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Huang W, Lu Y, Ren B, Zeng F, Liu Y, Lu L, Li L. Identification and Expression Analysis of UPS Gene Family in Potato. Genes (Basel) 2024; 15:870. [PMID: 39062649 PMCID: PMC11275393 DOI: 10.3390/genes15070870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Ureide permeases (UPSs) mediate the transport of ureides, including allantoin and allantoate, which act as nitrogen-transporting compounds in plants and have recently been found to play a role in cellular signaling. To date, UPSs have not been reported in potato, and their identification is important for further function studies and for understanding molecular mechanisms of plant adverse responses. Based on potato genomic data, we identified 10 StUPS genes in potato (Solanum tuberosum L.). Then, we conducted a comprehensive study of the identified StUPS genes using bioinformatics methods. Genome phylogenetic and genomic localization analyses revealed that StUPSs can be classified into four categories, are highly homologous to Arabidopsis thaliana UPS members, and are distributed on three chromosomes. The six StUPS genes were investigated by RT-qPCR, and the findings indicated that all of these genes are involved in the response to several stresses, including low nitrogen, cold, ABA, salt, H2O2, and drought. This study establishes a strong theoretical framework for investigating the function of potato UPS genes, as well as the molecular mechanisms underlying the responses of these genes to various environmental stresses.
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Affiliation(s)
| | | | | | | | | | | | - Liqin Li
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (Y.L.); (B.R.); (F.Z.); (Y.L.); (L.L.)
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2
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Qin H, Xiao M, Li Y, Huang R. Ethylene Modulates Rice Root Plasticity under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:432. [PMID: 38337965 PMCID: PMC10857340 DOI: 10.3390/plants13030432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
Plants live in constantly changing environments that are often unfavorable or stressful. Root development strongly affects plant growth and productivity, and the developmental plasticity of roots helps plants to survive under abiotic stress conditions. This review summarizes the progress being made in understanding the regulation of the phtyohormone ethylene in rice root development in response to abiotic stresses, highlighting the complexity associated with the integration of ethylene synthesis and signaling in root development under adverse environments. Understanding the molecular mechanisms of ethylene in regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions.
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Affiliation(s)
- Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.L.); (R.H.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Minggang Xiao
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China;
| | - Yuxiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.L.); (R.H.)
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.L.); (R.H.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
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3
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Gao Q, Yin X, Wang F, Zhang C, Xiao F, Wang H, Hu S, Liu W, Zhou S, Chen L, Dai X, Liang M. Jacalin-related lectin 45 (OsJRL45) isolated from 'sea rice 86' enhances rice salt tolerance at the seedling and reproductive stages. BMC PLANT BIOLOGY 2023; 23:553. [PMID: 37940897 PMCID: PMC10634080 DOI: 10.1186/s12870-023-04533-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the most widely cultivated grain crops in the world that meets the caloric needs of more than half the world's population. Salt stress seriously affects rice production and threatens food security. Therefore, mining salt tolerance genes in salt-tolerant germplasm and elucidating their molecular mechanisms in rice are necessary for the breeding of salt tolerant cultivars. RESULTS In this study, a salt stress-responsive jacalin-related lectin (JRL) family gene, OsJRL45, was identified in the salt-tolerant rice variety 'sea rice 86' (SR86). OsJRL45 showed high expression level in leaves, and the corresponding protein mainly localized to the endoplasmic reticulum. The knockout mutant and overexpression lines of OsJRL45 revealed that OsJRL45 positively regulates the salt tolerance of rice plants at all growth stages. Compared with the wild type (WT), the OsJRL45 overexpression lines showed greater salt tolerance at the reproductive stage, and significantly higher seed setting rate and 1,000-grain weight. Moreover, OsJRL45 expression significantly improved the salt-resistant ability and yield of a salt-sensitive indica cultivar, L6-23. Furthermore, OsJRL45 enhanced the antioxidant capacity of rice plants and facilitated the maintenance of Na+-K+ homeostasis under salt stress conditions. Five proteins associated with OsJRL45 were screened by transcriptome and interaction network analysis, of which one, the transmembrane transporter Os10g0210500 affects the salt tolerance of rice by regulating ion transport-, salt stress-, and hormone-responsive proteins. CONCLUSIONS The OsJRL45 gene isolated from SR86 positively regulated the salt tolerance of rice plants at all growth stages, and significantly increased the yield of salt-sensitive rice cultivar under NaCl treatment. OsJRL45 increased the activity of antioxidant enzyme of rice and regulated Na+/K+ dynamic equilibrium under salinity conditions. Our data suggest that OsJRL45 may improve the salt tolerance of rice by mediating the expression of ion transport-, salt stress response-, and hormone response-related genes.
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Affiliation(s)
- Qinmei Gao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
- College of Chemistry and Chemical Engineering, Jishou University, Hunan, 416000, China
| | - Xiaolin Yin
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Feng Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Congzhi Zhang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Feicui Xiao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hongyan Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Shuchang Hu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Weihao Liu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Shiqi Zhou
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Liangbi Chen
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xiaojun Dai
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Manzhong Liang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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Rajkumari N, Chowrasia S, Nishad J, Ganie SA, Mondal TK. Metabolomics-mediated elucidation of rice responses to salt stress. PLANTA 2023; 258:111. [PMID: 37919614 DOI: 10.1007/s00425-023-04258-1] [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: 07/03/2023] [Accepted: 10/01/2023] [Indexed: 11/04/2023]
Abstract
MAIN CONCLUSION Role of salinity responsive metabolites of rice and its wild species has been discussed. Salinity stress is one of the important environmental stresses that severely affects rice productivity. Although, several vital physio-biochemical and molecular responses have been activated in rice under salinity stress which were well described in literatures, the mechanistic role of salt stress and microbes-induced metabolites to overcome salt stress in rice are less studied. Nevertheless, over the years, metabolomic studies have allowed a comprehensive analyses of rice salt stress responses. Hence, we review the salt stress-triggered alterations of various metabolites in rice and discuss their significant roles toward salinity tolerance. Some of the metabolites such as serotonin, salicylic acid, ferulic acid and gentisic acid may act as signaling molecules to activate different downstream salt-tolerance mechanisms; whereas, the other compounds such as amino acids, sugars and organic acids directly act as protective agents to maintain osmotic balance and scavenger of reactive oxygen species during the salinity stress. The quantity, type, tissues specificity and time of accumulation of metabolites induced by salinity stress vary between salt-sensitive and tolerant rice genotypes and thus, contribute to their different degrees of salt tolerance. Moreover, few tolerance metabolites such as allantoin, serotonin and melatonin induce unique pathways for activation of defence mechanisms in salt-tolerant varieties of rice, suggesting their potential roles as the universal biomarkers for salt tolerance. Therefore, these metabolites can be applied exogenously to the sensitive genotypes of rice to enhance their performance under salt stress. Furthermore, the microbes of rhizosphere also participated in rice salt tolerance either directly or indirectly by regulating their metabolic pathways. Thus, this review for the first time offers valuable and comprehensive insights into salt-induced spatio-temporal and genotype-specific metabolites in different genotypes of rice which provide a reference point to analyze stress-gene-metabolite relationships for the biomarker designing in rice. Further, it can also help to decipher several metabolic systems associated with salt tolerance in rice which will be useful in developing salt-tolerance cultivars by conventional breeding/genetic engineering/exogenous application of metabolites.
