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Iman MN, Haslam DE, Liang L, Guo K, Joshipura K, Pérez CM, Clish C, Tucker KL, Manson JE, Bhupathiraju SN, Fukusaki E, Lasky-Su J, Putri SP. Multidisciplinary approach combining food metabolomics and epidemiology identifies meglutol as an important bioactive metabolite in tempe, an Indonesian fermented food. Food Chem 2024; 446:138744. [PMID: 38432131 PMCID: PMC11247955 DOI: 10.1016/j.foodchem.2024.138744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 03/05/2024]
Abstract
This study introduces a multidisciplinary approach to investigate bioactive food metabolites often overlooked due to their low concentrations. We integrated an in-house food metabolite library (n = 494), a human metabolite library (n = 891) from epidemiological studies, and metabolite pharmacological databases to screen for food metabolites with potential bioactivity. We identified six potential metabolites, including meglutol (3-hydroxy-3-methylglutarate), an understudied low-density lipoprotein (LDL)-lowering compound. We further focused on meglutol as a case study to showcase the range of characterizations achievable with this approach. Green pea tempe was identified to contain the highest meglutol concentration (21.8 ± 4.6 mg/100 g). Furthermore, we identified a significant cross-sectional association between plasma meglutol (per 1-standard deviation) and lower LDL cholesterol in two Hispanic adult cohorts (n = 1,628) (β [standard error]: -5.5 (1.6) mg/dl, P = 0.0005). These findings highlight how multidisciplinary metabolomics can serve as a systematic tool for discovering and enhancing bioactive metabolites in food, such as meglutol, with potential applications in personalized dietary approaches for disease prevention.
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Affiliation(s)
- Marvin N Iman
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan
| | - Danielle E Haslam
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kai Guo
- Center for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Kaumudi Joshipura
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Center for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Cynthia M Pérez
- Department of Biostatistics and Epidemiology, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Clary Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard, USA
| | - Katherine L Tucker
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, USA
| | - JoAnn E Manson
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shilpa N Bhupathiraju
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Japan
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Japan.
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Ding Y, Tao M, Xu L, Wang C, Wang J, Zhao C, Xiao Z, Wang Z. Impacts of nano-acetamiprid pesticide on faba bean root metabolic response and soil health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:171976. [PMID: 38547984 DOI: 10.1016/j.scitotenv.2024.171976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/23/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024]
Abstract
The associated benefits and potential environmental risks of nanopesticides on plant and soil health, particularly in comparison with traditional pesticides, have not been systematically elucidated. Herein, we investigated the impacts of the as-synthesized nano-acetamiprid (Nano-Ace, 20 nm) at low (10 mg/L), medium (50 mg/L), high (100 mg/L) doses and the corresponding high commercial acetamiprid (Ace, 100 mg/L) on the physiological and metabolic response of faba bean (Vicia faba L.) plants, as well as on rhizosphere bacterial communities and functions over short-, medium- and long-term exposures. Overall, Nano-Ace exposure contributed to basic metabolic pathways (e.g., flavonoids, amino acids, TCA cycle intermediate, etc.) in faba bean roots across the whole exposure period. Moreover, Nano-Ace exposure enriched rhizosphere beneficial bacteria (e.g., Streptomyces (420.7%), Pseudomonas (33.8%), Flavobacterium (23.3%)) and suppressed pathogenic bacteria (e.g., Acidovorax (44.5%)). Additionally, Nano-Ace exposure showed a trend of low promotion and high inhibition of soil enzyme activities (e.g., invertase, urease, arylsulfatase, alkaline phosphatase) involved in soil C, N, S, and P cycling, while the inhibition was generally weaker than that of conventional Ace. Altogether, this study indicated that the redox-responsive nano-acetamiprid pesticide possessed high safety for host plants and soil health.
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Affiliation(s)
- Ying Ding
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Mengna Tao
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Lanqing Xu
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Jinghong Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Chunjie Zhao
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Zhenggao Xiao
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China.
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
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Zhou X, Ma Y, Miao R, Li C, Liu Z, Zhang D, Chen S, Luo J, Tang W. Physiological responses and transcriptomic analysis of StCPD gene overexpression in potato under salt stresses. FRONTIERS IN PLANT SCIENCE 2024; 15:1297812. [PMID: 38434433 PMCID: PMC10906663 DOI: 10.3389/fpls.2024.1297812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
Introduction The potato (Solanum tuberosum L.), one of the most vital food crops worldwide, is sensitive to salinity. Brassinosteroids (BRs) are crucial in tolerance to various abiotic stresses. The constitutive photomorphogenesis and dwarf (CPD) gene encodes C-3 oxidase, which is a rate-limiting enzyme that controls the synthesis of BRs. Methods In this study, we used StCPD gene overexpression (T) and un-transgenic (NT) plants obtained from our former research to illustrate adaptive resistance to salt stress at levels of phenotype; cell ultrastructure, physiology, and biochemistry; hormone; and transcription. Results Results showed the accumulation of 2,4-epibrassionolide (EBL) in T potatoes. We found that under high salt situations, the changed Na+/K+ transporter gene expression was linked with the prevalent ionic responses in T plants, which led to lower concentrations of K+ and higher concentrations of Na+ in leaves. Furthermore, RNA-sequencing (RNA-seq) data elucidated that gene expressions in NT and T plants were significantly changed with 200-mM NaCl treatment for 24 h and 48 h, compared with the 0-h treatment. Functional enrichment analysis suggested that most of the differentially expressed genes (DEGs) were related to the regulation of BR-related gene expression, pigment metabolism process, light and action, and plant hormone signal transduction. Discussion These findings suggested that StCPD gene overexpression can alleviate the damage caused by salt stress and enhance the salt resistance of potato plantlets. Our study provides an essential reference for further research on BR regulation of plant molecular mechanisms in potatoes with stress tolerance.
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Affiliation(s)
- Xiangyan Zhou
- State Key Laboratory of Aridland Crop Science/College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yanming Ma
- State Key Laboratory of Aridland Crop Science/College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rong Miao
- State Key Laboratory of Aridland Crop Science/College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Caijuan Li
- State Key Laboratory of Aridland Crop Science/College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ziliang Liu
- State Key Laboratory of Aridland Crop Science/College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Zhang
- State Key Laboratory of Aridland Crop Science/College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Sijin Chen
- State Key Laboratory of Aridland Crop Science/College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiaqi Luo
- Qinzhou District Agricultural Technology Comprehensive Service Center in Tianshui City, Tianshui, China
| | - Wenhui Tang
- Zhuanglang Agricultural Technology Extension Center in Pingliang City, Pingliang, China
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Zhang Y, Qiao D, Zhang Z, Li Y, Shi S, Yang Y. Calcium signal regulated carbohydrate metabolism in wheat seedlings under salinity stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:123-136. [PMID: 38435855 PMCID: PMC10902238 DOI: 10.1007/s12298-024-01413-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024]
Abstract
This study aimed to explore the mechanism by which calcium (Ca) signal regulated carbohydrate metabolism and exogenous Ca alleviated salinity toxicity. Wheat seedlings were treated with sodium chloride (NaCl, 150 mM) alone or combined with 500 μM calcium chloride (CaCl2), lanthanum chloride (LaCl3) and/or ethylene glycol tetraacetic acid (EGTA) to primarily analyse carbohydrate starch and sucrose metabolism, as well as Ca signaling components. Treatment with NaCl, EGTA, or LaCl3 alone retarded wheat-seedling growth and decreased starch content accompanied by weakened ribulose-1,5-bisphosphate carboxylation/oxygenase (Rubisco) and Rubisco activase activities, as well as enhanced glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, alpha-amylase, and beta-amylase activities. However, it increased the sucrose level, up-regulated the sucrose phosphate synthase (SPS) and sucrose synthase (SuSy) activities and TaSPS and TaSuSy expression together, but down-regulated the acid invertase (SA-Inv) and alkaline/neutral invertase (A/N-Inv) activities and TaSA-Inv and TaA/N-Inv expression. Except for unchanged A/N-Inv activities and TaA/N-Inv expression, adding CaCl2 effectively blocked the sodium salt-induced changes of these parameters, which was partially eliminated by EGTA or LaCl3 presence. Furthermore, NaCl treatment also significantly inhibited Ca-dependent protein kinases and Ca2+-ATPase activities and their gene expression in wheat leaves, which was effectively relieved by adding CaCl2. Taken together, CaCl2 application effectively alleviated the sodium salt-induced retardation of wheat-seedling growth by enhancing starch anabolism and sucrose catabolism, and intracellular Ca signal regulated the enzyme activities and gene expression of starch and sucrose metabolism in the leaves of sodium salt-stressed wheat seedlings.
