shi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory for Tea Plant Biology and Resource Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| | - Gui Xin Li
- College of Agronomy and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nicholas P. Harberd
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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13
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Huang D, Gong Z, Chen X, Wang H, Tan R, Mao Y. Transcriptomic responses to aluminum stress in tea plant leaves. Sci Rep 2021; 11:5800. [PMID: 33707704 PMCID: PMC7952733 DOI: 10.1038/s41598-021-85393-1] [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: 07/14/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Tea plant (Camellia sinensis) is a well-known Al-accumulating plant, showing a high level of aluminum (Al) tolerance. However, the molecular mechanisms of Al tolerance and accumulation are poorly understood. We carried out transcriptome analysis of tea plant leaves in response to three different Al levels (0, 1, 4 mM, for 7 days). In total, 794, 829 and 585 differentially expressed genes (DEGs) were obtained in 4 mM Al vs. 1 mM Al, 0 Al vs. 1 mM Al, and 4 mM Al vs. 0 Al comparisons, respectively. Analysis of genes related to polysaccharide and cell wall metabolism, detoxification of reactive oxygen species (ROS), cellular transport, and signal transduction were involved in the Al stress response. Furthermore, the transcription factors such as zinc finger, myeloblastosis (MYB), and WRKY played a critical role in transcriptional regulation of genes associated with Al resistance in tea plant. In addition, the genes involved in phenolics biosynthesis and decomposition were overwhelmingly upregulated in the leaves treated with either 0 Al and 4 mM Al stress, indicating they may play an important role in Al tolerance. These results will further help us to understand mechanisms of Al stress and tolerance in tea plants regulated at the transcriptional level.
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Affiliation(s)
- Danjuan Huang
- grid.410632.20000 0004 1758 5180Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Ziming Gong
- grid.410632.20000 0004 1758 5180Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Xun Chen
- grid.410632.20000 0004 1758 5180Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Hongjuan Wang
- grid.410632.20000 0004 1758 5180Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Rongrong Tan
- grid.410632.20000 0004 1758 5180Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yingxin Mao
- grid.410632.20000 0004 1758 5180Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
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14
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Zhang X, Liu P, Qing C, Yang C, Shen Y, Ma L. Comparative transcriptome analyses of maize seedling root responses to salt stress. PeerJ 2021; 9:e10765. [PMID: 33717668 PMCID: PMC7934676 DOI: 10.7717/peerj.10765] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
Salt stress affects crop yield by limiting growth and delaying development. In this study, we constructed 16 transcriptome libraries from maize seedling roots using two maize lines, with contrasting salt tolerance, that were exposed to salt stress for 0, 6, 18 and 36 h. In total, 6,584 differential expression genes (DEGs; 3,669 upregulated, 2,915 downregulated) were induced in the salt-sensitive line and 6,419 DEGs (3,876 upregulated, 2,543 downregulated) were induced in the salt-tolerant line. Several DEGs common to both lines were enriched in the ABA signaling pathway, which was presumed to coordinate the process of maize salt response. A total of 459 DEGs were specifically induced in the salt-tolerant line and represented candidate genes responsible for high salt-tolerance. Expression pattern analysis for these DEGs indicated that the period between 0 and 6 h was a crucial period for the rapid response of the tolerant genes under salt stress. Among these DEGs, several genes, Aux/IAA, SAUR, and CBL-interacting kinase have been reported to regulate salt tolerance. In addition, the transcription factors WRKY, bZIP and MYB acted as regulators in the salt-responsive regulatory network of maize roots. Our findings will contribute to understanding of the mechanism on salt response and provide references for functional gene revelation in plants.