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Affiliation(s)
- Nitasana Rajkumari
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India
- ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Soni Chowrasia
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India
- Department of Bioscience and Biotechnology, Banastahli Vidyapith, Tonk, Rajasthan, 304022, India
| | - Jyoti Nishad
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India
| | - Showkat Ahmad Ganie
- Plant Molecular Sciences and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, Surrey, UK
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India.
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Kaur R, Chandra J, Varghese B, Keshavkant S. Allantoin: A Potential Compound for the Mitigation of Adverse Effects of Abiotic Stresses in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3059. [PMID: 37687306 PMCID: PMC10489999 DOI: 10.3390/plants12173059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Stress-induced alterations vary with the species of plants, the intensity and duration of the exposure, and stressors availability in nature or soil. Purine catabolism acts as an inherent defensive mechanism against various abiotic stresses and plays a pivotal role in the stress acclimatisation of plants. The intermediate metabolite of purine catabolism, allantoin, compensates for soil nitrogen deficiency due to the low carbon/nitrogen ratio, thereby maintaining nitrogen homeostasis and supporting plant growth and development. Allantoin accounts for 90% of the total nitrogenous compound in legumes, while it contributes only 15% in non-leguminous plants. Moreover, studies on a variety of plant species have reported the differential accumulation of allantoin in response to abiotic stresses, endowing allantoin as a stress modulator. Allantoin functions as signalling molecule to stimulate stress-responsive genes (P5CS; pyrroline-5-carboxylase synthase) and ROS (reactive oxygen species) scavenging enzymes (antioxidant). Moreover, it regulates cross-talk between the abscisic acid and jasmonic acid pathway, and maintains ion homeostasis by increasing the accumulation of putrescine and/or spermine, consequently enhancing the tolerance against stress conditions. Further, key enzymes of purine catabolism (xanthine dehydrogenase and allantoinase) have also been explored by constructing various knockdown/knockout mutant lines to decipher their impact on ROS-mediated oxidative injury in plants. Thus, it is established that allantoin serves as a regulatory signalling metabolite in stress protection, and therefore a lower accumulation of allantoin also reduces plant stress tolerance mechanisms. This review gives an account of metabolic regulation and the possible contribution of allantoin as a photo protectant, osmoprotectant, and nitrogen recycler to reduce abiotic-stress-induced impacts on plants.
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Affiliation(s)
- Rasleen Kaur
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur 492 010, India; (R.K.); (S.K.)
| | - Jipsi Chandra
- Center for Basic Sciences, Pt. Ravishankar Shukla University, Raipur 492 010, India;
| | - Boby Varghese
- Centre for Academic Success in Science and Engineering, University of KwaZulu-Natal, Durban 4001, South Africa
| | - S. Keshavkant
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur 492 010, India; (R.K.); (S.K.)
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Liu Y, Gao S, Hu Y, Zhang T, Guo J, Shi L, Li M. Comparative study of leaf nutrient reabsorption by two different ecotypes of wild soybean under low-nitrogen stress. PeerJ 2023; 11:e15486. [PMID: 37397019 PMCID: PMC10312162 DOI: 10.7717/peerj.15486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/10/2023] [Indexed: 07/04/2023] Open
Abstract
Wild soybean (Glycine soja), the ancestor of cultivated soybean, has evolved into many ecotypes with different adaptations to adversity under the action of divergent evolution. Barren-tolerant wild soybean has developed adaptation to most nutrient-stress environments, especially with respect to low nitrogen (LN) conditions. This study describes the differences in physiological and metabolomic changes between common wild soybean (GS1) and barren-tolerant wild soybean(GS2) under LN stress. Compared with plants grown under the unstressed control (CK) conditions, the young leaves of barren-tolerant wild soybean under LN conditions maintained relatively stable chlorophyll, concentration and rates of photosynthesis and transpiration, as well as increased carotenoid content, whereas the net photosynthetic rate (PN) of GS1 decreased significantly 0.64-fold (p < 0.05) in the young leaves of GS1. The ratio of internal to atmospheric CO2 concentrations increased significantly 0.07-fold (p < 0.05), 0.09-fold (p < 0.05) in the young leaves of GS1 and GS2, respectively, and increased significantly 0.05-fold (p < 0.05) and 0.07-fold (p < 0.05) in the old leaves of GS1 and GS2, respectively, relative to the CK. The concentration of chlorophylls a and b decreased significantly 0.45-fold (p < 0.05), 0.13-fold (p > 0.05) in the young leaves of GS1 and GS2, respectively, and decreased significantly 0.74-fold (p < 0.01) and 0.60-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Under LN stress, nitrate concentration in the young leaves of GS1 and GS2 decreased significantly 0.69- and 0.50-fold (p < 0.01), respectively, relative to CK, and decreased significantly 2.10-fold and 1.77-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Barren-tolerant wild soybean increased the concentration of beneficial ion pairs. Under LN stress, Zn2+ significantly increased by 1.06- and 1.35-fold (p < 0.01) in the young and old leaves of GS2 (p < 0.01), but there was no significant change in GS1. The metabolism of amino acids and organic acids was high in GS2 young and old leaves, and the metabolites related to the TCA cycle were significantly increased. The 4-aminobutyric acid (GABA) concertation decreased significantly 0.70-fold (p < 0.05) in the young leaves of GS1 but increased 0.21-fold (p < 0.05) significantly in GS2. The relative concentration of proline increased significantly 1.21-fold (p < 0.01) and 2.85-fold (p < 0.01) in the young and old leaves of GS2. Under LN stress, GS2 could maintain photosynthesis rate and enhance the reabsorption of nitrate and magnesium in young leaves, compared to GS1. More importantly, GS2 exhibited increased amino acid and TCA cycle metabolism in young and old leaves. Adequate reabsorption of mineral and organic nutrients is an important strategy for barren-tolerant wild soybeans to survive under LN stress. Our research provides a new perspective on the exploitation and utilization of wild soybean resources.