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Affiliation(s)
- Ya Zhang
- School of Life Science, College of Life Science, Northwest Normal University, Lanzhou, 730070 Gansu People’s Republic of China
| | - Dan Qiao
- School of Life Science, College of Life Science, Northwest Normal University, Lanzhou, 730070 Gansu People’s Republic of China
| | - Zhe Zhang
- School of Life Science, College of Life Science, Northwest Normal University, Lanzhou, 730070 Gansu People’s Republic of China
| | - Yaping Li
- School of Life Science, College of Life Science, Northwest Normal University, Lanzhou, 730070 Gansu People’s Republic of China
| | - Shuqian Shi
- School of Life Science, College of Life Science, Northwest Normal University, Lanzhou, 730070 Gansu People’s Republic of China
| | - Yingli Yang
- School of Life Science, College of Life Science, Northwest Normal University, Lanzhou, 730070 Gansu People’s Republic of China
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Zhang X, Zhang Y, Chen Z, Gu P, Li X, Wang G. Exploring cell aggregation as a defense strategy against perchlorate stress in Chlamydomonas reinhardtii through multi-omics analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167045. [PMID: 37709088 DOI: 10.1016/j.scitotenv.2023.167045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Perchlorate (ClO4-) is a type of novel, widely distributed, and persistent inorganic pollutant. However, the impacts of perchlorate on freshwater algae remain unclear. In this study, the response and defense mechanisms of microalgae (Chlamydomonas reinhardtii) under perchlorate stress were investigated by integrating physiological and biochemical monitoring, transcriptomics, and metabolomics. Weighted gene co-expression network analysis (WGCNA) of transcriptome data was used to analyze the relationship between genes and phenotype and screen the key pathways. C. reinhardtii exhibited aggregate behavior when exposed to 100- and 200-mM perchlorate but was restored to its unicellular lifestyle when transferred to fresh medium. WGCNA results found that the "carbohydrate metabolism" and "lipid metabolism" pathways were closely related to cell aggregation phenotype. The differential expression genes (DEGs) and differentially accumulated metabolites (DAMs) of these pathways were upregulated, indicating that the lipid and carbohydrate metabolisms were enhanced in aggregated cells. Additionally, most genes and metabolites related to phytohormone abscisic acid (ABA) biosynthesis and the mitogen-activated protein kinase (MAPK) signaling pathway were significantly upregulated, indicating their crucial roles in the signal transmission of aggregated cells. Meanwhile, in aggregated cells, extracellular polymeric substances (EPS) and lipid contents increased, photosynthesis activity decreased, and the antioxidant system was activated. These characteristics contributed to C. reinhardtii's improved resistance to perchlorate stress. Above results demonstrated that cell aggregation behavior was the principal defense strategy of C. reinhardtii against perchlorate. Overall, this study sheds new light on the impact mechanisms of perchlorate to aquatic microalgae and provides multi-omics insights into the research of multicellular-like aggregation as an adaptation strategy to abiotic stress. These results are beneficial for assessing the risk of perchlorate in aquatic environments.
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Affiliation(s)
- Xianyuan Zhang
- Key Laboratory for Algae Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixiao Zhang
- Key Laboratory for Algae Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; School of Science, Tibet University, Lasha 850000, China
| | - Zixu Chen
- Key Laboratory for Algae Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peifan Gu
- Key Laboratory for Algae Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Li
- Key Laboratory for Algae Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Gaohong Wang
- Key Laboratory for Algae Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Raza A, Tabassum J, Fakhar AZ, Sharif R, Chen H, Zhang C, Ju L, Fotopoulos V, Siddique KHM, Singh RK, Zhuang W, Varshney RK. Smart reprograming of plants against salinity stress using modern biotechnological tools. Crit Rev Biotechnol 2023; 43:1035-1062. [PMID: 35968922 DOI: 10.1080/07388551.2022.2093695] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/08/2022] [Indexed: 01/19/2023]
Abstract
Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Zhejiang, China
| | - Ali Zeeshan Fakhar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Luo Ju
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Zhejiang, China
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology & Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Rakesh K Singh
- Crop Diversification and Genetics, International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch's Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia
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Xu H, Halford NG, Guo G, Chen Z, Li Y, Zhou L, Liu C, Xu R. Transcriptomic and Metabolomic Analyses Reveal the Importance of Lipid Metabolism and Photosynthesis Regulation in High Salinity Tolerance in Barley ( Hordeum vulgare L.) Leaves Derived from Mutagenesis Combined with Microspore Culture. Int J Mol Sci 2023; 24:16757. [PMID: 38069082 PMCID: PMC10705989 DOI: 10.3390/ijms242316757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Barley is the most salt-tolerant cereal crop. However, little attention has been paid to the salt-tolerant doubled haploids of barley derived from mutagenesis combined with isolated microspore culture. In the present study, barley doubled haploid (DH) line 20, which was produced by mutagenesis combined with isolated microspore culture, showed stably and heritably better salt tolerance than the wild type H30 in terms of fresh shoot weight, dry shoot weight, K+/Na+ ratio and photosynthetic characteristics. Transcriptome and metabolome analyses were performed to compare the changes in gene expression and metabolites between DH20 and H30. A total of 462 differentially expressed genes (DEGs) and 152 differentially accumulated metabolites (DAMs) were identified in DH20 compared to H30 under salt stress. Among the DAMs, fatty acids were the most accumulated in DH20 under salt stress. The integration of transcriptome and metabolome analyses revealed that nine key biomarkers, including two metabolites and seven genes, could distinguish DH20 and H30 when exposed to high salt. The pathways of linoleic acid metabolism, alpha-linolenic acid metabolism, glycerolipid metabolism, photosynthesis, and alanine, aspartate and glutamate metabolism were significantly enriched in DH20 with DEGs and DAMs in response to salt stress. These results suggest that DH20 may enhance resilience by promoting lipid metabolism, maintaining energy metabolism and decreasing amino acids metabolism. The study provided novel insights for the rapid generation of homozygous mutant plants by mutagenesis combined with microspore culture technology and also identified candidate genes and metabolites that may enable the mutant plants to cope with salt stress.
