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Li J, Ackah M, Amoako FK, Cui Z, Sun L, Li H, Tsigbey VE, Zhao M, Zhao W. Metabolomics and physio-chemical analyses of mulberry plants leaves response to manganese deficiency and toxicity reveal key metabolites and their pathways in manganese tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1349456. [PMID: 38911982 PMCID: PMC11192020 DOI: 10.3389/fpls.2024.1349456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/10/2024] [Indexed: 06/25/2024]
Abstract
Introduction Manganese (Mn) plays a pivotal role in plant growth and development. Aside aiding in plant growth and development, Mn as heavy metal (HM) can be toxic in soil when applied in excess. Morus alba is an economically significant plant, capable of adapting to a range of environmental conditions and possessing the potential for phytoremediation of contaminated soil by HMs. The mechanism by which M. alba tolerates Mn stresses remains obscure. Methods In this study, Mn concentrations comprising sufficiency (0.15 mM), higher regimes (1.5 mM and 3 mM), and deficiency (0 mM and 0.03 mM), were applied to M. alba in pot treatment for 21 days to understand M. alba Mn tolerance. Mn stress effects on the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), intercellular CO2 concentration (Ci), chlorophyll content, plant morphological traits, enzymatic and non-enzymatic parameters were analyzed as well as metabolome signatures via non-targeted LC-MS technique. Results Mn deficiency and toxicity decrease plant biomass, Pn, Ci, Gs, Tr, and chlorophyll content. Mn stresses induced a decline in the activities of catalase (CAT) and superoxide dismutase (SOD), while peroxidase (POD) activity, and leaf Mn content, increased. Soluble sugars, soluble proteins, malondialdehyde (MDA) and proline exhibited an elevation in Mn deficiency and toxicity concentrations. Metabolomic analysis indicates that Mn concentrations induced 1031 differentially expressed metabolites (DEMs), particularly amino acids, lipids, carbohydrates, benzene and derivatives and secondary metabolites. The DEMs are significantly enriched in alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, galactose metabolism, pantothenate and CoA biosynthesis, pentose phosphate pathway, carbon metabolism, etc. Discussion and conclusion The upregulation of Galactinol, Myo-inositol, Jasmonic acid, L-aspartic acid, Coproporphyrin I, Trigonelline, Pantothenol, and Pantothenate and their significance in the metabolic pathways makes them Mn stress tolerance metabolites in M. alba. Our findings reveal the fundamental understanding of DEMs in M. alba's response to Mn nutrition and the metabolic mechanisms involved, which may hold potential significance for the advancement of M. alba genetic improvement initiatives and phytoremediation programs.
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Affiliation(s)
- Jianbin Li
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Michael Ackah
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | | | - Zipei Cui
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - LongWei Sun
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Haonan Li
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Victor Edem Tsigbey
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Mengdi Zhao
- Department of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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Zhang H, Qi C, Li C, Huang D, Mao H, Lin X. Overexpression of high affinity K + transporter from Nitraria sibirica enhanced salt tolerance of transgenic plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112052. [PMID: 38417716 DOI: 10.1016/j.plantsci.2024.112052] [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: 11/03/2023] [Revised: 01/27/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Nitraria sibirica Pall is a halophytic shrub growing in desert steppe zones. It exhibits extraordinary adaptability to saline-alkali soil, drought, and sand burial. In this study, the high-affinity K+ transporter NsHKT1 was identified and found to play a key role in salt tolerance in N. sibirica. NsHKT1 was used to improve salt tolerance in a poplar hybrid. The expression characteristics of NsHKT1 were analyzed by transforming Arabidopsis and poplar with the β-glucuronidase (GUS) gene driven by the NsHKT1 promoter. The results showed that NsHKT1 expression was induced by various abiotic stresses and phytohormones. GUS expression was also detected in the reproductive organs of transgenic Arabidopsis, indicating its function in regulating plant reproductive growth. Transgenic 84 K poplar plants overexpressing NsHKT1 exhibited less damage, higher antioxidant capacity, higher chlorophyll and proline levels, and lower malondialdehyde content compared with non-transgenic plants under salt stress. These results are consistent with the salt tolerance results for transgenic Arabidopsis overexpressing NsHKT1, indicating that NsHKT1 plays a key role in salt tolerance in herbaceous and ligneous plants. Inductively coupled plasma-optical emission spectrometry showed a significantly lower leaf Na+ content in transgenic poplar than in the non-transgenic line, revealing that NsHKT1, as a member of HKT family subclass 1, was highly selective to Na+ and prevented shoot Na+ accumulation. Transcriptome analysis indicated that differentially expressed genes in transgenic poplars under salt stress were associated mainly with the isoflavonoid, cutin, suberine, wax, anthocyanin, flavonoid, and cyanoamino biosynthesis pathways, as well as the MAPK signaling pathway, indicating that NsHKT1 not only regulates ion homeostasis but also influences secondary metabolism and signal transaction in transgenic plants.
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Affiliation(s)
- Haidong Zhang
- Key Laboratory of Herbage and Endemic Crop Biology of Ministry Education, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Caifen Qi
- Key Laboratory of Herbage and Endemic Crop Biology of Ministry Education, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Chaoran Li
- Key Laboratory of Herbage and Endemic Crop Biology of Ministry Education, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Duoman Huang
- Key Laboratory of Herbage and Endemic Crop Biology of Ministry Education, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Huiping Mao
- Key Laboratory of Herbage and Endemic Crop Biology of Ministry Education, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China.
| | - Xiaofei Lin
- Key Laboratory of Herbage and Endemic Crop Biology of Ministry Education, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China.