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Affiliation(s)
- Yuan Liu
- Northeast Normal University, Changchun, China
- ChiFeng University, ChiFeng, China
| | - Shujuan Gao
- Northeast Normal University, Changchun, China
| | - Yunan Hu
- Northeast Normal University, Changchun, China
| | - Tao Zhang
- Northeast Normal University, Changchun, China
| | - Jixun Guo
- Northeast Normal University, Changchun, China
| | | | - Mingxia Li
- ChangChun Normal University, Changchun, China
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Chowrasia S, Nishad J, Mahato R, Kiran K, Rajkumari N, Panda AK, Rawal HC, Barman M, Mondal TK. Allantoin improves salinity tolerance in Arabidopsis and rice through synergid activation of abscisic acid and brassinosteroid biosynthesis. PLANT MOLECULAR BIOLOGY 2023:10.1007/s11103-023-01350-8. [PMID: 37184674 DOI: 10.1007/s11103-023-01350-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/02/2023] [Indexed: 05/16/2023]
Abstract
Soil salinity stress is one of the major bottlenecks for crop production. Although, allantoin is known to be involved in nitrogen metabolism in plants, yet several reports in recent time indicate its involvement in various abiotic stress responses including salinity stress. However, the detail mechanism of allantoin involvement in salinity stress tolerance in plants is not studied well. Moreover, we demonstrated the role of exogenous application of allantoin as well as increased concentration of endogenous allantoin in rendering salinity tolerance in rice and Arabidopsis respectively, via., induction of abscisic acid (ABA) and brassinosteroid (BR) biosynthesis pathways. Exogenous application of allantoin (10 µM) provides salt-tolerance to salt-sensitive rice genotype (IR-29). Transcriptomic data after exogenous supplementation of allantoin under salinity stress showed induction of ABA (OsNCED1) and BR (Oscytochrome P450) biosynthesis genes in IR-29. Further, the key gene of allantoin biosynthesis pathway i.e., urate oxidase of the halophytic species Oryza coarctata was also found to induce ABA and BR biosynthesis genes when over-expressed in transgenic Arabidopsis. Thus, indicating that ABA and BR biosynthesis pathways were involved in allantoin mediated salinity tolerance in both rice and Arabidopsis. Additionally, it has been found that several physio-chemical parameters such as biomass, Na+/K+ ratio, MDA, soluble sugar, proline, allantoin and chlorophyll contents were also associated with the allantoin-mediated salinity tolerance in urate oxidase overexpressed lines of Arabidopsis. These findings depicted the functional conservation of allantoin for salinity tolerance in both plant clades.
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Affiliation(s)
- Soni Chowrasia
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Jyoti Nishad
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Rekha Mahato
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kanti Kiran
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Nitasana Rajkumari
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Alok Kumar Panda
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Hukam C Rawal
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Mandira Barman
- ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- LBS Centre, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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Xu S, Cui J, Cao H, Liang S, Ma T, Liu H, Wang J, Yang L, Xin W, Jia Y, Zou D, Zheng H. Identification of candidate genes for salinity tolerance in Japonica rice at the seedling stage based on genome-wide association study and linkage mapping. FRONTIERS IN PLANT SCIENCE 2023; 14:1184416. [PMID: 37235029 PMCID: PMC10206223 DOI: 10.3389/fpls.2023.1184416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023]
Abstract
Background Salinity tolerance plays a vital role in rice cultivation because the strength of salinity tolerance at the seedling stage directly affects seedling survival and final crop yield in saline soils. Here, we combined a genome-wide association study (GWAS) and linkage mapping to analyze the candidate intervals for salinity tolerance in Japonica rice at the seedling stage. Results We used the Na+ concentration in shoots (SNC), K+ concentration in shoots (SKC), Na+/K+ ratio in shoots (SNK), and seedling survival rate (SSR) as indices to assess the salinity tolerance at the seedling stage in rice. The GWAS identified the lead SNP (Chr12_20864157), associated with an SNK, which the linkage mapping detected as being in qSK12. A 195-kb region on chromosome 12 was selected based on the overlapping regions in the GWAS and the linkage mapping. Based on haplotype analysis, qRT-PCR, and sequence analysis, we obtained LOC_Os12g34450 as a candidate gene. Conclusion Based on these results, LOC_Os12g34450 was identified as a candidate gene contributing to salinity tolerance in Japonica rice. This study provides valuable guidance for plant breeders to improve the response of Japonica rice to salt stress.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Detang Zou
- *Correspondence: Detang Zou, ; Hongliang Zheng,
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Wang G, Li J, Ji J, Zhang L, Li B, Zhang J, Wang X, Song W, Guan C. Combined application of allantoin and strain JIT1 synergistically or additively promotes the growth of rice under 2, 4-DCP stress by enhancing the phosphate solubility, improving soil enzyme activities and photosynthesis. JOURNAL OF PLANT PHYSIOLOGY 2023; 282:153941. [PMID: 36739690 DOI: 10.1016/j.jplph.2023.153941] [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: 07/01/2022] [Revised: 12/10/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Environmental pollution by 2, 4 dichlorophenol (2, 4-DCP) has become a widespread concern due to its detrimental influence on human and natural ecosystem. With the increasing accumulation of 2, 4-DCP in soil, it is of great significance to explore some appropriate approaches for enhancing plant tolerance to 2, 4-DCP stress. In the current study, a strain resistant to 2, 4-DCP was obtained from the tall fescue rhizosphere soil and named as Pseudomonas sp. JIT1. The strain JIT1 exhibited several remarkable plant growth-promoting traits, including the production of IAA, fixation of biological nitrogen and solubilization of phosphate. The inoculation of strain JIT1 significantly increased biomass, photosynthesis, antioxidant levels, chlorophyll contents and the osmotic substance contents in rice seedlings exposed to 2, 4-DCP. Meanwhile, inoculation of strain JIT1 also enhanced activities of soil alkaline phosphatase, urease, sucrase and cellulase. Moreover, under 2, 4-DCP stress, the content of allantoin in seedlings significantly increased and the pretreatment of exogenous allantoin noticeably ameliorated the negative effects caused by 2, 4-DCP stress in rice seedlings. Interesting, allantoin treatment also enhanced phosphate solubilization properties of strain JIT1. The chlorophyll contents, photosynthesis and osmotic substance further increased by combination use of strain JIT1 and allantoin, which improved the growth of seedlings, most likely to be attributed to the synergistic or additive effect between allantoin and strain JIT1. The results of this study highlight the important roles of combined use of strain JIT1 and allantoin for improving the tolerance of rice to 2, 4-DCP to stress.
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Affiliation(s)
- Gang Wang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Jiali Li
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Jing Ji
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Lishuang Zhang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Bowen Li
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Jiaqi Zhang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Xinya Wang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Wenju Song
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Chunfeng Guan
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
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de Moraes Pontes JG, da Silva Pinheiro MS, Fill TP. Unveiling Chemical Interactions Between Plants and Fungi Using Metabolomics Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:1-20. [PMID: 37843803 DOI: 10.1007/978-3-031-41741-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Metabolomics has been extensively used in clinical studies in the search for new biomarkers of human diseases. However, this approach has also been highlighted in agriculture and biological sciences, once metabolomics studies have been assisting researchers to deduce new chemical mechanisms involved in biological interactions that occur between microorganisms and plants. In this sense, the knowledge of the biological role of each metabolite (virulence factors, signaling compounds, antimicrobial metabolites, among others) and the affected biochemical pathways during the interaction contribute to a better understand of different ecological relationships established in nature. The current chapter addresses five different applications of the metabolomics approach in fungal-plant interactions research: (1) Discovery of biomarkers in pathogen-host interactions, (2) plant diseases diagnosis, (3) chemotaxonomy, (4) plant defense, and (5) plant resistance; using mass spectrometry and/or nuclear magnetic resonance spectroscopy, which are the techniques most used in metabolomics.
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Affiliation(s)
- João Guilherme de Moraes Pontes
- Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Laboratório de Biologia Química Microbiana (LaBioQuiMi), Campinas, SP, Brazil
| | - Mayra Suelen da Silva Pinheiro
- Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Laboratório de Biologia Química Microbiana (LaBioQuiMi), Campinas, SP, Brazil
| | - Taícia Pacheco Fill
- Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Laboratório de Biologia Química Microbiana (LaBioQuiMi), Campinas, SP, Brazil.