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Affiliation(s)
- Hongwei Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | | | - Guimei Guo
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Zhiwei Chen
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yingbo Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Longhua Zhou
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Chenghong Liu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Zhang Q, Zhang Y, Wang Y, Zou J, Lin S, Chen M, Miao P, Jia X, Cheng P, Pang X, Ye J, Wang H. Transcriptomic Analysis of the Effect of Pruning on Growth, Quality, and Yield of Wuyi Rock Tea. PLANTS (BASEL, SWITZERLAND) 2023; 12:3625. [PMID: 37896087 PMCID: PMC10610282 DOI: 10.3390/plants12203625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/14/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023]
Abstract
Pruning is an important agronomic measure in tea plantation management. In this study, we analyzed the effect of pruning on gene expression in tea leaves from a transcriptomics perspective and verified the results of a transcriptomic analysis in terms of changes in physiological indicators of tea leaves. The results showed that pruning enhanced the gene expression of nine metabolic pathways in tea leaves, including fatty acid synthesis and carbohydrate metabolism, nitrogen metabolism, protein processing in the endoplasmic reticulum, and plant hormone signal transduction, thereby promoting the growth of tea plants and increasing tea yield. However, pruning reduced the gene expression of nine metabolic pathways, including secondary metabolites biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, and sesquiterpenoid and triterpenoid biosynthesis, and lowered the content of caffeine, flavonoids, and free amino acids in tea plant leaves. In conclusion, pruning could promote the growth of tea plants and increase the yield of tea, but it was not conducive to the accumulation of some quality indicators in tea leaves, especially caffeine, flavonoids, and free amino acids, which, in turn, reduced the quality of tea. This study provides an important theoretical reference for the management of agronomic measures in tea plantations.
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Affiliation(s)
- Qi Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (Q.Z.)
| | - Ying Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (Q.Z.)
| | - Yuhua Wang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China (J.Z.)
| | - Jishuang Zou
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China (J.Z.)
| | - Shaoxiong Lin
- College of Life Science, Longyan University, Longyan 364012, China
| | - Meihui Chen
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (Q.Z.)
| | - Pengyao Miao
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (Q.Z.)
| | - Xiaoli Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (Q.Z.)
| | - Pengyuan Cheng
- College of Life Science, Longyan University, Longyan 364012, China
| | - Xiaomin Pang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (Q.Z.)
| | - Jianghua Ye
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (Q.Z.)
| | - Haibin Wang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (Q.Z.)
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Zixuan Z, Rongping D, Yingying Z, Yueyue L, Jiajing Z, Yue J, Tan M, Zengxu X. The phenotypic variation mechanisms of Atractylodes lancea post-cultivation revealed by conjoint analysis of rhizomic transcriptome and metabolome. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108025. [PMID: 37722282 DOI: 10.1016/j.plaphy.2023.108025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/07/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
The wild Atractylodes lancea rhizomes have been traditionally used as herbal medicine. As the increasingly exhaustion of wild A. lancea, the artificial cultivation mainly contributed to the medicinal material production. However, besides the phenotypic variation of rhizome phenotypic trait alteration, the qualities of cultivated A. lancea decrease compared with the wild counterpart. To unveil the physiological and molecular mechanism beneath the phenotypic variation, GC-MS-based volatile organic compounds (VOCs) profiling and RNAseq-based transcriptome analysis were conducted. The volatile metabolomics profiling revealed 65 differentially accumulated metabolites (DAMs) while the transcriptomic profiling identified 12 009 differentially expressed unigenes (DEGs) post-cultivation. The volatile active compounds including atractylone, and eudesmol accumulated more in wild rhizome than in the cultivated counterpart, and several unigenes in terpene synthesis were downregulated under cultivated condition. Compared with the wild A. lancea rhizome, the contents of bioactive Jasmonic Acid (JAs) in cultivated A. lancea rhizome were higher, and evidences that JAs negatively regulate the terpenes biosynthesis in the cultivated A. lancea rhizome were also provided. The combinational omics analysis further indicated the high correlation between the ten cultivation-suppressed VOCs and the cultivation-altered genes for sesquiterpenoids biosynthesis in A. lancea. The network of the cultivation-altered transcription factors (TFs) and the ten VOCs suggested TFs (e.g. Arabidopsis ERF13 homologs and WRKY50) are involved in the regulation of terpenes biosynthesis. These results laid a theoretical basis for developing geo-herbalism medicinal plants with "high quality and optimal shape".
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Affiliation(s)
- Zhang Zixuan
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Ding Rongping
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Zhang Yingying
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Liao Yueyue
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Zhao Jiajing
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Jia Yue
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Mingpu Tan
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Xiang Zengxu
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
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Sun M, Sun S, Jia Z, Zhang H, Ou C, Ma W, Wang J, Li M, Mao P. Genome-wide analysis and expression profiling of glyoxalase gene families in oat ( Avena sativa) indicate their responses to abiotic stress during seed germination. FRONTIERS IN PLANT SCIENCE 2023; 14:1215084. [PMID: 37396634 PMCID: PMC10308377 DOI: 10.3389/fpls.2023.1215084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Abiotic stresses have deleterious effects on seed germination and seedling establishment, leading to significant crop yield losses. Adverse environmental conditions can cause the accumulation of methylglyoxal (MG) within plant cells, which can negatively impact plant growth and development. The glyoxalase system, which consists of the glutathione (GSH)-dependent enzymes glyoxalase I (GLX1) and glyoxalase II (GLX2), as well as the GSH-independent glyoxalase III (GLX3 or DJ-1), plays a crucial role in detoxifying MG. However, genome-wide analysis of glyoxalase genes has not been performed for one of the agricultural important species, oat (Avena sativa). This study identified a total of 26 AsGLX1 genes, including 8 genes encoding Ni2+-dependent GLX1s and 2 genes encoding Zn2+-dependent GLX1s. Additionally, 14 AsGLX2 genes were identified, of which 3 genes encoded proteins with both lactamase B and hydroxyacylglutathione hydrolase C-terminal domains and potential catalytic activity, and 15 AsGLX3 genes encoding proteins containing double DJ-1 domains. The domain architecture of the three gene families strongly correlates with the clades observed in the phylogenetic trees. The AsGLX1, AsGLX2, and AsGLX3 genes were evenly distributed in the A, C, and D subgenomes, and gene duplication of AsGLX1 and AsGLX3 genes resulted from tandem duplications. Besides the core cis-elements, hormone responsive elements dominated the promoter regions of the glyoxalase genes, and stress responsive elements were also frequently observed. The subcellular localization of glyoxalases was predicted to be primarily in the cytoplasm, chloroplasts, and mitochondria, with a few presents in the nucleus, which is consistent with their tissue-specific expression. The highest expression levels were observed in leaves and seeds, indicating that these genes may play important roles in maintaining leaf function and ensuring seed vigor. Moreover, based on in silico predication and expression pattern analysis, AsGLX1-7A, AsGLX2-5D, AsDJ-1-5D, AsGLX1-3D2, and AsGLX1-2A were suggested as promising candidate genes for improving stress resistance or seed vigor in oat. Overall, the identification and analysis of the glyoxalase gene families in this study can provide new strategies for improving oat stress resistance and seed vigor.