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Affiliation(s)
- Xiaoxiang Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Wenjiang, China
| | - Peng Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Wenjiang, China
| | - Chunyan Qing
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Wenjiang, China
| | - Cong Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Wenjiang, China
| | - Yaou Shen
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Wenjiang, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Wenjiang, China
| | - Langlang Ma
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Wenjiang, China
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15
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Yamashita H, Fukuda Y, Yonezawa S, Morita A, Ikka T. Tissue ionome response to rhizosphere pH and aluminum in tea plants ( Camellia sinensis L.), a species adapted to acidic soils. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2020; 1:152-164. [PMID: 37283727 PMCID: PMC10168086 DOI: 10.1002/pei3.10028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/06/2020] [Accepted: 07/23/2020] [Indexed: 06/08/2023]
Abstract
The growth of tea plants (Camellia sinensis L.) is promoted by the presence of aluminum (Al), a beneficial element under acidic conditions, but the influence of rhizosphere pH on this interaction is not known. To understand the mechanisms underlying the adaptation to acidic rhizosphere conditions, we evaluated ionome profiles and the effect of pH on tea growth in hydroponic culture. The optimum pH for tea growth was around pH 4.2, and growth was inferior under a pH less than 3.8 or higher than 5.0. Under the optimum pH growth and Al accumulation were markedly stimulated by Al treatment. Al content and accumulation in new and mature leaves and new roots (the predominant tissues that accumulate minerals in tea plants) gradually declined with decrease in pH, especially in new roots. Ionome profiles drastically altered Al treatment, but changes were more pronounced in new roots than in new or mature leaves and did not depend on pH. Although the uptake of most cationic minerals in new roots was decreased by Al treatment, cationic mineral contents in new and mature leaves were not decreased by Al. In contrast to other plant species, the content and accumulation of manganese, despite it being a cationic nutrient, were significantly increased by Al treatment. These results indicated that one role of Al as a beneficial element was to maintain the shoot nutrient status by effectively utilizing Al-limited elements in the roots.
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Affiliation(s)
- Hiroto Yamashita
- Faculty of AgricultureShizuoka UniversityOhyaShizuokaJapan
- United Graduate School of Agricultural ScienceGifu UniversityYanagito, GifuJapan
| | - Yusuke Fukuda
- Faculty of AgricultureShizuoka UniversityOhyaShizuokaJapan
| | | | - Akio Morita
- Faculty of AgricultureShizuoka UniversityOhyaShizuokaJapan
| | - Takashi Ikka
- Faculty of AgricultureShizuoka UniversityOhyaShizuokaJapan
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16
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Chen Y, Jiang Y, Chen Y, Feng W, Liu G, Yu C, Lian B, Zhong F, Zhang J. Uncovering candidate genes responsive to salt stress in Salix matsudana (Koidz) by transcriptomic analysis. PLoS One 2020; 15:e0236129. [PMID: 32760076 PMCID: PMC7410171 DOI: 10.1371/journal.pone.0236129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
Salix matsudana, a member of Salicaceae, is an important ornamental tree in China. Because of its capability to tolerate high salt conditions, S. matsudana also plays an important ecological role when grown along Chinese coastal beaches, where the salinity content is high. Here, we aimed to elucidate the mechanism of higher salt tolerance in S. matsudana variety ‘9901’ by identifying the associated genes through RNA sequencing and comparing differential gene expression between the S. matsudana salt-tolerant and salt-sensitive samples treated with 150 mM NaCl. Transcriptomic comparison of the roots of the two samples revealed 2174 and 3159 genes responsive to salt stress in salt-sensitive and salt-tolerant sample, respectively. Real-time polymerase chain reaction analysis of 9 of the responsive genes revealed a strong, positive correlation with RNA sequencing data. The genes were enriched in several pathways, including carbon metabolism pathway, plant-pathogen interaction pathway, and plant hormone signal transduction pathway. Differentially expressed genes (DEGs) encoding transcription factors associated with abiotic stress responses and salt stress response network were identified; their expression levels differed between the two samples in response to salt stress. Hub genes were also revealed by weighted gene co-expression network (WGCNA) analysis. For functional analysis of the DEG encoding sedoheptulose-1,7-bisphosphatase (SBPase), the gene was overexpressed in transgenic Arabidopsis, resulting in increased photosynthetic rates, sucrose and starch accumulation, and enhanced salt tolerance. Further functional characterization of other hub DEGs will reveal the molecular mechanism of salt tolerance in S. matsudana and allow the application of S. matsudana in coastal afforestation.