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11
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Lu S, Jia Z, Meng X, Chen Y, Wang S, Fu C, Yang L, Zhou R, Wang B, Cao Y. Combined Metabolomic and Transcriptomic Analysis Reveals Allantoin Enhances Drought Tolerance in Rice. Int J Mol Sci 2022; 23:ijms232214172. [PMID: 36430648 PMCID: PMC9699107 DOI: 10.3390/ijms232214172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Drought is a misfortune for agriculture and human beings. The annual crop yield reduction caused by drought exceeds the sum of all pathogens. As one of the gatekeepers of China's "granary", rice is the most important to reveal the key drought tolerance factors in rice. Rice seedlings of Nipponbare (Oryza sativa L. ssp. Japonica) were subjected to simulated drought stress, and their root systems were analyzed for the non-targeted metabolome and strand-specific transcriptome. We found that both DEGs and metabolites were enriched in purine metabolism, and allantoin accumulated significantly in roots under drought stress. However, few studies on drought tolerance of exogenous allantoin in rice have been reported. We aimed to further determine whether allantoin can improve the drought tolerance of rice. Under the treatment of exogenous allantoin at different concentrations, the drought resistant metabolites of plants accumulated significantly, including proline and soluble sugar, and reactive oxygen species (ROS) decreased and reached a significant level in 100 μmol L-1. To this end, a follow-up study was identified in 100 μmol L-1 exogenous allantoin and found that exogenous allantoin improved the drought resistance of rice. At the gene level, under allantoin drought treatment, we found that genes of scavenge reactive oxygen species were significantly expressed, including peroxidase (POD), catalase (CATA), ascorbate peroxidase 8 (APX8) and respiratory burst oxidase homolog protein F (RbohF). This indicates that plants treated by allantoin have better ability to scavenge reactive oxygen species to resist drought. Alternative splicing analysis revealed a total of 427 differentially expressed alternative splicing events across 320 genes. The analysis of splicing factors showed that gene alternative splicing could be divided into many different subgroups and play a regulatory role in many aspects. Through further analysis, we restated the key genes and enzymes in the allantoin synthesis and catabolism pathway, and found that the expression of synthetase and hydrolase showed a downward trend. The pathway of uric acid to allantoin is completed by uric acid oxidase (UOX). To find out the key transcription factors that regulate the expression of this gene, we identified two highly related transcription factors OsERF059 and ONAC007 through correlation analysis. They may be the key for allantoin to enhance the drought resistance of rice.
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Affiliation(s)
- Shuai Lu
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Zichang Jia
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Xiangfeng Meng
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Yaoyu Chen
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Surong Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Chaozhen Fu
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lei Yang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Rong Zhou
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
- Correspondence: (B.W.); (Y.C.)
| | - Yunying Cao
- School of Life Sciences, Nantong University, Nantong 226019, China
- Correspondence: (B.W.); (Y.C.)
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12
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Wang J, Li Y, Wang Y, Du F, Zhang Y, Yin M, Zhao X, Xu J, Yang Y, Wang W, Fu B. Transcriptome and Metabolome Analyses Reveal Complex Molecular Mechanisms Involved in the Salt Tolerance of Rice Induced by Exogenous Allantoin. Antioxidants (Basel) 2022; 11:antiox11102045. [PMID: 36290768 PMCID: PMC9598814 DOI: 10.3390/antiox11102045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Allantoin is crucial for plant growth and development as well as adaptations to abiotic stresses, but the underlying molecular mechanisms remain unclear. In this study, we comprehensively analyzed the physiological indices, transcriptomes, and metabolomes of rice seedlings following salt, allantoin, and salt + allantoin treatments. The results revealed that exogenous allantoin positively affects the salt tolerance by increasing the contents of endogenous allantoin with antioxidant activities, increasing the reactive oxygen species (ROS)–scavenging capacity, and maintaining sodium and potassium homeostasis. The transcriptome analysis detected the upregulated expression genes involved in ion transport and redox regulation as well as the downregulated expression of many salt-induced genes related to transcription and post-transcriptional regulation, carbohydrate metabolism, chromosome remodeling, and cell wall organization after the exogenous allantoin treatment of salt-stressed rice seedlings. Thus, allantoin may mitigate the adverse effects of salt stress on plant growth and development. Furthermore, a global metabolite analysis detected the accumulation of metabolites with antioxidant activities and intermediate products of the allantoin biosynthetic pathway in response to exogenous allantoin, implying allantoin enhances rice salt tolerance by inducing ROS scavenging cascades. These results have clarified the transcript-level and metabolic processes underlying the allantoin-mediated salt tolerance of rice.
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Affiliation(s)
- Juan Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Life Sciences, China Agricultural University, Beijing 100193, China
| | - Yingbo Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinxiao Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fengping Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yue Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ming Yin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongqing Yang
- College of Life Sciences, China Agricultural University, Beijing 100193, China
- Correspondence: (Y.Y.); (W.W.); (B.F.)
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
- Correspondence: (Y.Y.); (W.W.); (B.F.)
| | - Binying Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (Y.Y.); (W.W.); (B.F.)
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13
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Zhou L, Zong Y, Li L, Wu S, Duan M, Lu R, Liu C, Chen Z. Integrated analysis of transcriptome and metabolome reveals molecular mechanisms of salt tolerance in seedlings of upland rice landrace 17SM-19. FRONTIERS IN PLANT SCIENCE 2022; 13:961445. [PMID: 36186007 PMCID: PMC9515574 DOI: 10.3389/fpls.2022.961445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/18/2022] [Indexed: 06/16/2023]
Abstract
Salt stress is a major abiotic stress that threatens global rice production. It is particularly important to improve salt tolerance in upland rice because of its growth environment. Upland rice landrace 17SM-19 with high salt tolerance was obtained from a previous study. In this study, an integrated analysis of transcriptome and metabolome was performed to determine the responses of the rice seedling to salt stress. When treated with 100 mm NaCl, the rice seedling growth was significantly inhibited at 5 d, with inhibition first observed in shoot dry weight (SDW). Changes in potassium (K+) content were associated with changes in SDW. In omics analyses, 1,900 differentially expressed genes (DEGs) and 659 differentially abundant metabolites (DAMs) were identified at 3 d after salt stress (DAS), and 1,738 DEGs and 657 DAMs were identified at 5 DAS. Correlation analyses between DEGs and DAMs were also conducted. The results collectively indicate that salt tolerance of upland rice landrace 17SM-19 seedlings involves many molecular mechanisms, such as those involved with osmotic regulation, ion balance, and scavenging of reactive oxygen species.