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Yang Y, Song H, Yao P, Zhang S, Jia H, Ye X. NtLTPI.38, a plasma membrane-localized protein, mediates lipid metabolism and salt tolerance in Nicotiana tabacum. Int J Biol Macromol 2023; 242:125007. [PMID: 37217046 DOI: 10.1016/j.ijbiomac.2023.125007] [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: 11/27/2022] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
Non-specific lipid transfer proteins (nsLTPs) typically have conserved structural resemblance, low sequence identity, and broad biological functions in plant growth and stress resistance. Here, a plasma membrane-localized nsLTP, NtLTPI.38, was identified in tobacco plants. Multi-omics integrated analysis revealed that NtLTPI.38 overexpression or knock out significantly changed glycerophospholipid and glycerolipid metabolism pathways. NtLTPI.38 overexpression remarkably increased phosphatidylcholine, phosphatidylethanolamine, triacylglycerol, and flavonoid levels, but decreased ceramides compared to wild type and mutant lines. Differentially expressed genes were associated with lipid metabolite and flavonoid synthesis. Many genes related to Ca2+ channels, abscisic acid (ABA) signal transduction, and ion transport pathways were upregulated in overexpressing plants. NtLTPI.38 overexpression in salt-stressed tobacco triggered a Ca2+ and K+ influx in leaves, increased the contents of chlorophyll, proline, flavonoids, and osmotic tolerance, and raised enzymatic antioxidant activities as well as the expression level of related genes. However, mutants accumulated more O2- and H2O2, exhibited ionic imbalance, gathered excess Na+, Cl-, and malondialdehyde, with more severe ion leakage. Therefore, NtLTPI.38 enhanced salt tolerance in tobacco by regulating lipid and flavonoid synthesis, antioxidant activity, ion homeostasis, and ABA signaling pathways.
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Affiliation(s)
- Yongxia Yang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Hao Song
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Panpan Yao
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Songtao Zhang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongfang Jia
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiefeng Ye
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
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Wang W, Guo J, Ma J, Wang Z, Zhang L, Wang Z, Meng M, Zhang C, Sun F, Xi Y. Comprehensive Transcriptomic and Metabolic Profiling of Agrobacterium- tumefaciens-Infected Immature Wheat Embryos. Int J Mol Sci 2023; 24:ijms24098449. [PMID: 37176157 PMCID: PMC10179373 DOI: 10.3390/ijms24098449] [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: 04/10/2023] [Revised: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
The transformation efficiency (TE) was improved by a series of special chemical and physical methods using immature embryos from the cultivar Fielder, with the PureWheat technique. To analyze the reaction of immature embryos infected, which seemed to provide the necessary by Agrobacterium tumefaciens in PureWheat, a combination of scanning electron microscopy (SEM), complete transcriptome analysis, and metabolome analysis was conducted to understand the progress. The results of the SEM analysis revealed that Agrobacterium tumefaciens were deposited under the damaged cortex of immature embryos as a result of pretreatment and contacted the receptor cells to improve the TE. Transcriptome analysis indicated that the differentially expressed genes were mainly enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, plant-pathogen interaction, plant hormone signal transduction, and the MAPK (Mitogen-activated protein kinase) signaling pathway. By analyzing the correlation between differentially expressed genes and metabolites, the expression of many genes and the accumulation of metabolites were changed in glucose metabolism and the TCA cycle (Citrate cycle), as well as the amino acid metabolism; this suggests that the infection of wheat embryos with Agrobacterium is an energy-demanding process. The shikimate pathway may act as a hub between glucose metabolism and phenylpropanoid metabolism during Agrobacterium infection. The downregulation of the F5H gene and upregulation of the CCR gene led to the accumulation of lignin precursors through phenylpropanoid metabolism. In addition, several metabolic pathways and oxidases were found to be involved in the infection treatment, including melatonin biosynthesis, benzoxazinoid biosynthesis, betaine biosynthesis, superoxide dismutase, and peroxidase, suggesting that wheat embryos may be under the stress of Agrobacterium and, thus, undergo an oxidative stress response. These findings explore the physiological and molecular changes of immature embryos during the co-culture stage of the PureWheat technique and provide insights for Agrobacterium-mediated transgenic wheat experiments.
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Affiliation(s)
- Weiwei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jinliang Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jiayang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhulin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Lining Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zixu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Min Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Fengli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yajun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
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Zhang Y, Zhang Q, Wang Y, Lin S, Chen M, Cheng P, Wang Y, Du M, Jia X, Wang H, Ye J. Effects of Magnesium on Transcriptome and Physicochemical Index of Tea Leaves. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091810. [PMID: 37176867 PMCID: PMC10181054 DOI: 10.3390/plants12091810] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Magnesium (Mg) is one of the essential elements for the growth of tea tree and is extremely important for its development. In this study, we investigated the effect of Mg on the transcriptome and physicochemical indexes of tea leaves, and the results showed that Mg could significantly affect the gene expression of tea leaves. The results of Orthogonal Partial Least-Squares Discriminant Analysis (OPLS-DA) model analysis showed that a total of 300 key genes (Variable Importance for the Projection, VIP > 1) were screened under different concentrations of Mg treatment, among which 140 genes were up-regulated and 160 genes were down-regulated. The bubble map was used to screen the characteristic genes from the above key genes, and a total of 121 representative characteristic genes were obtained, mainly involving 9 metabolic pathways. Among them, gene expression of three metabolic pathways, including porphyrin metabolism, alpha-linolenic acid metabolism and photosynthesis, showed an increasing trend with the increase of Mg concentration, while gene expression of four metabolic pathways, including biosynthesis of secondary metabolites, anthocyanin biosynthesis, ABC transporters, pentose and glucuronate interconversions, showed a decreasing trend. The results of physiological index analysis showed that with the increase of Mg concentration, the photosynthetic physiological index, theanine and soluble sugar content of tea leaves showed an increasing trend, while the content of tea polyphenol, flavone and caffeine showed a decreasing trend. The results of TOPSIS analysis showed that the physiological indexes of tea trees most affected by Mg were chlorophyll, tea polyphenols and flavonoids, while the metabolic pathways most affected by Mg on gene expression were the metabolic pathways and biosynthesis of secondary metabolites. It can be seen that the effects of Mg on tea tree were mainly related to photosynthesis and synthesis of secondary metabolites, and Mg was beneficial for improving the photosynthetic capacity of tea tree, enhancing the accumulation of primary metabolites, and thus increasing tea yield. However, Mg was not conducive to the synthesis of secondary metabolites of tea tree and the accumulation of main quality indexes of tea leaves.
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Affiliation(s)
- Ying Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qi Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China
| | - Yuhua Wang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shaoxiong Lin
- College of Life Science, Longyan University, Longyan 364012, China
| | - Meihui Chen
- College of Tea and Food, Wuyi University, Wuyishan 354300, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pengyuan Cheng
- College of Life Science, Longyan University, Longyan 364012, China
| | - Yuchao Wang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengru Du
- College of Tea and Food, Wuyi University, Wuyishan 354300, China
| | - Xiaoli Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China
| | - Haibin Wang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China
| | - Jianghua Ye
- College of Tea and Food, Wuyi University, Wuyishan 354300, China
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Feng Y, Liu L, Yu J, Chen R, Hu C, Wang H, Li D, Wang Z, Zhao Z. Combined transcriptomic and metabolomic analyses reveal the mechanism of debagged ‘Fuji’ apple sunburn. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Transcriptome Mechanisms of Tomato Seedlings Induced by Low-Red to Far-Red Light Ratio under Calcium Nitrate Stress. Int J Mol Sci 2023; 24:ijms24043738. [PMID: 36835148 PMCID: PMC9963801 DOI: 10.3390/ijms24043738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023] Open
Abstract
In recent times, the excessive accumulation of nitrate has been one of the main reasons for the secondary salinization of greenhouse soils. Light plays a key role in a plant's growth, development, and response to stress. A low-red to far-red (R:FR) light ratio could enhance plant salinity tolerance, but the mechanism at a molecular level is unclear. Thus, we analyzed the transcriptome responses of tomato seedlings to calcium nitrate stress under either a low R:FR ratio (0.7) or normal light conditions. Under calcium nitrate stress, a low R:FR ratio enhanced both the antioxidant defense system and the rapid physiological accumulation of proline in tomato leaves, which promoted plant adaptability. Using weighted gene co-expression network analysis (WGCNA), three modules including 368 differentially expressed genes (DEGs) were determined to be significantly associated with these plant traits. Functional annotations showed that the responses of these DEGs to a low R:FR ratio under excessive nitrate stress were enriched in the areas of hormone signal transduction, amino acid biosynthesis, sulfide metabolism, and oxidoreductase activity. Furthermore, we identified important novel hub genes encoding certain proteins, including FBNs, SULTRs, and GATA-like transcription factor, which may play a vital role in low R:FR light-induced salt responses. These findings offer a new perspective on the mechanisms and environmental implications behind low R:FR ratio light-modulated tomato saline tolerance.