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Affiliation(s)
- Yanhong Chen
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Yuna Jiang
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Yu Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wenxiang Feng
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Guoyuan Liu
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Chunmei Yu
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Bolin Lian
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Fei Zhong
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
| | - Jian Zhang
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, China
- * E-mail:
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17
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Pan J, Li D, Zhu J, Shu Z, Ye X, Xing A, Wen B, Ma Y, Zhu X, Fang W, Wang Y. Aluminum relieves fluoride stress through stimulation of organic acid production in Camellia sinensis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1127-1137. [PMID: 32549678 PMCID: PMC7266864 DOI: 10.1007/s12298-020-00813-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/10/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Tea plants (Camellia sinensis O. Kuntze) can hyperaccumulate fluoride (F) in leaves. Although, aluminum (Al) can alleviate F toxicity in C. sinensis, the mechanisms driving this process remain unclear. Here, we measured root length, root activity, soluble proteins content, and levels of peroxidase, superoxide dismutase, catalase, malondialdehyde (MDA), and chlorophyll in tea leaves after treatment with different F concentrations. In addition, we focused on the content of organic acids, the gene transcription of malate dehydrogenase (MDH), glycolate oxidase (GO) and citrate synthase (CS) and the relative enzyme activity involved in the tolerance to F in C. sinensis. We also examined the role of Al in this process by analyzing the content of these physiological indicators in tea leaves treated with F and Al. Our results demonstrate that increased MDA content, together with decreased chlorophyll content and soluble proteins are responsible for oxidative damage and metabolism inhibition at high F concentration. Moreover, increased antioxidant enzymes activity regulates ROS damage to protect tea leaves during F stress. Furthermore, exogenous Al alleviated F stress in tea leaves through the regulation of MDA content and antioxidant enzymes activity. In addition, organic acids in exudate stimulated root growth in tea plants exposed to low F concentrations are regulated by MDH, GO, and CS. In addition, Al can stimulate the exudation of organic acids, and may participate in regulating rhizosphere pH of the roots through the interaction with F, eventually leading to the response to F stress in C. sinensis.
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Affiliation(s)
- Junting Pan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dongqin Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiaojiao Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zaifa Shu
- Lishui Academy of Agricultural Sciences, Lishui, 323000 Zhejiang China
| | - Xiaoli Ye
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Anqi Xing
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Bo Wen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuhua Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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18
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Hu S, Chen Q, Guo F, Wang M, Zhao H, Wang Y, Ni D, Wang P. (Z)-3-Hexen-1-ol accumulation enhances hyperosmotic stress tolerance in Camellia sinensis. PLANT MOLECULAR BIOLOGY 2020; 103:287-302. [PMID: 32240472 DOI: 10.1007/s11103-020-00992-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Volatile components in fresh leaves are involved in the regulation of many stress responses, such as insect damage, fungal infection and high temperature. However, the potential function of volatile components in hyperosmotic response is largely unknown. Here, we found that 7-day hyperosmotic treatment specifically led to the accumulation of (Z)-3-hexen-1-ol, (E)-2-hexenal and methyl salicylate. Transcriptome and qRT-PCR analyses suggested the activation of linolenic acid degradation and methyl salicylate processes. Importantly, exogenous (Z)-3-hexen-1-ol pretreatment dramatically enhanced the hyperosmotic stress tolerance of tea plants and decreased stomatal conductance, whereas (E)-2-hexenal and methyl salicylate pretreatments did not exhibit such a function. qRT-PCR analysis revealed that exogenous ABA induced the expressions of related enzyme genes, and (Z)-3-hexen-1-ol could up-regulate the expressions of many DREB and RD genes. Moreover, exogenous (Z)-3-hexen-1-ol tremendously induced the expressions of specific LOX and ADH genes within 24 h. Taken together, hyperosmotic stress induced (Z)-3-hexen-1-ol accumulation in tea plant via the activation of most LOX, HPL and ADH genes, while (Z)-3-hexen-1-ol could dramatically enhance the hyperosmotic stress tolerance via the decrease of stomatal conductance and MDA, accumulation of ABA and proline, activation of DREB and RD gene expressions, and probably positive feedback regulation of LOXs and ADHs. KEY MESSAGE: Hyperosmotic stress induced (Z)-3-hexen-1-ol accumulation in Camellia sinensis via the up-regulation of most LOX, HPL and ADH genes, while (Z)-3-hexen-1-ol could dramatically enhance the hyperosmotic stress tolerance via the decrease of stomatal conductance, accumulation of proline, activation of DREB and RD gene expressions, and probably positive feedback regulation of LOXs and ADHs.