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Affiliation(s)
- Longhua Zhou
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Zong
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Luli Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Shujun Wu
- Crop Breeding & Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | | | - Ruiju Lu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chenghong Liu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhiwei Chen
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
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14
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Yi X, Sun X, Tian R, Li K, Ni M, Ying J, Xu L, Liu L, Wang Y. Genome-Wide Characterization of the Aquaporin Gene Family in Radish and Functional Analysis of RsPIP2-6 Involved in Salt Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:860742. [PMID: 35909741 PMCID: PMC9337223 DOI: 10.3389/fpls.2022.860742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Aquaporins (AQPs) constitute a highly diverse family of channel proteins that transport water and neutral solutes. AQPs play crucial roles in plant development and stress responses. However, the characterization and biological functions of RsAQPs in radish (Raphanus sativus L.) remain elusive. In this study, 61 non-redundant members of AQP-encoding genes were identified from the radish genome database and located on nine chromosomes. Radish AQPs (RsAQPs) were divided into four subfamilies, including 21 plasma membrane intrinsic proteins (PIPs), 19 tonoplast intrinsic proteins (TIPs), 16 NOD-like intrinsic proteins (NIPs), and 5 small basic intrinsic proteins (SIPs), through phylogenetic analysis. All RsAQPs contained highly conserved motifs (motifs 1 and 4) and transmembrane regions, indicating the potential transmembrane transport function of RsAQPs. Tissue- and stage-specific expression patterns of AQP gene analysis based on RNA-seq data revealed that the expression levels of PIPs were generally higher than TIPs, NIPs, and SIPs in radish. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) revealed that seven selected RsPIPs, according to our previous transcriptome data (e.g., RsPIP1-3, 1-6, 2-1, 2-6, 2-10, 2-13, and 2-14), exhibited significant upregulation in roots of salt-tolerant radish genotype. In particular, the transcriptional levels of RsPIP2-6 dramatically increased after 6 h of 150 mM NaCl treatment during the taproot thickening stage. Additionally, overexpression of RsPIP2-6 could enhance salt tolerance by Agrobacterium rhizogenes-mediated transgenic radish hairy roots, which exhibited the mitigatory effects of plant growth reduction, leaf relative water content (RWC) reduction and alleviation of O2- in cells, as shown by nitro blue tetrazolium (NBT) staining, under salt stress. These findings are helpful for deeply dissecting the biological function of RsAQPs on the salt stress response, facilitating practical application and genetic improvement of abiotic stress resistance in radish.
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Affiliation(s)
- Xiaofang Yi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaochuan Sun
- College of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an, China
| | - Rong Tian
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kexin Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Meng Ni
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiali Ying
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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15
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Zhou T, Wu P, Yue C, Huang J, Zhang Z, Hua Y. Transcriptomic Dissection of Allotetraploid Rapeseed (Brassica napus L.) in Responses to Nitrate and Ammonium Regimes and Functional Analysis of BnaA2.Gln1;4 in Arabidopsis. PLANT & CELL PHYSIOLOGY 2022; 63:755-769. [PMID: 35325216 DOI: 10.1093/pcp/pcac037] [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: 02/22/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Plant roots acquire nitrogen predominantly as two inorganic forms, nitrate (NO3-) and ammonium (NH4+), to which plants respond differentially. Rapeseed (Brassica napus L.) is an important oil-crop species with very low nitrogen-use efficiency (NUE), the regulatory mechanism of which was elusive due to the vastness and complexity of the rapeseed genome. In this study, a comparative transcriptomic analysis was performed to investigate the differential signatures of nitrogen-starved rapeseed in responses to NO3- and NH4+ treatments and to identify the key genes regulating rapeseed NUE. The two nitrogen sources differentially affected the shoot and root transcriptome profiles, including those of genome-wide nitrogen transporter and transcription factor (TF)-related genes. Differential expression profiling showed that BnaA6.NRT2;1 and BnaA7.AMT1;3 might be the core transporters responsible for efficient NO3- and NH4+ uptake, respectively; the TF genes responsive to inorganic nitrogen, specifically responding to NO3-, and specifically responsive to NH4+ were also identified. The genes which were commonly and most significantly affected by both NO3- and NH4+ treatments were related to glutamine metabolism. Among the glutamine synthetase (GS) family genes, we found BnaA2.Gln1;4, significantly responsive to low-nitrogen conditions and showed higher transcription abundance and GS activity in the leaf veins, flower sepals, root cortex and stele, silique petiole and stem tissues. These characters were significantly different from those of AtGln1;4. The heterologous overexpression of BnaA2.Gln1;4 in Arabidopsis increased plant biomass, NUE, GS activity and total amino acid concentrations under both sufficient- and low-nitrogen conditions. Overall, this study provided novel information about the genes involved in the adaptation to different nitrogen regimes and identified some promising candidate genes for enhancing NUE in rapeseed.
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Affiliation(s)
- Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Pengjia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Caipeng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Jinyong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Zhenhua Zhang
- College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha 430128, PR China
| | - Yingpeng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
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16
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Li Y, Zhou J, Li Z, Qiao J, Quan R, Wang J, Huang R, Qin H. SALT AND ABA RESPONSE ERF1 improves seed germination and salt tolerance by repressing ABA signaling in rice. PLANT PHYSIOLOGY 2022; 189:1110-1127. [PMID: 35294556 PMCID: PMC9157093 DOI: 10.1093/plphys/kiac125] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/24/2022] [Indexed: 05/13/2023]
Abstract
Rice (Oryza sativa) germination and seedling establishment, particularly in increasingly saline soils, are critical to ensure successful crop yields. Seed vigor, which determines germination and seedling growth, is a complex trait affected by exogenous (environmental) and endogenous (hormonal) factors. Here, we used genetic and biochemical analyses to uncover the role of an APETALA2-type transcription factor, SALT AND ABA RESPONSE ERF1 (OsSAE1), as a positive regulator of seed germination and salt tolerance in rice by repressing the expression of ABSCISIC ACID-INSENSITIVE5 (OsABI5). ossae1 knockout lines exhibited delayed seed germination, enhanced sensitivity to abscisic acid (ABA) during germination and in early seedling growth, and reduced seedling salt tolerance. OsSAE1 overexpression lines exhibited the converse phenotype, with increased seed germination and salt tolerance. In vivo and in vitro assays indicated that OsSAE1 binds directly to the promoter of OsABI5, a major downstream component of the ABA signaling pathway and acts as a major regulator of seed germination and stress response. Genetic analyses revealed that OsABI5-mediated ABA signaling functions downstream of OsSAE1. This study provides important insights into OsSAE1 regulation of seed vigor and salt tolerance and facilitates the practical use of OsSAE1 in breeding salt-tolerant varieties suitable for direct seeding cultivation.
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Affiliation(s)
- Yuxiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiahao Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhe Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinzhu Qiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruidang Quan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Juan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
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17
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A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms. PLANTS 2022; 11:plants11111430. [PMID: 35684203 PMCID: PMC9182744 DOI: 10.3390/plants11111430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 01/04/2023]
Abstract
Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.
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18
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Dai L, Li P, Li Q, Leng Y, Zeng D, Qian Q. Integrated Multi-Omics Perspective to Strengthen the Understanding of Salt Tolerance in Rice. Int J Mol Sci 2022; 23:ijms23095236. [PMID: 35563627 PMCID: PMC9105537 DOI: 10.3390/ijms23095236] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022] Open
Abstract
Salt stress is one of the major constraints to rice cultivation worldwide. Thus, the development of salt-tolerant rice cultivars becomes a hotspot of current rice breeding. Achieving this goal depends in part on understanding how rice responds to salt stress and uncovering the molecular mechanism underlying this trait. Over the past decade, great efforts have been made to understand the mechanism of salt tolerance in rice through genomics, transcriptomics, proteomics, metabolomics, and epigenetics. However, there are few reviews on this aspect. Therefore, we review the research progress of omics related to salt tolerance in rice and discuss how these advances will promote the innovations of salt-tolerant rice breeding. In the future, we expect that the integration of multi-omics salt tolerance data can accelerate the solution of the response mechanism of rice to salt stress, and lay a molecular foundation for precise breeding of salt tolerance.