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Shen J, Xiao X, Zhong D, Lian H. Potassium humate supplementation improves photosynthesis and agronomic and yield traits of foxtail millet. Sci Rep 2024; 14:9508. [PMID: 38664476 PMCID: PMC11045805 DOI: 10.1038/s41598-024-57354-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Foxtail millet is a highly nutritious crop, which is widely cultivated in arid and semi-arid areas worldwide. Humic acid (HA), as a common plant growth regulator, is used as an organic fertilizer and feed additive in agricultural production. However, the impact of potassium humate KH on the photosynthetic rate and yield of foxtail millet has not yet been studied. We explored the effects of KH application on the morphology, photosynthetic ability, carbon and nitrogen metabolism, and yield of foxtail millet. A field experiment was performed using six concentrations of KH (0, 20, 40, 80, 160, and 320 kg ha-1) supplied foliarly at the booting stage in Zhangza 10 cultivar (a widely grown high-yield variety). The results showed that KH treatment increased growth, chlorophyll content (SPAD), photosynthetic rate (Pn), transpiration rate (Tr), and stomatal conductance (Gs). In addition, soluble protein content, sugar content, and nitrate reductase activity increased in KH-treated plants. With increased KH concentration, the effects became more evident and the peak values of each factor were achieved at 80 kg ha-1. Photosynthetic rate showed significant correlation with SPAD, Tr, Gs, and soluble protein content, but was negatively correlated with intercellular CO2 concentration. Compared to that of the control, the yield of foxtail millet under the T2, T3, T4, and T5 (40, 80, 160, and 320 kg ha-1 of KH) treatments significantly increased by 6.0%, 12.7%, 10.5%, and 8.6%, respectively. Yield exhibited a significant positive correlation with Tr, Pn, and Gs. Overall, KH enhances photosynthetic rate and yield of foxtail millet, therefore it may be conducive to stable millet production. These findings may provide a theoretical basis for the green and efficient production of millet fields.
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Affiliation(s)
- Jie Shen
- Department of Life Sciences, Changzhi University, Changzhi, 046011, China
| | - Xiaolu Xiao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Dandan Zhong
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China
| | - Huida Lian
- Department of Life Sciences, Changzhi University, Changzhi, 046011, China.
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Han M, Niu M, Gao T, Shen Y, Zhou X, Zhang Y, Liu L, Chai M, Sun G, Wang Y. Responsive Alternative Splicing Events of Opisthopappus Species against Salt Stress. Int J Mol Sci 2024; 25:1227. [PMID: 38279226 PMCID: PMC10816081 DOI: 10.3390/ijms25021227] [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: 11/06/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
Salt stress profoundly affects plant growth, prompting intricate molecular responses, such as alternative splicing (AS), for environmental adaptation. However, the response of AS events to salt stress in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear, which is a Taihang Mountain cliff-dwelling species. Using RNA-seq data, differentially expressed genes (DEGs) were identified under time and concentration gradients of salt stress. Two types of AS, skipped exon (SE) and mutually exclusive exons (MXE), were found. Differentially alternative splicing (DAS) genes in both species were significantly enriched in "protein phosphorylation", "starch and sucrose metabolism", and "plant hormone signal transduction" pathways. Meanwhile, distinct GO terms and KEGG pathways of DAS occurred between two species. Only a small subset of DAS genes overlapped with DEGs under salt stress. Although both species likely adopted protein phosphorylation to enhance salt stress tolerance, they exhibited distinct responses. The results indicated that the salt stress mechanisms of both Opisthopappus species exhibited similarities and differences in response to salt stress, which suggested that adaptive divergence might have occurred between them. This study initially provides a comprehensive description of salt responsive AS events in Opisthopappus and conveys some insights into the molecular mechanisms behind species tolerance on the Taihang Mountains.
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Affiliation(s)
- Mian Han
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Mengfan Niu
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Ting Gao
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Yuexin Shen
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Xiaojuan Zhou
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Yimeng Zhang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Li Liu
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Min Chai
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Genlou Sun
- Department of Botany, Saint Mary’s University, Halifax, NS B3H 3C3, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
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Su Y, Liu L, Ma H, Yuan Y, Zhang D, Lu X. Metabolomic Analysis of the Effect of Freezing on Leaves of Malus sieversii (Ledeb.) M.Roem. Histoculture Seedlings. Int J Mol Sci 2023; 25:310. [PMID: 38203481 PMCID: PMC10778857 DOI: 10.3390/ijms25010310] [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: 11/16/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Malus sieversii (Ledeb.) M.Roem. is the ancestor of cultivated apples, and is an excellent germplasm resource with high resistance to cold. Artificial refrigerators were used to simulate the low temperature of -3 °C to treat Malus sieversii (Ledeb.) M.Roem. histoculture seedlings. Observations were performed to find the effects of freezing stress on the status of open or closed stomata, photosystems, and detection of metabolomic products in leaves of Malus sieversii (Ledeb.) M.Roem. histoculture seedlings. The percentage of closed stomata in the Malus sieversii (Ledeb.) M.Roem. histoculture seedlings increased, the maximum fluorescence (Fm') excited by a strong light (saturating pulse) was weakened relative to the real-time fluorescence in its vicinity, and the quantum yield of unregulated energy dissipation was increased in PSII under freezing stress. The metabolites in the leaves of the Malus sieversii (Ledeb. M.Roem.) histoculture seedlings were analyzed by ultra-performance liquid chromatography-tandem mass spectrometry using CK, T12h, T36 h, and HF24h. Results demonstrated that cold stress in the Malus sieversii (Ledeb.) M.Roem. histoculture seedlings led to wilting, leaf stomatal closure, and photosystem damage. There were 1020 metabolites identified as lipids (10.2%), nucleotides and their derivatives (5.2%), phenolic acids (19.12%), flavonoids (24.51%), amino acids and their derivatives (7.75%), alkaloids (5.39%), terpenoids (8.24%), lignans (3.04%), organic acids (5.88%), and tannins (0.88%). There were 110 differential metabolites at CKvsT12h, 113 differential metabolites at CKvsT36h, 87 differential metabolites at T12hvsT36h, 128 differential metabolites at CKvsHF24h, 121 differential metabolites at T12hvsHF24h, and 152 differential metabolites at T36hvsHF24h. The differential metabolites in the leaves of the Malus sieversii (Ledeb.) M.Roem. seedlings grown under low-temperature stress mainly involved glycolysis, amino acid metabolism, lipid metabolism, pyrimidine metabolism, purine metabolism, and secondary metabolite metabolism. The Malus sieversii (Ledeb.) M.Roem. seedlings responded to the freezing stress by coordinating with each other through these metabolic pathways. The metabolic network of the leaves of the Malus sieversii (Ledeb.) M.Roem. histoculture seedlings under low temperature stress was also proposed based on the above pathways to deepen understanding of the response of metabolites of Malus sieversii (Ledeb.) M.Roem. to low-temperature stress and to lay a theoretical foundation for the development and utilization of Malus sieversii (Ledeb.) M.Roem. cultivation resources.