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Affiliation(s)
- Shuangling Hu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Fei Guo
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Mingle Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Hua Zhao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yu Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Dejiang Ni
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Pu Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.
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Jiang X, Zhao H, Guo F, Shi X, Ye C, Yang P, Liu B, Ni D. Transcriptomic analysis reveals mechanism of light-sensitive albinism in tea plant Camellia sinensis 'Huangjinju'. BMC PLANT BIOLOGY 2020; 20:216. [PMID: 32410639 PMCID: PMC7227349 DOI: 10.1186/s12870-020-02425-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/30/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND Camellia sinensis 'Huangjinju' is an albino tea variety developed recently in China. Young leaves of 'Huangjinju' demonstrate bright yellow when cultivated under natural sunlight, but regreens under reduced light intensity. To elucidate the physiological and molecular mechanisms of this light-sensitive albinism, we compared leaf pigmentation, metabolites, cellular ultrastructure and transcriptome between plants cultured under natural sunlight and shade. RESULTS Shading treatment doubled the chlorophyll concentration and regreened albino leaves; carotenoid also increased by 30%. Electron microscopy analyses showed that chloroplast not only increased in number but also in size with a complete set of components. In addition, regreened leaves also had a significantly higher concentration of polyphenols and catechins than albino leaves. At transcriptomic level, a total of 507 genes were differentially expressed in response to light condition changes. The most enriched pathways include light harvest protein complex, response to stimuli, oxidation-reduction process, generation of precursor metabolites and energy response. CONCLUSION The integrated strategy in this study allows a mechanistic understanding of leaf albinism in light-sensitive tea plants and suggested the regulation of gene networks involved in pigmentation and protein processing. Results from this study provide valuable information to this area and can benefit the domestication and artificial breeding to develop new albino tea varieties.
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Affiliation(s)
- Xinfeng Jiang
- College of Horticulture and Forestry Science, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
- Jiangxi Sericulture and Tea Research Institute, Nanchang, 330202, Jiangxi, China
| | - Hua Zhao
- College of Horticulture and Forestry Science, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Fei Guo
- College of Horticulture and Forestry Science, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Xuping Shi
- Jiangxi Sericulture and Tea Research Institute, Nanchang, 330202, Jiangxi, China
| | - Chuan Ye
- Jiangxi Sericulture and Tea Research Institute, Nanchang, 330202, Jiangxi, China
| | - Puxiang Yang
- Jiangxi Sericulture and Tea Research Institute, Nanchang, 330202, Jiangxi, China
| | - Benying Liu
- Yunnan Provincial Key Laboratory of Tea Science, Jinghong, 666100, Yunnan, China
| | - Dejiang Ni
- College of Horticulture and Forestry Science, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China.
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20
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Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PLANTS 2020; 9:plants9050591. [PMID: 32384671 PMCID: PMC7285221 DOI: 10.3390/plants9050591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Alessia Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
- Correspondence: ; Tel.: +39-081-253-9492
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21
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Muhammad II, Kong SL, Akmar Abdullah SN, Munusamy U. RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism. Int J Mol Sci 2019; 21:E167. [PMID: 31881735 PMCID: PMC6981605 DOI: 10.3390/ijms21010167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.