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Wang X, Yin J, Wang J, Li J. Integrative analysis of transcriptome and metabolome revealed the mechanisms by which flavonoids and phytohormones regulated the adaptation of alfalfa roots to NaCl stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1117868. [PMID: 36818861 PMCID: PMC9936617 DOI: 10.3389/fpls.2023.1117868] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Salinity critically affects the growth and development of alfalfa (Medicago sativa), making it necessary to understand the molecular mechanism of alfalfa's adaptation to salt stress. METHODS In this study, alfalfa roots were subjected to salt stress and transcriptomics and metabolomics analyses were performed. RESULTS The results showed that flavonoid synthesis, hormone synthesis, and transduction pathways may be involved in the alfalfa salt stress adaptation reaction, and that they are related. Combined analysis of differential genes and differential metabolites found that dihydroquercetin and beta-ring hydroxylase (LUT5), ABA responsive element binding factor 2 (ABF2), protein phosphatase PP2C (PP2C) and abscisic acid (ABA) receptor PYL2 (PYL), luteolinidin was significantly correlated with PP2C and phytochrome-interacting factor 4 (PIF4) and (+)-7-isomethyl jasmonate were significantly correlated with flavonol synthase (FLS) gene. (+)-7-isomethyl jasmonate and homoeriodictyol chalcone were significantly correlated with peroxidase (POD). POD was significantly up-regulated under NaCl stress for 6 and 24 h. Moreover, flavonoids, gibberellin (GA), jasmonic acid (JA) and ABA were suggested to play an important role in alfalfa's response to salt stress. Further, GA,ABA, and JA may be involved in the regulation of flavonoids to improve alfalfa's salt tolerance, and JA may be a key signal to promote the synthesis of flavonoids. DISCUSSION This study revealed the possible molecular mechanism of alfalfa adaptation to salt stress, and identified a number of salt-tolerance candidate genes from the synthesis and signal transduction pathways of flavonoids and plant hormones, providing new insights into the regulatory network of alfalfa response to salt stress.
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Li H, Kong F, Tang T, Luo Y, Gao H, Xu J, Xing G, Li L. Physiological and Transcriptomic Analyses Revealed That Humic Acids Improve Low-Temperature Stress Tolerance in Zucchini ( Cucurbita pepo L.) Seedlings. PLANTS (BASEL, SWITZERLAND) 2023; 12:548. [PMID: 36771631 PMCID: PMC9921430 DOI: 10.3390/plants12030548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/07/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Zucchini (Cucurbita pepo L.) is one of the main vegetable crops grown under protected cultivation in northern China. Low-temperature (LT) stress severely inhibits the growth of zucchini seedlings, resulting in reductions in yield and quality. Here, using three kinds of different humic acids, including coal-based humic acid (CHA), fulvic acid (FA), and biochemical humic acid (BHA), we investigated the effects of humic acids against LT stress (5 °C) in zucchini seedlings. Treatment with all three kinds of humic acids improves LT stress tolerance by decreasing oxidative damage through increases in antioxidative enzyme activities and the contents of soluble sugar and proline in zucchini seedlings, especially after BHA application. Comparative transcriptomic analysis revealed that a total of 17 differentially expressed genes (DEGs) were commonly induced in the leaves of FA-, CHA-, and BHA-treated zucchini seedlings under LT stress, including calmodulin, ethylene-responsive transcription factors (TFs), peroxidases, and 10 TFs, including two NAC and seven WRKY genes. Altogether, these results indicated that supplementation with humic acids reprograms plant metabolism and modulates the expression of genes involved in ROS scavenging, phytohormone metabolism, or signaling pathways, finally improving LT stress tolerance in zucchini seedlings.
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Ling L, Li M, Chen N, Ren G, Qu L, Yue H, Wu X, Zhao J. Genome-Wide Analysis and Expression of the GRAS Transcription Factor Family in Avena sativa. Genes (Basel) 2023; 14:genes14010164. [PMID: 36672905 PMCID: PMC9858933 DOI: 10.3390/genes14010164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The GRAS transcription factor is an important transcription factor in plants. In recent years, more GRAS genes have been identified in many plant species. However, the GRAS gene family has not yet been studied in Avena sativa. We identified 100 members of the GRAS gene family in A. sativa (Avena sativa), named them AsGRAS1~AsGRAS100 according to the positions of 21 chromosomes, and classified them into 9 subfamilies. In this study, the motif and gene structures were also relatively conserved in the same subfamilies. At the same time, we found a great deal related to the stress of cis-acting promoter regulatory elements (MBS, ABRE, and TC-rich repeat elements). qRT-PCR suggested that the AsGRAS gene family (GRAS gene family in A. sativa) can regulate the response to salt, saline-alkali, and cold and freezing abiotic stresses. The current study provides original and detailed information about the AsGRAS gene family, which contributes to the functional characterization of GRAS proteins in other plants.
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Jia C, Guo B, Wang B, Li X, Yang T, Li N, Wang J, Yu Q. Integrated metabolomic and transcriptomic analysis reveals the role of phenylpropanoid biosynthesis pathway in tomato roots during salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1023696. [PMID: 36570882 PMCID: PMC9773889 DOI: 10.3389/fpls.2022.1023696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
As global soil salinization continues to intensify, there is a need to enhance salt tolerance in crops. Understanding the molecular mechanisms of tomato (Solanum lycopersicum) roots' adaptation to salt stress is of great significance to enhance its salt tolerance and promote its planting in saline soils. A combined analysis of the metabolome and transcriptome of S. lycopersicum roots under different periods of salt stress according to changes in phenotypic and root physiological indices revealed that different accumulated metabolites and differentially expressed genes (DEGs) associated with phenylpropanoid biosynthesis were significantly altered. The levels of phenylpropanoids increased and showed a dynamic trend with the duration of salt stress. Ferulic acid (FA) and spermidine (Spd) levels were substantially up-regulated at the initial and mid-late stages of salt stress, respectively, and were significantly correlated with the expression of the corresponding synthetic genes. The results of canonical correlation analysis screening of highly correlated DEGs and construction of regulatory relationship networks with transcription factors (TFs) for FA and Spd, respectively, showed that the obtained target genes were regulated by most of the TFs, and TFs such as MYB, Dof, BPC, GRAS, and AP2/ERF might contribute to the regulation of FA and Spd content levels. Ultimately, FA and Spd attenuated the harm caused by salt stress in S. lycopersicum, and they may be key regulators of its salt tolerance. These findings uncover the dynamics and possible molecular mechanisms of phenylpropanoids during different salt stress periods, providing a basis for future studies and crop improvement.