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Affiliation(s)
| | | | | | | | | | - Xiaoyan Lu
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Agricultural College of Shihezi University, Shihezi 832003, China; (Y.S.); (L.L.); (H.M.); (Y.Y.); (D.Z.)
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Zhang M, Xing Y, Ma J, Zhang Y, Yu J, Wang X, Jia X. Investigation of the response of Platycodongrandiflorus (Jacq.) A. DC to salt stress using combined transcriptomics and metabolomics. BMC PLANT BIOLOGY 2023; 23:589. [PMID: 38001405 PMCID: PMC10675982 DOI: 10.1186/s12870-023-04536-w] [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: 01/26/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023]
Abstract
BACKGROUND Platycodon grandiflorus (Jacq.) A. DC is a famous traditional Chinese medicine in China and an authentic medicine in Inner Mongolia. It has been traditionally used as an expectorant in cough and also has anti-inflammatory and other pharmacological effects. As a homologous plant of medicine and food, P. grandiflorus is widely planted in Northeast China. Soil salinity isa limiting factor for its cultivation. In this study, we comprehensively described the physiological characteristics of P. grandiflorus and combined transcriptomics and metabolomics to study the response of roots of P. grandiflorus to salt stress. RESULTS Overall, 8,988 differentially expressed genes were activated and significantly altered the metabolic processes. In total, 428 differentially abundant metabolites were affected by salt stress. After moderate and severe salt stress, most of the differentially abundant metabolites were enriched in the L-phenylalanine metabolic pathway. Through the comprehensive analysis of the interaction between key genes and metabolites, the main pathways such as lignin compound biosynthesis and triterpene saponin biosynthesis were completed. The relative content of compounds related to lignin biosynthesis, such as caffeic acid, coniferin, and syringing, increased under salt stress, and the related genes such as PAL, C4H, and the key enzyme gene UGT72E2 were activated to adapt to the salt stress. Platycodon saponin is one of the major triterpene saponins in P. grandiflorus, and Platycodin D is its most abundant major bioactive component. Under severe salt stress, Platycodin D level increased by nearly 1.77-fold compared with the control group. Most of the genes involved insynthetic pathway of Platycodin D, such as HMGCR, GGPS, SE, and LUP, were upregulated under salt stress. CONCLUSION Salt stress led to a decrease in the biomass and affected the activities of antioxidant enzymes and contents of osmotic regulators in the plant. These results provided not only novel insights into the underlying mechanisms of response of P. grandiflorus to salt stress but also a foundation for future studies on the function of genes related to salt tolerance in the triterpenoid saponin biosynthesis pathway.
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Affiliation(s)
- Meixi Zhang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Yushu Xing
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Jiannan Ma
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Ying Zhang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Juan Yu
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Xiaoqin Wang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China.
| | - Xin Jia
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China.
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Shen J, Wang X, Song H, Wang M, Niu T, Lei H, Qin C, Liu A. Physiology and transcriptomics highlight the underlying mechanism of sunflower responses to drought stress and rehydration. iScience 2023; 26:108112. [PMID: 37860690 PMCID: PMC10583116 DOI: 10.1016/j.isci.2023.108112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/15/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
Drought can adversely influence the crop growth and production. Accordingly, sunflowers have strong adaptability to drought; hence, we conducted analyses for sunflower seedlings with drought stress and rehydration drought acclimation through physiological measurements and transcriptomics. It showed that drought can cause the accumulation of ROS and enhance the activity of antioxidant enzymes and the content of osmolytes. After rehydration, the contents of ROS and MDA were significantly reduced concomitant with increased antioxidant activity and osmotic adjustment. Totally, 2,589 DEGs were identified among treatments. Functional enrichment analysis showed that DEGs were mainly involved in plant hormone signal transduction, MAPK signaling, and biosynthesis of secondary metabolites. Comparison between differentially spliced genes and DEGs indicated that bHLH025, NAC53, and SINAT3 may be pivotal genes involved in sunflower drought resistance. Our results not only highlight the underlying mechanism of drought stress and rehydration in sunflower but also provide a theoretical basis for crop genetic breeding.
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Affiliation(s)
- Jie Shen
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Xi Wang
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Huifang Song
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Mingyang Wang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Tianzeng Niu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Haiying Lei
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Cheng Qin
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
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Zhang P, Zhang F, Wu Z, Cahaeraduqin S, Liu W, Yan Y. Analysis on the salt tolerance of Nitraria sibirica Pall. based on Pacbio full-length transcriptome sequencing. PLANT CELL REPORTS 2023; 42:1665-1686. [PMID: 37479883 DOI: 10.1007/s00299-023-03052-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
KEY MESSAGE Nitraria sibirica Pall. regulates its tolerance to salt stress mainly by adjusting ion balance, modifying cell wall structure, and activating signal transduction pathways. N. sibirica, as a typical halophyte, can not only effectively restore saline-alkali land, but also has high economic value. However, studies on its salt tolerance at combining molecular and physiological levels were limited. In this study, the salt tolerance of N. sibirica was analyzed based on Pacbio full-length transcriptome sequencing, and the salt tolerance in the physiological level was verified by key genes. The results showed that 89,017 full-length transcripts were obtained, of which 84,632 sequences were annotated. A total of 86,482 coding sequences (CDS) were predicted and 6561 differentially expressed genes (DEGs) were identified. DEGs were significantly enriched in "sodium ion homeostasis", "response to osmotic stress", "reactive oxygen species metabolic process", "defense response by cell wall thickening", "signal transduction", etc. The expression levels for most of these DEGs increased under salt stress. A total of 69 key genes were screened based on weighted gene co-expression network analysis (WGCNA), of which 33 were first reported on salt tolerance. Moreover, NsRabE1c gene with the highest expression level was selected to verify its salt tolerance. Over-expression of NsRabE1c gene enhanced the germination potential and root length of transgenic Arabidopsis thaliana plants without salt treatment as compared to those of Col-0 and AtRabE1c mutant. The expression levels of NsRabE1c decreased in the growth stagnation phase, while significantly increased in the growth recovery phase under salt stress. We predicted that NsRabE1c gene help N. sibirica resist salt stress through the regulation of plant growth. The results of this study deepen the understanding of salinity resistance in N. sibirica.