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Affiliation(s)
- Isiaka Ibrahim Muhammad
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Sze Ling Kong
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Siti Nor Akmar Abdullah
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Selangor 43400, Malaysia
| | - Umaiyal Munusamy
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
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Li FD, Tong W, Xia EH, Wei CL. Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species. BMC Bioinformatics 2019; 20:553. [PMID: 31694521 PMCID: PMC6836513 DOI: 10.1186/s12859-019-3166-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022] Open
Abstract
Background Tea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), which belong to the genus Camellia of family Theaceae. In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes. Results We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. Although the total number of assembled transcripts increased with increasing sequencing data, the proportion of unassembled transcripts became saturated as revealed by plant BUSCO datasets. Among the five representative assemblers, the Bridger package shows the best performance in both assembly completeness and accuracy as evaluated by the BUSCO datasets and genome alignment. In addition, we showed that Bridger and BinPacker harbored the shortest runtimes followed by SOAPdenovo and Trans-ABySS. Conclusions The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry.
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Affiliation(s)
- Fang-Dong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.,School of Science, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - En-Hua Xia
- 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.
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23
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Samarth, Lee R, Song J, Macknight RC, Jameson PE. Identification of flowering-time genes in mast flowering plants using De Novo transcriptomic analysis. PLoS One 2019; 14:e0216267. [PMID: 31412034 PMCID: PMC6693765 DOI: 10.1371/journal.pone.0216267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/22/2019] [Indexed: 11/18/2022] Open
Abstract
Mast flowering is synchronised highly variable flowering by a population of perennial plants over a wide geographical area. High seeding years are seen as a threat to native and endangered species due to high predator density caused by the abundance of seed. An understanding of the molecular pathways that influence masting behaviour in plants could provide better prediction of a forthcoming masting season and enable conservation strategies to be deployed. The goal of this study was to identify candidate flowering genes that might be involved in regulating mast flowering. To achieve this, high-throughput large-scale RNA-sequencing was performed on two masting plant species, Celmisia lyallii (Asteraceae), and Chionochloa pallens (Poaceae) to develop a reference transcriptome for functional and molecular analysis. An average total of 33 million 150 base-paired reads, for both species, were assembled using the Trinity pipeline, resulting in 151,803 and 348,649 transcripts respectively for C. lyallii and C. pallens. For both species, about 56% of the unigenes were annotated with gene descriptions to known proteins followed by Gene Ontology analysis, categorising them on the basis of putative biological processes, molecular function, and cellular localization. A total of 543 transcripts from C. lyallii and 470 transcripts from C. pallens were also mapped to unique flowering-time proteins identified in Arabidopsis thaliana, suggesting the conservation of the flowering network in these wild alpine plants growing in natural field conditions. Expression analysis of several selected homologous flowering-pathway genes showed seasonal and photoperiodic variations. These genes can further be analysed to understand why seasonal cues, such as the increasing photoperiod in spring, that triggers the annual flowering of most plants, are insufficient to always trigger flowering in masting plants and to uncover the molecular basis of how additional cues (such as temperature during the previous growing seasons) then determines flowering in mast years.
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Affiliation(s)
- Samarth
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Robyn Lee
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Jiancheng Song
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- School of Life Sciences, Yantai University, Yantai, China
| | | | - Paula E. Jameson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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24
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Samarth, Jameson PE. Selection of reference genes for flowering pathway analysis in the masting plants, Celmisia lyallii and Chionochloa pallens, under variable environmental conditions. Sci Rep 2019; 9:9767. [PMID: 31278277 PMCID: PMC6611903 DOI: 10.1038/s41598-019-45780-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/13/2019] [Indexed: 12/20/2022] Open
Abstract
Mast flowering is characterised by mass synchronised flowering at irregular intervals over a wide geographical area. An understanding of the molecular drivers of mast flowering requires expression analysis of key developmentally regulated gene(s). Reverse transcription-quantitative PCR is the gold standard technique used to assess expression of target gene(s) and to validate high-throughput sequencing data. Selection and validation of appropriate reference gene(s), used as normalisation factors in transcript abundance analysis, is an essential step to avoid ambiguous expression results. Eight candidate reference genes were assessed to select the best internal normalisation factors in naturally growing masting plants Chionochloa pallens and Celmisia lyallii. Statistical packages geNorm, Normfinder, BestKeeper, ΔCt and RefFinder were used to determine the expression stability in plants translocated to different altitudes and sampled across the season. GAPDH and PP2a in Celmisia and ExP and THP in Chionochloa were found to be the best pairs of reference genes for normalisation of the gene expression data. Our study revealed environmentally-induced changes in reference gene expression, information that will be utilised as we investigate flowering phenology of masting plants under global climatic change.