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Affiliation(s)
- Chunping Jia
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Bin Guo
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Xin Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Qinghui Yu
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
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Sun M, Sun S, Jia Z, Ma W, Mao C, Ou C, Wang J, Zhang H, Hong L, Li M, Jia S, Mao P. Genome-Wide Analysis and Expression Profiling of Glutathione Reductase Gene Family in Oat ( Avena sativa) Indicate Their Responses to Abiotic Stress during Seed Imbibition. Int J Mol Sci 2022; 23:ijms231911650. [PMID: 36232950 PMCID: PMC9569478 DOI: 10.3390/ijms231911650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2022] Open
Abstract
Abiotic stress disturbs plant cellular redox homeostasis, inhibiting seed germination and plant growth. This is a crucial limitation to crop yield. Glutathione reductase (GR) is an important component of the ascorbate-glutathione (AsA-GSH) cycle which is involved in multiple plant metabolic processes. In the present study, GRs in A. sativa (AsGRs) were selected to explore their molecular characterization, phylogenetic relationship, and RNA expression changes during seed imbibition under abiotic stress. Seven AsGR genes were identified and mapped on six chromosomes of A, C, and D subgenomes. Phylogenetic analysis and subcellular localization of AsGR proteins divided them into two sub-families, AsGR1 and AsGR2, which were predicted to be mainly located in cytoplasm, mitochondrion, and chloroplast. Cis-elements relevant to stress and hormone responses are distributed in promoter regions of AsGRs. Tissue-specific expression profiling showed that AsGR1 genes were highly expressed in roots, leaves, and seeds, while AsGR2 genes were highly expressed in leaves and seeds. Both AsGR1 and AsGR2 genes showed a decreasing-increasing expression trend during seed germination under non-stress conditions. In addition, their responses to drought, salt, cold, copper, H2O2, and ageing treatments were quite different during seed imbibition. Among the seven AsGR genes, AsGR1-A, AsGR1-C, AsGR2-A, and AsGR2-D responded more significantly, especially under drought, ageing, and H2O2 stress. This study has laid the ground for the functional characterization of GR and the improvement of oat stress tolerance and seed vigor.
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Chen Z, Zhong W, Zhou Y, Ji P, Wan Y, Shi S, Yang Z, Gong Y, Mu F, Chen S. Integrative analysis of metabolome and transcriptome reveals the improvements of seed quality in vegetable soybean (Glycine max (L.) Merr.). PHYTOCHEMISTRY 2022; 200:113216. [PMID: 35487251 DOI: 10.1016/j.phytochem.2022.113216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Vegetable soybean is derived from grain soybean. Seeds of vegetable soybean are bigger, sweeter, and have smoother texture and better flavor than those of grain soybean. To better understand the improvements of seed quality in vegetable soybean, comparative metabolome and transcriptome analyses were performed in the developing seeds between grain (Williams 82) and vegetable (Jiaoda 133) soybeans. A total of 299 differential metabolites were identified between two genotypes, with an increase in free amino acids, carbohydrates, sterols, and flavonoids and a decrease in fatty acid in vegetable soybean. Thousands of differentially expressed genes (DEGs) were identified by transcriptome analysis. DEGs were used for weighted gene co-expression network analysis (WGCNA), yielding 16 co-expression modules. The expression patterns of DEGs within these modules were distinct between two genotypes. Functional enrichment analysis revealed that metabolic pathways, including alanine, aspartate and glutamate metabolism, fatty acid degradation, starch and sucrose metabolism, sucrose transport, and flavonoid biosynthesis, were up-regulated, whereas photosynthesis, arginine biosynthesis, arginine and proline metabolism, glycolysis/gluconeogenesis, and fatty acid biosynthesis were down-regulated in vegetable soybean. Reasonably, the alterations of metabolic pathways corresponding to DEGs partly explained the formation of differential metabolites. These findings provide a better understanding of seed development and breeding improvements of vegetable soybean.
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Affiliation(s)
- Zhengjie Chen
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Wenjuan Zhong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Yonghang Zhou
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Peicheng Ji
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Yonglu Wan
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Shengjia Shi
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Zehu Yang
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Yiyun Gong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Fangsheng Mu
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Siwei Chen
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
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22
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Zhang S, Yin F, Li J, Ren S, Liang X, Zhang Y, Wang L, Wang M, Zhang C. Transcriptomic and metabolomic investigation of metabolic disruption in Vigna unguiculata L. triggered by acetamiprid and cyromazine. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113675. [PMID: 35617907 DOI: 10.1016/j.ecoenv.2022.113675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
A variety of pesticides are often used in agricultural management to control target pests but may trigger disruptions in the metabolism of nontarget organisms, ultimately affecting crop quality. Acetamiprid (ACE) and cyromazine (CYR) are two frequently used insecticides on cowpea, so it is critical to understand whether these two insecticides cause metabolic disorders in cowpea quality changes and the mechanism by which they do so. Here, we used metabolomic and transcriptomic methods to explore the mechanisms of the effects of ACE, CYR, and their mixture (MIX) on cowpea. In this study, ACE, CYR and MIX had no significant effects on plant biomass or growth status but decreased the contents of starch, soluble protein, and total flavonoids. All treatments reduced the total flavonoid content, but MIX showed the largest reduction of 10.02%. Metabolomic and transcriptomic analyses revealed that ACE markedly affected amino acid metabolism, and CYR and MIX affected sugar metabolism and flavonoid synthesis pathways. ACE and CYR reduced the levels of alanine, glutamic acid, isoleucine and phenylalanine and the expression of amino acid-related genes in cowpea, while MIX significantly increased the levels of most amino acids. All pesticide treatments reduced saccharide levels and related genes, with the most pronounced reduction in the MIX treatment. Exposure to ACE decreased the content of naringenin chalcone and quercetin and increased the content of anthocyanins in cowpeas, while MIX caused a significant decrease in the contents of quercetin and anthocyanins. According to the current study, single and mixed pesticides had different effects on the active ingredients of cowpea, with MIX causing the most significant decrease in the metabolite content of cowpea. These results provide important insights from a molecular perspective on how neonicotinoids and triazine insecticides affect cowpea metabolism.
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Affiliation(s)
- Shanying Zhang
- College of Food Science and Engineering, Hainan University, 570228 Haikou, China; Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Fengman Yin
- College of Life Sciences, Hainan University, Haikou 570228, China
| | - Jiahao Li
- College of Food Science and Engineering, Hainan University, 570228 Haikou, China; Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, China; Laboratory of Quality and Safety Risk Assessment for Agro-products (Haikou), Ministry of Agriculture, China
| | - Saihao Ren
- College of Food Science and Engineering, Hainan University, 570228 Haikou, China; Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Xiaoyu Liang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Laboratory of Quality and Safety Risk Assessment for Agro-products (Haikou), Ministry of Agriculture, China
| | - Yu Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Laboratory of Quality and Safety Risk Assessment for Agro-products (Haikou), Ministry of Agriculture, China
| | - Lifeng Wang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture and Rural Afairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Meng Wang
- College of Food Science and Engineering, Hainan University, 570228 Haikou, China; Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
| | - Chenghui Zhang
- College of Food Science and Engineering, Hainan University, 570228 Haikou, China; Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, China; Laboratory of Quality and Safety Risk Assessment for Agro-products (Haikou), Ministry of Agriculture, China.