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Affiliation(s)
- Panpan Zhang
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Fengxiang Zhang
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Zhiheng Wu
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Sunaer Cahaeraduqin
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Liu
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Yongqing Yan
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
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Sun M, Wei S, Liu J, Wang L, Zhang Y, Hu L, Piao J, Liang Z, Jiang H, Xin D, Zhao Y, Chen Q, Foyer CH, Liu C, Qi Z. The impact of GmTSA and GmALS on soybean salt tolerance: uncovering the molecular landscape of amino acid and secondary metabolism pathways. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:212. [PMID: 37740151 DOI: 10.1007/s00122-023-04461-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023]
Abstract
KEY MESSAGE GmTSA and GmALS were screened out for salt stress in soybean and explore the poteintial amino acid secondary metabolism pathways. Soybean (Glycine max L.) is an oil and protein crop of global importance, and salinity has significant effects on soybean growth. Here, a population of soybean chromosome segment substitution lines was screened to identify highly salt-tolerant lines. In total, 24 quantitative trait loci (QTLs) on seven chromosomes were associated with salt tolerance, and CSSL_R71 was selected for further analysis. Although numerous genes were differentially expressed in CSSL_R71 in response to salt statically no differently, transcript levels of classical salt-response genes, including those of the salt overly sensitive pathway. Rather, salt tolerance in CSSL_R71 was associated with changes in amino acid and lipid metabolism. In particular, changes in p-coumaric acid, shikimic acid, and pyrrole-2-carboxylic acid levels accompanied salt tolerance in CSSL_R71. Eleven differentially expressed genes (DEGs) related to amino acid and secondary metabolism were identified as candidate genes on the substituted chromosome fragment. Six of these showed differences in coding sequence between the parental genotypes. Crucially, overexpression of GmTSA (Glyma.03G158400, tryptophan synthase) significantly enhanced salt tolerance in soybean hairy roots, whereas overexpression of GmALS (Glyma.13G241000, acetolactate synthase) decreased salt tolerance. Two KASP markers were developed for GmALS and used to genotype salt-tolerant and salt-sensitive lines in the CSSL population. Non-synonymous mutations were directly associated with salt tolerance. Taken together, these data provide evidence that changes in amino acid and secondary metabolism have the potential to confer salt tolerance in soybean.
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Affiliation(s)
- Minghao Sun
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Siming Wei
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jiarui Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Luyao Wang
- Institute of Rural Revitalization Science and Technology, Heilongjiang Academy of Agricultural Sciences, Harbin, 150028, China
| | - Yu Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Limin Hu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jingxi Piao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhao Liang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, 130033, China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Ying Zhao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, UK.
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
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Niu T, Zhang J, Li J, Gao X, Ma H, Gao Y, Chang Y, Xie J. Effects of exogenous glycine betaine and cycloleucine on photosynthetic capacity, amino acid composition, and hormone metabolism in Solanum melongena L. Sci Rep 2023; 13:7626. [PMID: 37165051 PMCID: PMC10172174 DOI: 10.1038/s41598-023-34509-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/03/2023] [Indexed: 05/12/2023] Open
Abstract
Although exogenous glycine betaine (GB) and cycloleucine (Cyc) have been reported to affect animal cell metabolism, their effects on plant growth and development have not been studied extensively. Different concentrations of exogenous glycine betaine (20, 40, and 60 mmol L-1) and cycloleucine (10, 20, and 40 mmol L-1), with 0 mmol L-1 as control, were used to investigate the effects of foliar spraying of betaine and cycloleucine on growth, photosynthesis, chlorophyll fluorescence, Calvin cycle pathway, abaxial leaf burr morphology, endogenous hormones, and amino acid content in eggplant. We found that 40 mmol L-1 glycine betaine had the best effect on plant growth and development; it increased the fresh and dry weight of plants, increased the density of abaxial leaf hairs, increased the net photosynthetic rate and Calvin cycle key enzyme activity of leaves, had an elevating effect on chlorophyll fluorescence parameters, increased endogenous indoleacetic acid (IAA) content and decreased abscisic acid (ABA) content, and increased glutamate, serine, aspartate, and phenylalanine contents. However, cycloleucine significantly inhibited plant growth; plant apical dominance disappeared, plant height and dry and fresh weights decreased significantly, the development of abaxial leaf hairs was hindered, the net photosynthetic rate and Calvin cycle key enzyme activities were inhibited, the endogenous hormones IAA and ABA content decreased, and the conversion and utilization of glutamate, arginine, threonine, and glycine were affected. Combined with the experimental results and plant growth phenotypes, 20 mmol L-1 cycloleucine significantly inhibited plant growth. In conclusion, 40 mmol L-1 glycine betaine and 20 mmol L-1 cycloleucine had different regulatory effects on plant growth and development.
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Affiliation(s)
- Tianhang Niu
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Jing Zhang
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Jing Li
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Xiaoping Gao
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Hongyan Ma
- Lanzhou New Area Agricultural Science and Technology Development Co., Ltd., Lanzhou, 730000, China
| | - Yanqiang Gao
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Youlin Chang
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China.