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Affiliation(s)
- Samarth
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Paula E Jameson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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25
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Fan K, Wang M, Gao Y, Ning Q, Shi Y. Transcriptomic and ionomic analysis provides new insight into the beneficial effect of Al on tea roots' growth and nutrient uptake. PLANT CELL REPORTS 2019; 38:715-729. [PMID: 30911819 DOI: 10.1007/s00299-019-02401-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
Transcriptome profiling of roots indicated that genes involved in cell wall modification, cytoskeleton, H+ exchange and K+ influx played important roles in tea root growth under Al addition. Tea (Camellia sinensis) is considered as an Al accumulator species. It can accumulate a high concentration of Al in mature leaves without any symptom of toxicity, even improve roots' growth and nutrient uptake. However, the molecular mechanisms underlying this tolerance remain unclear. Here, we investigated the accumulation of elements and transcriptional profiles in tea roots treated with various Al doses. The results showed that the growth of tea plants was improved by a low dose of Al (0.2, 0.4, 0.6, 1 mM); however, this beneficial effect disappeared when higher concentrations of Al were supplied (2, 4, 10 mM). Ionomic analysis suggested that accumulation of P and K increased under a low Al supply (< 1 mM), while Ca and Mg contents were negatively correlated with external Al doses. The RNA seq obtained 523,391 unigenes, among which 20,448 were annotated in all databases. In total, 1876 unigenes were expressed significantly different in any Al treatment. A large number of DEGs involved in cell growth and division, such as those linked to cell wall-modifying enzymes, actin cytoskeleton, cyclin and H+-ATPase were identified, suggesting that these pathways were involved in root growth under different Al supply. Furthermore, expression of transporters significantly changed in roots supplied with Al. Among them, HAK5, which is involved in K uptake by plants, had a significant positive correlation with the K content.
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Affiliation(s)
- Kai Fan
- Tea research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310058, China
| | - Min Wang
- Tea research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310058, China
| | - Yaoyao Gao
- Tea research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310058, China
| | - Qiuyan Ning
- Tea research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310058, China
| | - Yuanzhi Shi
- Tea research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310058, China.
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26
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Gao Y, Zhao M, Wu XH, Li D, Borthakur D, Ye JH, Zheng XQ, Lu JL. Analysis of Differentially Expressed Genes in Tissues of Camellia sinensis during Dedifferentiation and Root Redifferentiation. Sci Rep 2019; 9:2935. [PMID: 30814540 PMCID: PMC6393419 DOI: 10.1038/s41598-019-39264-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/21/2019] [Indexed: 12/04/2022] Open
Abstract
Tissue culture is very important for identifying the gene function of Camellia sinensis (L.) and exploiting novel germplasm through transgenic technology. Regeneration system of tea plant has been explored but not been well established since the molecular mechanism of tea plant regeneration is not clear yet. In this study, transcriptomic analysis was performed in the initial explants of tea plant and their dedifferentiated and redifferentiated tissues. A total of 93,607 unigenes were obtained through de novo assembly, and 7,193 differentially expressed genes (DEGs) were screened out from the 42,417 annotated unigenes. Much more DEGs were observed during phase transition rather than at growth stages of callus. Our KOG and KEGG analysis, and qPCR results confirmed that phase transition of tea plant was closely related to the mechanism that regulate expression of genes encoding the auxin- and cytokinin-responsive proteins, transcription factor MYB15 and ethylene-responsive transcription factor ERF RAP2-12. These findings provide a reliable foundation for elucidating the mechanism of the phase transition and may help to optimize the regeneration system by regulating the gene expression pattern.
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Affiliation(s)
- Ying Gao
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Min Zhao
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Xiao-Han Wu
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Da Li
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | | | - Jian-Hui Ye
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Xin-Qiang Zheng
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Jian-Liang Lu
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China.