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Affiliation(s)
- Liping Dai
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
| | - Peiyuan Li
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
| | - Qing Li
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
| | - Yujia Leng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Y.L.); (Q.Q.)
| | - Dali Zeng
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A & F University, Hangzhou 311300, China
| | - Qian Qian
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
- Correspondence: (Y.L.); (Q.Q.)
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19
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Zhou J, Qiao J, Wang J, Quan R, Huang R, Qin H. OsQHB Improves Salt Tolerance by Scavenging Reactive Oxygen Species in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:848891. [PMID: 35599895 PMCID: PMC9115556 DOI: 10.3389/fpls.2022.848891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
Soil salinity is a major environmental stress that restricts the growth and yield of crops. Mining the key genes involved in the balance of rice salt tolerance and yield will be extremely important for us to cultivate salt-tolerance rice varieties. In this study, we report a WUSCHEL-related homeobox (WOX) gene, quiescent-center-specific homeobox (OsQHB), positively regulates yield-related traits and negatively regulates salt tolerance in rice. Mutation in OsQHB led to a decrease in plant height, tiller number, panicle length, grain length and grain width, and an increase in salt tolerance. Transcriptome and qPCR analysis showed that reactive oxygen species (ROS) scavenging-related genes were regulated by OsQHB. Moreover, the osqhb mutants have higher ROS-scavenging enzymes activities and lower accumulation of ROS and malondialdehyde (MDA) under salt stress. Thus, our findings provide new insights into the role of rice WOX gene family in rice development and salt tolerance, and suggest that OsQHB is a valuable target for improving rice production in environments characterized by salt stress.
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Affiliation(s)
- Jiahao Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinzhu Qiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, China
| | - Ruidang Quan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, China
| | - Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, China
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20
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Kumar P, Choudhary M, Halder T, Prakash NR, Singh V, V. VT, Sheoran S, T. RK, Longmei N, Rakshit S, Siddique KHM. Salinity stress tolerance and omics approaches: revisiting the progress and achievements in major cereal crops. Heredity (Edinb) 2022; 128:497-518. [DOI: 10.1038/s41437-022-00516-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
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21
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Huang Y, Zhou J, Li Y, Quan R, Wang J, Huang R, Qin H. Salt Stress Promotes Abscisic Acid Accumulation to Affect Cell Proliferation and Expansion of Primary Roots in Rice. Int J Mol Sci 2021; 22:ijms221910892. [PMID: 34639232 PMCID: PMC8509385 DOI: 10.3390/ijms221910892] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 01/16/2023] Open
Abstract
The primary root is the basic component of the root system and plays a key role in early seedling growth in rice. Its growth is easily affected by environmental cues, such as salt stress. Abscisic acid (ABA) plays an essential role in root development, but the molecular mechanism underlying ABA-regulated root growth in response to salt stress remains poorly understood. In this study, we report that salt stress inhibits primary root elongation and promotes primary root swelling. Moreover, salt stress induces the expression of ABA-responsive genes and ABA accumulation in the primary root, revealing that ABA plays an essential role in salt-modulated root growth. Transgenic lines of OsSAPK10-OE and OsABIL2-OE, which constitutively express OsSAPK10 or OsABIL2, with enhanced or attenuated ABA signaling, show increased and decreased sensitivity to salt, correspondingly. Microscopic analysis indicates that salt and ABA inhibits cell proliferation and promotes cell expansion in the root apical meristem. Transcriptome analysis showed that ABA induces the expression of EXPANSIN genes. Further investigations indicate that ABA exerts these effects largely through ABA signaling. Thus, our findings deepen our understanding of the role of ABA in controlling primary root growth in response to salt stress, and this knowledge can be used by breeders to cultivate rice varieties suitable for saline–alkali land.
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Affiliation(s)
- Yingying Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (J.Z.); (Y.L.); (R.Q.); (J.W.); (R.H.)
| | - Jiahao Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (J.Z.); (Y.L.); (R.Q.); (J.W.); (R.H.)
| | - Yuxiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (J.Z.); (Y.L.); (R.Q.); (J.W.); (R.H.)
| | - Ruidang Quan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (J.Z.); (Y.L.); (R.Q.); (J.W.); (R.H.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Juan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (J.Z.); (Y.L.); (R.Q.); (J.W.); (R.H.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (J.Z.); (Y.L.); (R.Q.); (J.W.); (R.H.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (J.Z.); (Y.L.); (R.Q.); (J.W.); (R.H.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
- Correspondence:
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Wang Y, Huang L, Du F, Wang J, Zhao X, Li Z, Wang W, Xu J, Fu B. Comparative transcriptome and metabolome profiling reveal molecular mechanisms underlying OsDRAP1-mediated salt tolerance in rice. Sci Rep 2021; 11:5166. [PMID: 33664392 PMCID: PMC7933422 DOI: 10.1038/s41598-021-84638-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/18/2021] [Indexed: 11/09/2022] Open
Abstract
Integration of transcriptomics and metabolomics data can provide detailed information for better understanding the molecular mechanisms underlying salt tolerance in rice. In the present study, we report a comprehensive analysis of the transcriptome and metabolome of rice overexpressing the OsDRAP1 gene, which encodes an ERF transcription factor and was previously identified to be conferring drought tolerance. Phenotypic analysis showed that OsDRAP1 overexpression (OE) improved salt tolerance by increasing the survival rate under salt stress. OsDRAP1 affected the physiological indices such as superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) to enhance redox homeostasis and membrane stability in response to salt stress. Higher basal expression of OsDRAP1 resulted in differential expression of genes that potentially function in intrinsic salt tolerance. A core set of genes with distinct functions in transcriptional regulation, organelle gene expression and ion transport were substantially up-regulated in the OE line in response to salt stress, implying their important role in OsDRAP1-mediated salt tolerance. Correspondingly, metabolome profiling detected a number of differentially metabolites in the OE line relative to the wild type under salt stress. These metabolites, including amino acids (proline, valine), organic acids (glyceric acid, phosphoenolpyruvic acid and ascorbic acid) and many secondary metabolites, accumulated to higher levels in the OE line, demonstrating their role in salt tolerance. Integration of transcriptome and metabolome analysis highlights the crucial role of amino acids and carbohydrate metabolism pathways in OsDRAP1-mediated salt tolerance.
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Affiliation(s)
- Yinxiao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China
| | - Liyu Huang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China.,School of Agriculture, Yunnan University, Kunming, Yunnan, China.,Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, 650091, Yunnan, China
| | - Fengping Du
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China
| | - Juan Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China.,School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China. .,School of Agronomy, Anhui Agricultural University, Hefei, China.
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China.
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China.