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11
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Han M, Cui R, Wang D, Huang H, Rui C, Malik WA, Wang J, Zhang H, Xu N, Liu X, Lei Y, Jiang T, Sun L, Ni K, Fan Y, Zhang Y, Wang J, Chen X, Lu X, Yin Z, Wang S, Guo L, Zhao L, Chen C, Ye W. Combined transcriptomic and metabolomic analyses elucidate key salt-responsive biomarkers to regulate salt tolerance in cotton. BMC PLANT BIOLOGY 2023; 23:245. [PMID: 37161359 PMCID: PMC10170727 DOI: 10.1186/s12870-023-04258-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 04/28/2023] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cotton is an important industrial crop and a pioneer crop for saline-alkali land restoration. However, the molecular mechanism underlying the cotton response to salt is not completely understood. METHODS Here, we used metabolome data and transcriptome data to analyze the salt tolerance regulatory network of cotton and metabolic biomarkers. RESULTS In this study, cotton was stressed at 400 m M NaCl for 0 h, 3 h, 24 h and 48 h. NaCl interfered with cotton gene expression, altered metabolite contents and affected plant growth. Metabolome analysis showed that NaCl stress increased the contents of amino acids, sugars and ABA, decreased the amount of vitamin and terpenoids. K-means cluster analysis of differentially expressed genes showed that the continuously up-regulated genes were mainly enriched in metabolic pathways such as flavonoid biosynthesis and amino acid biosynthesis. CONCLUSION The four metabolites of cysteine (Cys), ABA(Abscisic acid), turanose, and isopentenyladenine-7-N-glucoside (IP7G) were consistently up-regulated under salt stress, which may indicate that they are potential candidates for cotton under salt stress biomarkers. Combined transcriptome and metabolome analysis revealed accumulation of cysteine, ABA, isopentenyladenine-7-N-glucoside and turanose were important for salt tolerance in cotton mechanism. These results will provide some metabolic insights and key metabolite biomarkers for salt stress tolerance, which may help to understanding of the metabolite response to salt stress in cotton and develop a foundation for cotton to grow better in saline soil.
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Affiliation(s)
- Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Ruifeng Cui
- Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Cun Rui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Waqar Afzal Malik
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Jing Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Hong Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Nan Xu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Xiaoyu Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Yuqian Lei
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Tiantian Jiang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Liangqing Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Kesong Ni
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Zujun Yin
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China.
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12
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Zhang H, Hu A, Wu H, Zhu J, Zhang J, Cheng T, Shabala S, Zhang H, Yang X. Integrated metabolome and transcriptome analysis unveils novel pathway involved in the fruit coloration of Nitraria tangutorum Bobr. BMC PLANT BIOLOGY 2023; 23:65. [PMID: 36721098 PMCID: PMC9890838 DOI: 10.1186/s12870-023-04076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The desert shrub Nitraria tangutorum Bobr. is important for its resistance to salt and alkali in Northwest China. It is an ecologically important species in this region and provides edible and medicinal berries. This study showed a mutant of N. tangutorum (named Jincan, JC) that has a strong yellow pericarp vs red in a wild type (represented by NT). RESULTS In this study, the secondary metabolic and molecular mechanisms responsible for Nitraria fruit coloration were investigated using LC-MS-based widely targeted metabolomics and transcriptomics data. As a result of our study, 122 and 104 flavonoid metabolites were differentially expressed throughout the mature and transition stages between JC and NT, respectively. Furthermore, two cyanidin derivatives (cyanidin 3-O-glucoside and cyanidin-3-O-(2''-O-glucosyl) glucoside) and one pelargonidin derivative (pelargonidin-3-O-glucoside) were identified only in the NT phenotype. The functional genes F3H (flavanone 3-hydroxylase), F3'H (flavonoid 3'-hydroxylase) and UFGT (flavonoid 3-O-glucosyltransferase) and the transcription factors MYB, bHLH, NAC and bZIP were significantly downregulated in JC. Meanwhile, the activity of UFGT was extremely low in both periods of JC, with a five-fold higher enzymatic activity of UFGT in RT than in YT. In summary, due to the lack of catalysis of UGFT, yellow fruit of JC could not accumulate sufficient cyanidin and pelargonidin derivatives during fruit ripening. CONCLUSION Taken together, our data provide insights into the mechanism for the regulation of anthocyanin synthesis and N. tangutorum fruit coloration and provide a theoretical basis to develop new strategies for developing bioactive compounds from N. tangutorum fruits.
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Affiliation(s)
- Huilong Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, 10091, China
- The Comprehensive Experimental Center, Chinese Academy of Forestry in Yellow River Delta, Dongying, 257000, China
| | - Aishuang Hu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, 10091, China
- The Comprehensive Experimental Center, Chinese Academy of Forestry in Yellow River Delta, Dongying, 257000, China
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Tangshan, 063299, China
| | - Haiwen Wu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, 10091, China
- The Comprehensive Experimental Center, Chinese Academy of Forestry in Yellow River Delta, Dongying, 257000, China
| | - Jianfeng Zhu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, 10091, China
- The Comprehensive Experimental Center, Chinese Academy of Forestry in Yellow River Delta, Dongying, 257000, China
| | - Jingbo Zhang
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, 015200, China
| | - Tielong Cheng
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, 7001, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Huaxin Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, 10091, China
- The Comprehensive Experimental Center, Chinese Academy of Forestry in Yellow River Delta, Dongying, 257000, China
| | - Xiuyan Yang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, 10091, China.
- The Comprehensive Experimental Center, Chinese Academy of Forestry in Yellow River Delta, Dongying, 257000, China.