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23
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Chen X, Xu Z, Zhao B, Yang Y, Mi J, Zhao Z, Liu J. Physiological and Proteomic Analysis Responsive Mechanisms for Salt Stress in Oat. FRONTIERS IN PLANT SCIENCE 2022; 13:891674. [PMID: 35783977 PMCID: PMC9240473 DOI: 10.3389/fpls.2022.891674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Oat is considered as a moderately salt-tolerant crop that can be used to improve saline and alkaline soils. Previous studies have focused on short-term salt stress exposure, and the molecular mechanisms of salt tolerance in oat have not yet been elucidated. In this study, the salt-tolerant oat cultivar Vao-9 and the salt-sensitive oat cultivar Bai5 were treated with 6 days of 0 and 150 mmol L-1 salt stress (nNaCl:nNa2SO4 = 1:1). Label-Free technology was then used to analyze the differentially expressed proteins in leaves under 0 and 150 mmol L-1 salt stress. The obtained results indicated that total of 2,631 proteins were identified by mass spectrometry in the four samples. The salt-tolerant cultivar Vao-9 mainly enhances its carbohydrate and energy metabolism through the pentose and glucuronate interconversions, and carbon fixation pathways in prokaryotes, thereby reducing the damage caused by salt stress. In addition, the down-regulation of ribosomes expression and the up-regulated expression of HSPs and CRT are all through the regulation of protein synthesis in response to salt stress. However, GABA metabolism presents a different synthesis pattern in Bai5 and Vao-9. The main KEGG function of differential expressed protein (DEP) in Bai5 is classified into protein processing in the endoplasmic reticulum, estrogen signaling pathway, antigen processing and presentation, longevity regulating pathway-multiple species, arginine and proline metabolism, beta-alanine metabolism, vitamin B6 metabolism, salmonella infection, chloroalkane and chloroalkene degradation, and limonene and pinene degradation. Moreover, the main KEGG functions of DEP in Vao-9 are classified as ribosome and carbon fixation pathways in prokaryotes, pentose and glucuronate interconversions, GABA ergic synapse, and taurine and hypotaurine metabolism. The results obtained in this study provide an important basis for further research on the underlying mechanisms of salt response and tolerance in oat and other plant species.
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Affiliation(s)
- Xiaojing Chen
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Zhongshan Xu
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Baoping Zhao
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Yanming Yang
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Junzhen Mi
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Zhou Zhao
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Jinghui Liu
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
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Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement. Metabolites 2022; 12:metabo12060511. [PMID: 35736444 PMCID: PMC9228725 DOI: 10.3390/metabo12060511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/04/2023] Open
Abstract
Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.
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25
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Zhang MX, Bai R, Nan M, Ren W, Wang CM, Shabala S, Zhang JL. Evaluation of salt tolerance of oat cultivars and the mechanism of adaptation to salinity. JOURNAL OF PLANT PHYSIOLOGY 2022; 273:153708. [PMID: 35504119 DOI: 10.1016/j.jplph.2022.153708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Soil salinity is a threat to agricultural production worldwide. Oat (Avena sativa L.) is an irreplaceable crop in areas with fragile ecological conditions. However, there is a lack of research on salt tolerance evaluation of oat germplasm resources. Therefore, the purpose of this work was to evaluate the salt tolerance of oat cultivars and investigate the mechanism of salt-tolerant oat cultivars' adaptation to salinity. Salt tolerance of 100 oat cultivars was evaluated, and then two salt-tolerant cultivars and two salt-sensitive cultivars were used to compare their physiological responses and expression patterns of Na+- and K+-transport-related genes under salinity. Principal component analysis and membership function analysis had good predictability for salt tolerance evaluation of oat and other crops. The 100 oat cultivars were clustered into three categories, with three salt tolerance levels. Under saline condition, salt-tolerant cultivars maintained higher growth rate, leaf cell membrane integrity, and osmotic adjustment capability via enhancing the activities of antioxidant enzymes and accumulating more osmotic regulators. Furthermore, salt-tolerant cultivars had stronger capability to restrict root Na + uptake through reducing AsAKT1 and AsHKT2;1 expression, exclude more Na+ from root through increasing AsSOS1 expression, compartmentalize more Na + into root vacuoles through increasing AsNHX1 and AsVATP-P1 expression, and absorb more K+ through increasing AsKUP1 expression, compared with salt-sensitive cultivars. The evaluation procedure developed in this work can be applied for screening cereal crop cultivars with higher salt tolerance, and the elucidated mechanism of oat adaptation to salinity lays a foundation for identifying more functional genes related to salt tolerance.
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Affiliation(s)
- Ming-Xu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering, Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Rong Bai
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering, Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Ming Nan
- Gansu Academy of Agricultural Sciences, Lanzhou, 730070, People's Republic of China
| | - Wei Ren
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering, Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Chun-Mei Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, People's Republic of China
| | - Sergey Shabala
- Department of Horticulture, Foshan University, Foshan, 528000, PR China; School of Land and Food, University of Tasmania, Private Bag 54, Hobart, Tasmania, 7001, Australia.
| | - Jin-Lin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering, Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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26
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Li Z, Cheng B, Liu W, Feng G, Zhao J, Zhang L, Peng Y. Global Metabolites Reprogramming Induced by Spermine Contributing to Salt Tolerance in Creeping Bentgrass. Int J Mol Sci 2022; 23:ijms23094472. [PMID: 35562863 PMCID: PMC9104555 DOI: 10.3390/ijms23094472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/08/2022] [Accepted: 04/15/2022] [Indexed: 12/04/2022] Open
Abstract
Soil salinization has become a serious challenge to modern agriculture worldwide. The purpose of the study was to reveal salt tolerance induced by spermine (Spm) associated with alterations in water and redox homeostasis, photosynthetic performance, and global metabolites reprogramming based on analyses of physiological responses and metabolomics in creeping bentgrass (Agrostis stolonifera). Plants pretreated with or without 0.5 mM Spm were subjected to salt stress induced by NaCl for 25 days in controlled growth chambers. Results showed that a prolonged period of salt stress caused a great deal of sodium (Na) accumulation, water loss, photoinhibition, and oxidative damage to plants. However, exogenous application of Spm significantly improved endogenous spermidine (Spd) and Spm contents, followed by significant enhancement of osmotic adjustment (OA), photosynthesis, and antioxidant capacity in leaves under salt stress. The Spm inhibited salt-induced Na accumulation but did not affect potassium (K) content. The analysis of metabolomics demonstrated that the Spm increased intermediate metabolites of γ-aminobutyric acid (GABA) shunt (GABA, glutamic acid, and alanine) and tricarboxylic acid (TCA) cycle (aconitic acid) under salt stress. In addition, the Spm also up-regulated the accumulation of multiple amino acids (glutamine, valine, isoleucine, methionine, serine, lysine, tyrosine, phenylalanine, and tryptophan), sugars (mannose, fructose, sucrose-6-phosphate, tagatose, and cellobiose), organic acid (gallic acid), and other metabolites (glycerol) in response to salt stress. These metabolites played important roles in OA, energy metabolism, signal transduction, and antioxidant defense under salt stress. More importantly, the Spm enhanced GABA shunt and the TCA cycle for energy supply in leaves. Current findings provide new evidence about the regulatory roles of the Spm in alleviating salt damage to plants associated with global metabolites reprogramming and metabolic homeostasis.
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Affiliation(s)
- Zhou Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.L.); (B.C.); (W.L.); (G.F.); (J.Z.)
| | - Bizhen Cheng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.L.); (B.C.); (W.L.); (G.F.); (J.Z.)