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23
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Du B, Ma Y, Yáñez-Serrano AM, Arab L, Fasbender L, Alfarraj S, Albasher G, Hedrich R, White PJ, Werner C, Rennenberg H. Physiological responses of date palm (Phoenix dactylifera) seedlings to seawater and flooding. THE NEW PHYTOLOGIST 2021; 229:3318-3329. [PMID: 33259640 DOI: 10.1111/nph.17123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/22/2020] [Indexed: 06/12/2023]
Abstract
In their natural environment along coast lines, date palms are exposed to seawater inundation and, hence, combined stress by salinity and flooding. To elucidate the consequences of this combined stress on foliar gas exchange and metabolite abundances in leaves and roots, date palm seedlings were exposed to flooding with seawater and its major constituents under controlled conditions. Seawater flooding significantly reduced CO2 assimilation, transpiration and stomatal conductance, but did not affect isoprene emission. A similar effect was observed upon NaCl exposure. By contrast, flooding with distilled water or MgSO4 did not affect CO2 /H2 O gas exchange or stomatal conductance significantly, indicating that neither flooding itself, nor seawater sulfate, contributed greatly to stomatal closure. Seawater exposure increased Na and Cl contents in leaves and roots, but did not affect sulfate contents significantly. Metabolite analyses revealed reduced abundances of foliar compatible solutes, such as sugars and sugar alcohols, whereas nitrogen compounds accumulated in roots. Reduced transpiration upon seawater exposure may contribute to controlling the movement of toxic ions to leaves and, therefore, can be seen as a mechanism to cope with salinity. The present results indicate that date palm seedlings are tolerant towards seawater exposure to some extent, and highly tolerant to flooding.
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Affiliation(s)
- Baoguo Du
- College of Life Science and Biotechnology, Mianyang Normal University, Mianxing Road West 166, Mianyang, 621000, China
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 53, Freiburg, 79110, Germany
| | - Yuhua Ma
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Ningda Road 251, Xining, 810016, China
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 53, Freiburg, 79110, Germany
| | - Ana Maria Yáñez-Serrano
- Ecosystem Physiology, University of Freiburg, Georges-Köhler-Allee 53/54, Freiburg, 79110, Germany
| | - Leila Arab
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 53, Freiburg, 79110, Germany
| | - Lukas Fasbender
- Ecosystem Physiology, University of Freiburg, Georges-Köhler-Allee 53/54, Freiburg, 79110, Germany
| | - Saleh Alfarraj
- King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Gadah Albasher
- King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, Würzburg, 97082, Germany
| | - Philip J White
- King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Christiane Werner
- Ecosystem Physiology, University of Freiburg, Georges-Köhler-Allee 53/54, Freiburg, 79110, Germany
| | - Heinz Rennenberg
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 53, Freiburg, 79110, Germany
- King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
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24
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Advances and Challenges in the Breeding of Salt-Tolerant Rice. Int J Mol Sci 2020; 21:ijms21218385. [PMID: 33182265 PMCID: PMC7664944 DOI: 10.3390/ijms21218385] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/06/2020] [Accepted: 11/07/2020] [Indexed: 12/16/2022] Open
Abstract
Soil salinization and a degraded ecological environment are challenging agricultural productivity and food security. Rice (Oryza sativa), the staple food of much of the world’s population, is categorized as a salt-susceptible crop. Improving the salt tolerance of rice would increase the potential of saline-alkali land and ensure food security. Salt tolerance is a complex quantitative trait. Biotechnological efforts to improve the salt tolerance of rice hinge on a detailed understanding of the molecular mechanisms underlying salt stress tolerance. In this review, we summarize progress in the breeding of salt-tolerant rice and in the mapping and cloning of genes and quantitative trait loci (QTLs) associated with salt tolerance in rice. Furthermore, we describe biotechnological tools that can be used to cultivate salt-tolerant rice, providing a reference for efforts aimed at rapidly and precisely cultivating salt-tolerance rice varieties.
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25
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26
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Muthuramalingam P, Jeyasri R, Selvaraj A, Pandian SK, Ramesh M. Integrated transcriptomic and metabolomic analyses of glutamine metabolism genes unveil key players in Oryza sativa (L.) to ameliorate the unique and combined abiotic stress tolerance. Int J Biol Macromol 2020; 164:222-231. [PMID: 32682969 DOI: 10.1016/j.ijbiomac.2020.07.143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
Abstract
Plants can be considered to biosynthesize the specialized metabolites to adapt to various environmental stressors mainly on abiotic stresses (AbS). Among specialized metabolites, glutamine (Gln) is an essential plant metabolite to achieve sustainable plant growth, yield and food security. In this pilot study, swe employed computational metabolomics genome wide association survey (cmGWAS) of Gln metabolite profiling in Oryza sativa, targeting at the identification of abiotic stress responsible (AbSR) - Gln metabolite producing genes (GlnMPG). Identified 5 AbSR-GlnMPG alter the metabolite levels and play a predominant role in delineating the physiological significance of rice. These genes were systematically analysed for their biological features via OryzaCyc. Spatio-temporal and plant hormonal expression pattern of AbSR-GlnMPG was analysed and their differential expression profiling were noted in 48 different tissues and hormones, respectively. Furthermore, comparative ideogram of these genes revealed the chromosomal synteny with C4 grass genomes. Molecular crosstalks of these proteins, unravelled the various metabolic interaction. The systems expression profiling of AbSR-GlnMPG will lead to unravel the metabolite signaling and putative responses in multiple AbS. On the whole, this holistic study provides deeper insights on biomolecular features of AbSR-GlnMPG, which could be analysed further to decipher their functional metabolisms in AbS dynamism.
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Affiliation(s)
- Pandiyan Muthuramalingam
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India; Department of Systems Biology, Science Research Centre, Yonsei University, Seoul 03722, South Korea
| | - Rajendran Jeyasri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Anthonymuthu Selvaraj
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | | | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India.
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27
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Schaarschmidt S, Lawas LMF, Glaubitz U, Li X, Erban A, Kopka J, Jagadish SVK, Hincha DK, Zuther E. Season Affects Yield and Metabolic Profiles of Rice ( Oryza sativa) under High Night Temperature Stress in the Field. Int J Mol Sci 2020; 21:E3187. [PMID: 32366031 PMCID: PMC7247591 DOI: 10.3390/ijms21093187] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Rice (Oryza sativa) is the main food source for more than 3.5 billion people in the world. Global climate change is having a strong negative effect on rice production. One of the climatic factors impacting rice yield is asymmetric warming, i.e., the stronger increase in nighttime as compared to daytime temperatures. Little is known of the metabolic responses of rice to high night temperature (HNT) in the field. Eight rice cultivars with contrasting HNT sensitivity were grown in the field during the wet (WS) and dry season (DS) in the Philippines. Plant height, 1000-grain weight and harvest index were influenced by HNT in both seasons, while total grain yield was only consistently reduced in the WS. Metabolite composition was analysed by gas chromatography-mass spectrometry (GC-MS). HNT effects were more pronounced in panicles than in flag leaves. A decreased abundance of sugar phosphates and sucrose, and a higher abundance of monosaccharides in panicles indicated impaired glycolysis and higher respiration-driven carbon losses in response to HNT in the WS. Higher amounts of alanine and cyano-alanine in panicles grown in the DS compared to in those grown in the WS point to an improved N-assimilation and more effective detoxification of cyanide, contributing to the smaller impact of HNT on grain yield in the DS.