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13
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Li C, Li Y, Chu P, Hao-hao Z, Wei Z, Cheng Y, Liu X, Zhao F, Li YJ, Zhang Z, Zheng Y, Mu Z. Effects of salt stress on sucrose metabolism and growth in Chinese rose ( Rosa chinensis). BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2116356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Caihua Li
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Yuhuan Li
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Peiyu Chu
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Zhao Hao-hao
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Zunmiao Wei
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Yan Cheng
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Xianxian Liu
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Fengzhou Zhao
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Yan-jun Li
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Zhiwen Zhang
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Yi Zheng
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Zhongsheng Mu
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
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14
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Hu A, Yang X, Zhu J, Wang X, Liu J, Wang J, Wu H, Zhang H, Zhang H. Selection and validation of appropriate reference genes for RT-qPCR analysis of Nitraria sibirica under various abiotic stresses. BMC PLANT BIOLOGY 2022; 22:592. [PMID: 36526980 PMCID: PMC9758788 DOI: 10.1186/s12870-022-03988-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Nitraria sibirica Pall. is a halophytic shrub with strong environmental adaptability that can survive in extremely saline-alkali and drought-impacted environments. Gene expression analysis aids in the exploration of the molecular mechanisms of plant responses to abiotic stresses. RT-qPCR is the most common technique for studying gene expression. Stable reference genes are a prerequisite for obtaining accurate target gene expression results in RT-qPCR analysis. RESULTS In this study, a total of 10 candidate reference genes were selected from the transcriptome of N. sibirica, and their expression stability in leaves and roots under different treatment conditions (salt, alkali, drought, cold, heat and ABA) was evaluated with the geNorm, NormFinder, BestKeeper, comparative ΔCt and RefFinder programs. The results showed that the expression stability of the candidate reference genes was dependent on the tissue and experimental conditions tested. ACT7 combined with R3H, GAPDH, TUB or His were the most stable reference genes in the salt- or alkali-treated leaves, salt-treated roots and drought-treated roots, respectively; R3H and GAPDH were the most suitable combination for drought-treated leaves, heat-treated root samples and ABA-treated leaves; DIM1 and His maintained stable expression in roots under alkali stress; and TUB combined with R3H was stable in ABA-treated roots. TBCB and GAPDH exhibited stable expression in heat-treated leaves; TBCB, R3H, and ERF3A were stable in cold-treated leaves; and the three most stable reference genes for cold-treated roots were TBCB, ACT11 and DIM1. The reliability of the selected reference genes was further confirmed by evaluating the expression patterns of the NsP5CS gene under the six treatment conditions. CONCLUSION This study provides a theoretical reference for N. sibirica gene expression standardization and quantification under various abiotic stress conditions and will help to reveal the molecular mechanisms that confer stress tolerance to N. sibirica.
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Affiliation(s)
- Aishuang Hu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, 063299, Tangshan, China
- Hebei saline-alkali Land Greening Technology Innovation Center, 063299, Tangshan, China
| | - Xiuyan Yang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Jianfeng Zhu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Xiuping Wang
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, 063299, Tangshan, China
- Hebei saline-alkali Land Greening Technology Innovation Center, 063299, Tangshan, China
| | - Jiaxin Liu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Jiping Wang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Haiwen Wu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Huilong Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China.
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China.
| | - Huaxin Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China.
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China.
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15
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Lu L, Wu X, Tang Y, Zhu L, Hao Z, Zhang J, Li X, Shi J, Chen J, Cheng T. Halophyte Nitraria billardieri CIPK25 promotes photosynthesis in Arabidopsis under salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1052463. [PMID: 36589077 PMCID: PMC9800929 DOI: 10.3389/fpls.2022.1052463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The calcineurin B-like (CBL)-interacting protein kinases (CIPKs), a type of plant-specific genes in the calcium signaling pathway, function in response to adverse environments. However, few halophyte derived CIPKs have been studied for their role in plant physiological and developmental adaptation during abiotic stresses, which inhibits the potential application of these genes to improve environmental adaptability of glycophytes. In this study, we constructed Nitraria billardieri CIPK25 overexpressing Arabidopsis and analyzed the seedling development under salt treatment. Our results show that Arabidopsis with NbCIPK25 expression exhibits more vigorous growth than wild type plants under salt condition. To gain insight into the molecular mechanisms underlying salt tolerance, we profiled the transcriptome of WT and transgenic plants via RNA-seq. GO and KEGG analyses revealed that upregulated genes in NbCIPK25 overexpressing seedlings under salt stress are enriched in photosynthesis related terms; Calvin-cycle genes including glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) are significantly upregulated in transgenic plants, which is consistent with a decreased level of NADPH (GAPDH substrate) and increased level of NADP+. Accordingly, NbCIPK25 overexpressing plants exhibited more efficient photosynthesis; soluble sugar and proteins, as photosynthesis products, showed a higher accumulation in transgenic plants. These results provide molecular insight into how NbCIPK25 promotes the expression of genes involved in photosynthesis, thereby maintaining plant growth under salt stress. Our finding supports the potential application of halophyte-derived NbCIPK25 in genetic modification for better salt adaptation.
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Affiliation(s)
- Lu Lu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinru Wu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yao Tang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jingbo Zhang
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, Inner Mongolia, China
| | - Xinle Li
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, Inner Mongolia, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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16
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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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17
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Wang J, Shi D, Bai Y, Zhang T, Wu Y, Liu Z, Jiang L, Ye L, Peng Z, Yuan H, Liu Y. Comprehensive proteomic and metabolomic analysis uncover the response of okra to drought stress. PeerJ 2022; 10:e14312. [PMID: 36444379 PMCID: PMC9700456 DOI: 10.7717/peerj.14312] [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: 07/08/2022] [Accepted: 10/06/2022] [Indexed: 11/24/2022] Open
Abstract
The response of okra to drought stress is very complicated, and the molecular mechanisms underlying this process remains ambiguous up to now. In this study, different degrees of water-stress responses of okra leaf were explained by using transcriptomics and metabolomic approaches. The photosynthesis and glycometabolism in okra leaf were both adversely affected by drought stress, leading to inhibition of the carbohydrate metabolic process, and then influencing the secondary plant metabolism. Further, drought stress disturbed amino acid metabolism, especially for the tyrosine-derived pathway as well as arginine and proline metabolism, which have been shown to be significantly enriched under water withholding conditions based on multi-omics conjoint analysis (transcriptome, proteome and metabolome). In-depth analysis of the internal linkages between differentially expressed transcripts, proteins, and metabolites decidedly indicate that tyrosine metabolism could confer tolerance to drought stress by influencing carbon and nitrogen metabolism. These findings provide a whole framework of the regulation and relationships of major transcripts and peptides related to secondary metabolism, particularly, the role of critical proteins and metabolite involved in the change of amino acid metabolism in response to drought stress.