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.L.); (B.C.); (W.L.); (G.F.); (J.Z.)
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.L.); (B.C.); (W.L.); (G.F.); (J.Z.)
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.L.); (B.C.); (W.L.); (G.F.); (J.Z.)
| | - Liquan Zhang
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, 49 Xilinguole Road, Hohhot 010020, China
- Correspondence: (L.Z.); (Y.P.)
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.L.); (B.C.); (W.L.); (G.F.); (J.Z.)
- Correspondence: (L.Z.); (Y.P.)
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Yan H, Nie Y, Cui K, Sun J. Integrative Transcriptome and Metabolome Profiles Reveal Common and Unique Pathways Involved in Seed Initial Imbibition Under Artificial and Natural Salt Stresses During Germination of Halophyte Quinoa. FRONTIERS IN PLANT SCIENCE 2022; 13:853326. [PMID: 35498713 PMCID: PMC9039654 DOI: 10.3389/fpls.2022.853326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/28/2022] [Indexed: 05/31/2023]
Abstract
Salt stress is a major environmental factor that seriously restricts quinoa seed germination. However, the key regulatory mechanisms underlying the effect of salt stress on the initial imbibition stage of quinoa seeds are unclear. In this study, dry seeds (0 h) and imbibed (8 h) seeds with 450 mM NaCl (artificial salt) and 100% brackish water of Yellow River Estuary (BW, natural salt) were used to assess the key salt responses based on germination, transcriptome, and metabolome analyses. The results indicated that the capacity of germinating seeds to withstand these two salt stresses was similar due to the similarities in the germination percentage, germination index, mean germination time, and germination phenotypes. Combined omics analyses revealed that the common and unique pathways were induced by NaCl and BW. Starch and sucrose metabolism were the only commonly enriched pathways in which the genes were significantly changed. Additionally, amino sugar and nucleotide sugar metabolism, and ascorbate and aldarate metabolism were preferably enriched in the NaCl group. However, glutathione metabolism tended to enrich in the BW group where glutathione peroxidase, peroxiredoxin 6, and glutathione S-transferase were significantly regulated. These findings suggest that the candidates involved in carbohydrate metabolism and antioxidant defense can regulate the salt responses of seed initial imbibition, which provide valuable insights into the molecular mechanisms underlying the effect of artificial and natural salt stresses.
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Affiliation(s)
| | | | | | - Juan Sun
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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28
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Ahmad P, Venema K, Corpas FJ. Unravelling salt tolerance mechanisms in plants: From lab to field. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 176:31-33. [PMID: 35190337 DOI: 10.1016/j.plaphy.2022.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Parvaiz Ahmad
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Kees Venema
- Group of Ion Homeostasis and Membrane Transport. Department of Biochemistry, Cell and Molecular Biology of Plants, Estacíon Experimental Del Zaidín, CSIC, C/ Profesor Albareda, 1, 18008, Granada, Spain.
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture. Department of Biochemistry, Cell and Molecular Biology of Plants, Estacíon Experimental Del Zaidín, CSIC, C/ Profesor Albareda, 1, 18008, Granada, Spain
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29
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Comprehensive Transcriptome Analysis Uncovers Distinct Expression Patterns Associated with Early Salinity Stress in Annual Ryegrass ( Lolium Multiflorum L.). Int J Mol Sci 2022; 23:ijms23063279. [PMID: 35328700 PMCID: PMC8948850 DOI: 10.3390/ijms23063279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/15/2022] [Indexed: 02/07/2023] Open
Abstract
Soil salination is likely to reduce crop production worldwide. Annual ryegrass (Lolium multiflorum L.) is one of the most important forages cultivated in temperate and subtropical regions. We performed a time-course comparative transcriptome for salinity-sensitive (SS) and salinity-insensitive (SI) genotypes of the annual ryegrass at six intervals post-stress to describe the transcriptional changes and identify the core genes involved in the early responses to salt stress. Our study generated 215.18 Gb of clean data and identified 7642 DEGs in six pairwise comparisons between the SS and SI genotypes of annual ryegrass. Function enrichment of the DEGs indicated that the differences in lipid, vitamins, and carbohydrate metabolism are responsible for variation in salt tolerance of the SS and SI genotypes. Stage-specific profiles revealed novel regulation mechanisms in salinity stress sensing, phytohormones signaling transduction, and transcriptional regulation of the early salinity responses. High-affinity K+ (HAKs) and high-affinity K1 transporter (HKT1) play different roles in the ionic homeostasis of the two genotypes. Moreover, our results also revealed that transcription factors (TFs), such as WRKYs, ERFs, and MYBs, may have different functions during the early signaling sensing of salt stress, such as WRKYs, ERFs, and MYBs. Generally, our study provides insights into the mechanisms of the early salinity response in the annual ryegrass and accelerates the breeding of salt-tolerant forage.
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30
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Tang Y, Li S, Yan J, Peng Y, Weng W, Yao X, Gao A, Cheng J, Ruan J, Xu B. Bioactive Components and Health Functions of Oat. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2022.2029477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yong Tang
- College of Agriculture, Guizhou University, Guizhou, P. R. China
| | - Shijuan Li
- College of Plant Protection, Gansu Agricultural University, Lanzhou, P. R. China
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing in Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, P. R. China
| | - Yan Peng
- College of Agriculture, Guizhou University, Guizhou, P. R. China
| | - Wenfeng Weng
- College of Agriculture, Guizhou University, Guizhou, P. R. China
| | - Xin Yao
- College of Agriculture, Guizhou University, Guizhou, P. R. China
| | - Anjing Gao
- College of Agriculture, Guizhou University, Guizhou, P. R. China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guizhou, P. R. China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guizhou, P. R. China
| | - Bingliang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou, P. R. China
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Liu J, Zhang X, Sheng J. Integrative Analysis of the Transcriptome and Metabolome Reveals the Mechanism of Saline–Alkali Stress Tolerance in Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Saline–alkali stress is a major abiotic stress affecting the quality and yield of crops. Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao (A. mongholicus) is a well-known medicine food homology species with various pharmacological effects and health benefits that can grow well in saline–alkali soil. However, the molecular mechanisms underlying the adaptation of A. mongholicus plants to saline–alkali stress have not yet been clarified. Here, A. mongholicus plants were exposed to long-term saline–alkali stress (200 mmol·L -1 mixed saline–alkali solution), which limited the growth of A. mongholicus. The roots of A. mongholicus could resist long-term saline–alkali stress by increasing the activity of antioxidant enzymes and the content of osmolytes. Transcriptome analysis (via the Illumina platform) and metabolome analysis (via the Nexera UPLC Series QE Liquid Mass Coupling System) revealed that saline–alkali stress altered the activity of various metabolic pathways (e.g., amino acid metabolism, carbohydrate metabolism, lipid metabolism, and biosynthesis of other secondary metabolites). A total of 3,690 differentially expressed genes (DEGs) and 997 differentially accumulated metabolites (DAMs) were identified in A. mongholicus roots under saline–alkali stress, and flavonoid-related DEGs and DAMs were significantly up-regulated. Pearson correlation analysis revealed significant correlations between DEGs and DAMs related to flavonoid metabolism. MYB transcription factors might also contribute to the regulation of flavonoid biosynthesis. Overall, the results indicate that A. mongholicus plants adapt to saline–alkali stress by up-regulating the biosynthesis of flavonoids, which enhances the medicinal value of A. mongholicus.
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