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27
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Jia Y, Bai JQ, Liu ML, Jiang ZF, Wu Y, Fang MF, Li ZH. Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers. PLANT DIVERSITY 2019; 41:1-6. [PMID: 30931411 PMCID: PMC6412102 DOI: 10.1016/j.pld.2019.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 05/28/2023]
Abstract
Notopterygium incisum C. C. Ting ex H. T. Chang (Apiaceae) is an endangered perennial herb in China. The lack of transcriptomic and genomic resources for N. incisum greatly hinders studies of its population genetics and conservation. In this study, we employed RNA-seq technology to characterize transcriptomes for the flowers, leaves, and stems of this endangered herb. A total of 56 million clean reads were assembled into 120,716 unigenes with an N50 length of 850 bp. Among these unigenes, 70,245 (58.19%) were successfully annotated and 65,965 (54.64%) were identified as coding sequences based on their similarities with sequences in public databases. We identified 21 unigenes that had significant relationships with cold tolerance in N. incisum according to gene ontology (GO) annotation analysis. In addition, 13,149 simple sequence repeats (SSRs) and 85,681 single nucleotide polymorphisms were detected as potential molecular genetic markers. Ninety-six primer pairs of SSRs were randomly selected to validate their amplification efficiency and polymorphism. Nineteen SSR loci exhibited polymorphism in three natural populations of N. incisum. These results provide valuable resources to facilitate future functional genomics and conservation genetics studies of N. incisum.
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Affiliation(s)
- Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ji-Qing Bai
- Shaanxi University of Chinese Medicine, Xianyang 712046, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhen-Fang Jiang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Min-Feng Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
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Guo P, Qi YP, Huang WL, Yang LT, Huang ZR, Lai NW, Chen LS. Aluminum-responsive genes revealed by RNA-Seq and related physiological responses in leaves of two Citrus species with contrasting aluminum-tolerance. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 158:213-222. [PMID: 29704792 DOI: 10.1016/j.ecoenv.2018.04.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 05/25/2023]
Abstract
Little is known about the physiological and molecular responses of leaves to aluminum (Al)-toxicity. Seedlings of Al-intolerant Citrus grandis and Al-tolerant Citrus sinensis were supplied daily with nutrient solution containing 0 mM (control) and 1.0 mM (Al-toxicity) AlCl3·6H2O for 18 weeks. We found that Al-treatment only decreased CO2 assimilation in C. grandis leaves, and that the Al-induced alterations of gene expression profiles were less in C. sinensis leaves than those in C. grandis leaves, indicating that C. sinensis seedlings were more tolerant to Al-toxicity than C. grandis ones. Al concentration was similar between Al-treated C. sinensis and C. grandis roots, but it was higher in Al-treated C. grandis stems and leaves than that in Al-treated C. sinensis stems and leaves. Al-treated C. sinensis seedlings accumulated relatively more Al in roots and transported relatively little Al to shoots. This might be responsible for the higher Al-tolerance of C. sinensis. Further analysis showed that the following several aspects might account for the higher Al-tolerance of C. sinensis, including: (a) Al-treated C. sinensis leaves had higher capacity to maintain the homeostasis of energy and phosphate, the stability of lipid composition and the integrity of cell wall than did Al-treated C. grandis leaves; (b) Al-triggered production of reactive oxygen species (ROS) and the other cytotoxic compounds was less in Al-treated C. sinensis leaves than that in Al-treated C. grandis leaves, because Al-toxicity decreased CO2 assimilation only in C. grandis leaves; accordingly, more upregulated genes involved in the detoxifications of ROS, aldehydes and methylglyoxal were identified in Al-treated C. grandis leaves; in addition, flavonoid concentration was increased only in Al-treated C. grandis leaves; (c) Al-treated C. sinensis leaves could keep a better balance between protein phosphorylation and dephosphorylation than did Al-treated C. grandis leaves; and (d) both the equilibrium of hormones and hormone-mediated signal transduction were greatly disrupted in Al-treated C. grandis leaves, but less altered in Al-treated C. sinensis leaves. Finally, we discussed the differences in Al-responsive genes between Citrus roots and leaves.