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18
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Lu L, Wu X, Wang P, Zhu L, Liu Y, Tang Y, Hao Z, Lu Y, Zhang J, Shi J, Cheng T, Chen J. Halophyte Nitraria billardieri CIPK25 mitigates salinity-induced cell damage by alleviating H 2O 2 accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:961651. [PMID: 36003812 PMCID: PMC9393555 DOI: 10.3389/fpls.2022.961651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The plant-specific module of calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) play a crucial role in plant adaptation to different biotic and abiotic stresses in various plant species. Despite the importance of the CBL-CIPK module in regulating plant salt tolerance, few halophyte CIPK orthologs have been studied. We identified NbCIPK25 in the halophyte Nitraria billardieri as a salt-responsive gene that may improve salt tolerance in glycophytes. Sequence analyses indicated that NbCIPK25 is a typical CIPK family member with a conserved NAF motif, which contains the amino acids: asparagine, alanine, and phenylalanine. NbCIPK25 overexpression in salt-stressed transgenic Arabidopsis seedlings resulted in enhanced tolerance to salinity, a higher survival rate, longer newly grown roots, more root meristem cells, and less damaged root cells in comparison to wild-type (WT) plants. H2O2 accumulation and malondialdehyde (MDA) content were both deceased in NbCIPK25-transgenic plants under salt treatment. Furthermore, their proline content, an important factor for scavenging reactive oxygen species, accumulated at a significantly higher level. In concordance, the transcription of genes related to proline accumulation was positively regulated in transgenic plants under salt condition. Finally, we observed a stronger auxin response in salt-treated transgenic roots. These results provide evidence for NbCIPK25 improving salt tolerance by mediating scavenging of reactive oxygen species, thereby protecting cells from oxidation and maintaining plant development under salt stress. These findings suggest the potential application of salt-responsive NbCIPK25 for cultivating glycophytes with a higher salt tolerance through genetic engineering.
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Affiliation(s)
- Lu Lu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinru Wu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Pengkai Wang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yuxin Liu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yao Tang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jingbo Zhang
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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19
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Li M, Zhang J, Bai Q, Fang L, Song H, Cao Y. Non-homologous End Joining-Mediated Insertional Mutagenesis Reveals a Novel Target for Enhancing Fatty Alcohols Production in Yarrowia lipolytica. Front Microbiol 2022; 13:898884. [PMID: 35547152 PMCID: PMC9082995 DOI: 10.3389/fmicb.2022.898884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Non-homologous end joining (NHEJ)-mediated integration is effective in generating random mutagenesis to identify beneficial gene targets in the whole genome, which can significantly promote the performance of the strains. Here, a novel target leading to higher protein synthesis was identified by NHEJ-mediated integration that seriously improved fatty alcohols biosynthesis in Yarrowia lipolytica. One batch of strains transformed with fatty acyl-CoA reductase gene (FAR) showed significant differences (up to 70.53-fold) in fatty alcohol production. Whole-genome sequencing of the high-yield strain demonstrated that a new target YALI0_A00913g ("A1 gene") was disrupted by NHEJ-mediated integration of partial carrier DNA, and reverse engineering of the A1 gene disruption (YlΔA1-FAR) recovered the fatty alcohol overproduction phenotype. Transcriptome analysis of YlΔA1-FAR strain revealed A1 disruption led to strengthened protein synthesis process that was confirmed by sfGFP gene expression, which may account for enhanced cell viability and improved biosynthesis of fatty alcohols. This study identified a novel target that facilitated synthesis capacity and provided new insights into unlocking biosynthetic potential for future genetic engineering in Y. lipolytica.
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Affiliation(s)
- Mengxu Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Jinlai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Qiuyan Bai
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Lixia Fang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
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20
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Bano N, Fakhrah S, Mohanty CS, Bag SK. Transcriptome Meta-Analysis Associated Targeting Hub Genes and Pathways of Drought and Salt Stress Responses in Cotton ( Gossypium hirsutum): A Network Biology Approach. FRONTIERS IN PLANT SCIENCE 2022; 13:818472. [PMID: 35548277 PMCID: PMC9083274 DOI: 10.3389/fpls.2022.818472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/21/2022] [Indexed: 06/12/2023]
Abstract
Abiotic stress tolerance is an intricate feature controlled through several genes and networks in the plant system. In abiotic stress, salt, and drought are well known to limit cotton productivity. Transcriptomics meta-analysis has arisen as a robust method to unravel the stress-responsive molecular network in crops. In order to understand drought and salt stress tolerance mechanisms, a meta-analysis of transcriptome studies is crucial. To confront these issues, here, we have given details of genes and networks associated with significant differential expression in response to salt and drought stress. The key regulatory hub genes of drought and salt stress conditions have notable associations with functional drought and salt stress-responsive (DSSR) genes. In the network study, nodulation signaling pathways 2 (NSP2), Dehydration-responsive element1 D (DRE1D), ethylene response factor (ERF61), cycling DOF factor 1 (CDF1), and tubby like protein 3 (TLP3) genes in drought and tubby like protein 1 (TLP1), thaumatin-like proteins (TLP), ethylene-responsive transcription factor ERF109 (EF109), ETS-Related transcription Factor (ELF4), and Arabidopsis thaliana homeodomain leucine-zipper gene (ATHB7) genes in salt showed the significant putative functions and pathways related to providing tolerance against drought and salt stress conditions along with the significant expression values. These outcomes provide potential candidate genes for further in-depth functional studies in cotton, which could be useful for the selection of an improved genotype of Gossypium hirsutum against drought and salt stress conditions.