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Affiliation(s)
- Peng Guo
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China
| | - Wei-Lin Huang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeng-Rong Huang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ning-Wei Lai
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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29
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Zhang W, Sun P, He Q, Shu F, Deng H. Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice. PLoS One 2018; 13:e0199077. [PMID: 29924832 PMCID: PMC6010284 DOI: 10.1371/journal.pone.0199077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/31/2018] [Indexed: 11/18/2022] Open
Abstract
Panicle traits in rice impact yield and quality. The OsGRF4 gene encodes a growth-regulating factor controlling panicle traits, and was recently cloned. Gene expression profiling analysis can be used to study the molecular mechanisms underlying OsGRF4 regulation. Use of near-isogenic lines (NILs) reduces genetic background noise in omics studies. We compared transcriptome profiling of 7 cm long young panicles of NIL-Osgrf4 and NIL-OsGRF4 using RNAs sequence analyses. Eighty differentially expressed genes (DEGs) were identified. Our target gene OsGRF4 was up-regulated in NIL-OsGRF4 plants, which is consistent with a previous qPCR analysis. Hierarchical cluster analysis showed OsGRF4 is tightly clustered with the up-regulated DEG LOC_Os02g47320. Gene Ontology (GO) and KEGG analysis suggested that DEGs were primarily involved in somatic embryogenesis and chitinase activity. Two up-regulated DEGs, LOC_Os04g41680 and LOC_Os04g41620, were significantly enriched in the top 8 GO terms, and were over_represented in term of seed development, and may play key roles in grain shape regulation. The transcription factor Osmyb1 also exhibited differential expression between NILs, and may be is an important regulator of panicle traits. By searching reported functions of DEGs and by co-localization with previous identified quantitative trait loci (QTL), we determined that the pleiotropic gene OsGRF4 may also be involve in abiotic stress resistance. This study provides new candidates genes for further understanding the molecular mechanisms underlying rice panicle trait regulation.
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Affiliation(s)
- Wuhan Zhang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, China
- Collaborative Innovation Center of Grain and Oil Crops in South China, Changsha, China
- China National Japonica Rice Research and Development Center, Tianjin, China
| | - Pingyong Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Qiang He
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, China
- Collaborative Innovation Center of Grain and Oil Crops in South China, Changsha, China
| | - Fu Shu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, China
- Collaborative Innovation Center of Grain and Oil Crops in South China, Changsha, China
| | - Huafeng Deng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, China
- Collaborative Innovation Center of Grain and Oil Crops in South China, Changsha, China
- * E-mail:
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30
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Landi S, Esposito S. Nitrate Uptake Affects Cell Wall Synthesis and Modeling. FRONTIERS IN PLANT SCIENCE 2017; 8:1376. [PMID: 28848580 PMCID: PMC5550703 DOI: 10.3389/fpls.2017.01376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/24/2017] [Indexed: 05/27/2023]
Abstract
Nowadays, the relationship(s) about N assimilation and cell wall remodeling in plants remains generally unclear. Enzymes involved in cell wall synthesis/modification, and nitrogen transporters play a critical role in plant growth, differentiation, and response to external stimuli. In this review, a co-expression analysis of nitrate and ammonium transporters of Arabidopsis thaliana was performed in order to explore the functional connection of these proteins with cell-wall related enzymes. This approach highlighted a strict relationship between inorganic nitrogen transporters and cell wall formation, identifying a number of co-expressed remodeling enzymes. The enzymes involved in pectin and xyloglucan synthesis resulted particularly co-regulated together with nitrate carriers, suggesting a connection between nitrate assimilation and cell wall growth regulation. Major Facilitator Carriers, and one chloride channel, are similarly co-expressed with pectin lyase, pectinacetylesterase, and cellulose synthase. Contrarily, ammonium transporters show little or no connection with those genes involved in cell wall synthesis. Different aspects related to plant development, embryogenesis, and abiotic stress response will be discussed, given the importance in plant growth of cell wall synthesis and nitrate uptake. Intriguingly, the improvement of abiotic stress tolerance in crops concerns both these processes indicating the importance in sensing the environmental constraints and mediating a response. These evaluations could help to identify candidate genes for breeding purposes.
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