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Affiliation(s)
- Nasreen Bano
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shafquat Fakhrah
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Chandra Sekhar Mohanty
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sumit Kumar Bag
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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21
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Zhang H, Liu Z, Hu A, Wu H, Zhu J, Wang F, Cao P, Yang X, Zhang H. Full-Length Transcriptome Analysis of the Halophyte Nitraria sibirica Pall. Genes (Basel) 2022; 13:genes13040661. [PMID: 35456467 PMCID: PMC9032868 DOI: 10.3390/genes13040661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Nitraria sibirica Pall. is one of the pioneer tree species in saline–alkali areas due to its extreme salt tolerance. However, the lack of information on its genome limits the further exploration of the molecular mechanisms in N. sibirica under salt stress. Methods: In this study, we used single-molecule real-time (SMRT) technology based on the PacBio Iso-Seq platform to obtain transcriptome data from N. sibirica under salt treatment for the first time, which is helpful for our in-depth analysis of the salt tolerance and molecular characteristics of N. sibirica. Results: Our results suggested that a total of 234,508 circular consensus sequences (CCSs) with a mean read length of 2121 bp were obtained from the 19.26 Gb raw data. Furthermore, based on transcript cluster analysis, 93,713 consensus isoforms were obtained, including 92,116 high-quality isoforms. After removing redundant sequences, 49,240 non-redundant transcripts were obtained from high-quality isoforms. A total of 37,261 SSRs, 1816 LncRNAs and 47,314 CDSs, of which 40,160 carried complete ORFs, were obtained. Based on our transcriptome data, we also analyzed the coding genes of H+-PPase, and the results of both bioinformatics and functional analyses indicated that the gene prediction via full-length transcripts obtained by SMRT technology is reliable and effective. In summary, our research data obtained by SMRT technology provides more reliable and accurate information for the further analysis of the regulatory network and molecular mechanism of N. sibirica under salt stress.
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Affiliation(s)
- Huilong Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
| | - Zhen Liu
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou 061001, China
- Academy of Agriculture and Forestry Sciences, Cangzhou 061001, China
| | - Aishuang Hu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Tangshan 063299, China
| | - Haiwen Wu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
| | - Jianfeng Zhu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
| | - Fengzhi Wang
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou 061001, China
- Academy of Agriculture and Forestry Sciences, Cangzhou 061001, China
| | - Pingping Cao
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou 061001, China
- Academy of Agriculture and Forestry Sciences, Cangzhou 061001, China
| | - Xiuyan Yang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
| | - Huaxin Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
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22
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Chen Q, Xie H, Wei G, Guo X, Zhang J, Lu X, Tang Z. Metabolic differences of two constructive species in saline-alkali grassland in China. BMC PLANT BIOLOGY 2022; 22:53. [PMID: 35081916 PMCID: PMC8790901 DOI: 10.1186/s12870-021-03401-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/14/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Salinization of soil is an urgent problem that restricts agroforestry production and environmental protection. Substantial accumulation of metal ions or highly alkaline soil alters plant metabolites and may even cause plant death. To explore the differences in the response strategies between Suaeda salsa (S. salsa) and Puccinellia tenuiflora (P. tenuiflora), two main constructive species that survive in saline-alkali soil, their metabolic differences were characterized. RESULT Metabolomics was conducted to study the role of metabolic differences between S. salsa and P. tenuiflora under saline-alkali stress. A total of 68 significantly different metabolites were identified by GC-MS, including 9 sugars, 13 amino acids, 8 alcohols, and 34 acids. A more detailed analysis indicated that P. tenuiflora utilizes sugars more effectively and may be saline-alkali tolerant via sugar consumption, while S. salsa utilizes mainly amino acids, alcohols, and acids to resist saline-alkali stress. Measurement of phenolic compounds showed that more C6C3C6-compounds accumulated in P. tenuiflora, while more C6C1-compounds, phenolic compounds that can be used as signalling molecules to defend against stress, accumulated in S. salsa. CONCLUSIONS Our observations suggest that S. salsa resists the toxicity of saline-alkali stress using aboveground organs and that P. tenuiflora eliminates this toxicity via roots. S. salsa has a stronger habitat transformation ability and can provide better habitat for other plants.
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Affiliation(s)
- Qi Chen
- School of Life Sciences Nantong University, Nantong, China
| | - Huansong Xie
- School of Life Sciences Nantong University, Nantong, China
| | - Guanyun Wei
- School of Life Sciences Nantong University, Nantong, China
| | - Xiaorui Guo
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin, China
| | - Jian Zhang
- School of Life Sciences Nantong University, Nantong, China
| | - Xueyan Lu
- Northeast Agricultural University, Harbin, China.
| | - Zhonghua Tang
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin, China.
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23
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Metabolomics Analyses Reveal Metabolites Affected by Plant Growth-Promoting Endophytic Bacteria in Roots of the Halophyte Mesembryanthemum crystallinum. Int J Mol Sci 2021; 22:ijms222111813. [PMID: 34769244 PMCID: PMC8584320 DOI: 10.3390/ijms222111813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 01/07/2023] Open
Abstract
Mesembryanthemum crystallinum L. (common ice plant) is an edible halophyte. However, if ice plants are used to phytoremediate salinity soil, there are problems of slow initial growth, and a long period before active NaCl uptake occurs under higher salinity conditions. Application of endophytic bacteria may improve the problem, but there remain gaps in our understanding of how endophytic bacteria affect the growth and the biochemical and physiological characteristics of ice plants. The aims of this study were to identify growth-promoting endophytic bacteria from the roots of ice plants and to document the metabolomic response of ice plants after application of selected endophytic bacteria. Two plant growth-promoting endophytic bacteria were selected on the basis of their ability to promote ice plant growth. The two strains putatively identified as Microbacterium spp. and Streptomyces spp. significantly promoted ice plant growth, at 2-times and 2.5-times, respectively, compared with the control and also affected the metabolome of ice plants. The strain of Microbacterium spp. resulted in increased contents of metabolites related to the tricarboxylic acid cycle and photosynthesis. The effects of salt stress were alleviated in ice plants inoculated with the endobacterial strains, compared with uninoculated plants. A deeper understanding of the complex interplay among plant metabolites will be useful for developing microbe-assisted soil phytoremediation strategies, using Mesembryanthemum species.
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