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Affiliation(s)
- Stephanie Schaarschmidt
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Lovely Mae F. Lawas
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
- International Rice Research Institute, Metro Manila 1301, Philippines;
| | - Ulrike Glaubitz
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Xia Li
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Alexander Erban
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - S. V. Krishna Jagadish
- International Rice Research Institute, Metro Manila 1301, Philippines;
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Dirk K. Hincha
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Ellen Zuther
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
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28
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Yang C, Zhao W, Wang Y, Zhang L, Huang S, Lin J. Metabolomics Analysis Reveals the Alkali Tolerance Mechanism in Puccinellia tenuiflora Plants Inoculated with Arbuscular Mycorrhizal Fungi. Microorganisms 2020; 8:E327. [PMID: 32110985 PMCID: PMC7142761 DOI: 10.3390/microorganisms8030327] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/07/2020] [Accepted: 02/25/2020] [Indexed: 11/30/2022] Open
Abstract
Soil alkalization is a major environmental threat that affects plant distribution and yield in northeastern China. Puccinellia tenuiflora is an alkali-tolerant grass species that is used for salt-alkali grassland restoration. However, little is known about the molecular mechanisms by which arbuscular mycorrhizal fungi (AMF) enhance P. tenuiflora responses to alkali stress. Here, metabolite profiling in P. tenuiflora seedlings with or without arbuscular mycorrhizal fungi (AMF) under alkali stress was conducted using liquid chromatography combined with time-of-flight mass spectrometry (LC/TOF-MS). The results showed that AMF colonization increased seedling biomass under alkali stress. In addition, principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) demonstrated that non-AM and AM seedlings showed different responses under alkali stress. A heat map analysis showed that the levels of 88 metabolites were significantly changed in non-AM seedlings, but those of only 31 metabolites were significantly changed in AM seedlings. Moreover, the levels of a total of 62 metabolites were significantly changed in P. tenuiflora seedlings after AMF inoculation. The results suggested that AMF inoculation significantly increased amino acid, organic acid, flavonoid and sterol contents to improve osmotic adjustment and maintain cell membrane stability under alkali stress. P. tenuiflora seedlings after AMF inoculation produced more plant hormones (salicylic acid and abscisic acid) than the non-AM seedlings, probably to enhance the antioxidant system and facilitate ion balance under stress conditions. In conclusion, these findings provide new insights into the metabolic mechanisms of P. tenuiflora seedlings with arbuscular mycorrhizal fungi under alkali conditions and clarify the role of AM in the molecular regulation of this species under alkali stress.
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Affiliation(s)
- Chunxue Yang
- College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China; (C.Y.); (W.Z.); (Y.W.); (L.Z.); (S.H.)
| | - Wenna Zhao
- College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China; (C.Y.); (W.Z.); (Y.W.); (L.Z.); (S.H.)
| | - Yingnan Wang
- College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China; (C.Y.); (W.Z.); (Y.W.); (L.Z.); (S.H.)
| | - Liang Zhang
- College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China; (C.Y.); (W.Z.); (Y.W.); (L.Z.); (S.H.)
| | - Shouchen Huang
- College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China; (C.Y.); (W.Z.); (Y.W.); (L.Z.); (S.H.)
| | - Jixiang Lin
- College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China; (C.Y.); (W.Z.); (Y.W.); (L.Z.); (S.H.)
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
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29
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Asrar H, Hussain T, Qasim M, Nielsen BL, Gul B, Khan MA. Salt induced modulations in antioxidative defense system of Desmostachya bipinnata. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:113-124. [PMID: 31855817 DOI: 10.1016/j.plaphy.2019.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
This study addressed the interactions between salt stress and the antioxidant responses of a halophytic grass, Desmostachya bipinnata. Plants were grown in a semi-hydroponic system and treated with different NaCl concentrations (0 mM, 100 mM, 400 mM) for a month. ROS degradation enzyme activities were stimulated by addition of NaCl. Synthesis of antioxidant compounds, such as phenols, was enhanced in the presence of NaCl leading to accumulation of these compounds under moderate salinity. However, when the ROS production rate exceeded the capacity of enzyme-controlled degradation, antioxidant compounds were consumed and oxidative damage was indicated by significant levels of hydrogen peroxide at high salinity. The cellular concentration of salicylic acid increased upon salt stress, but since no direct interaction with ROS was detected, a messenger function may be postulated. High salinity treatment caused a significant decrease of plant growth parameters, whereas treatment with moderate salinity resulted in optimal growth. The activity and abundance of superoxide dismutase (SOD) increased with salinity, but the abundance of SOD isoforms was differentially affected, depending on the NaCl concentration applied. Detoxification of hydrogen peroxide (H2O2) was executed by catalase and guaiacol peroxidase at moderate salinity, whereas the enzymes detoxifying H2O2 through the ascorbate/glutathione cycle dominated at high salinity. The redox status of glutathione was impaired at moderate salinity, whereas the levels of both ascorbate and glutathione significantly decreased only at high salinity. Apparently, the maximal activation of enzyme-controlled ROS degradation was insufficient in comparison to the ROS production at high salinity. As a result, ROS-induced damage could not be prevented, if the applied stress exceeded a critical value in D. bipinnata plants.
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Affiliation(s)
- Hina Asrar
- Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, 75270, Pakistan
| | - Tabassum Hussain
- Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Qasim
- Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, 75270, Pakistan
| | - Brent L Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Bilquees Gul
- Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, 75270, Pakistan.
| | - M Ajmal Khan
- Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, 75270, Pakistan
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Qin H, Wang J, Chen X, Wang F, Peng P, Zhou Y, Miao Y, Zhang Y, Gao Y, Qi Y, Zhou J, Huang R. Rice OsDOF15 contributes to ethylene-inhibited primary root elongation under salt stress. THE NEW PHYTOLOGIST 2019; 223:798-813. [PMID: 30924949 DOI: 10.1111/nph.15824] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/17/2019] [Indexed: 05/22/2023]
Abstract
In early seedlings, the primary root adapts rapidly to environmental changes through the modulation of endogenous hormone levels. The phytohormone ethylene inhibits primary root elongation, but the underlying molecular mechanism of how ethylene-reduced root growth is modulated in environmental changes remains poorly understood. Here, we show that a novel rice (Oryza sativa) DOF transcription factor OsDOF15 positively regulates primary root elongation by regulating cell proliferation in the root meristem, via restricting ethylene biosynthesis. Loss-of-function of OsDOF15 impaired primary root elongation and cell proliferation in the root meristem, whereas OsDOF15 overexpression enhanced these processes, indicating that OsDOF15 is a key regulator of primary root elongation. This regulation involves the direct interaction of OsDOF15 with the promoter of OsACS1, resulting in the repression of ethylene biosynthesis. The control of ethylene biosynthesis by OsDOF15 in turn regulates cell proliferation in the root meristem. OsDOF15 transcription is repressed by salt stress, and OsDOF15-mediated ethylene biosynthesis plays a role in inhibition of primary root elongation by salt stress. Thus, our data reveal how the ethylene-inhibited primary root elongation is finely controlled by OsDOF15 in response to environmental signal, a novel mechanism of plants responding to salt stress and transmitting the information to ethylene biosynthesis to restrict root elongation.
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Affiliation(s)
- Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Juan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Xinbing Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fangfang Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Peng Peng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yun Zhou
- Institute of Plant Stress Biology, Collaborative Innovation Center of Crop Stress Biology, Henan University, Kaifeng, Henan, 475001, China
| | - Yuchen Miao
- Institute of Plant Stress Biology, Collaborative Innovation Center of Crop Stress Biology, Henan University, Kaifeng, Henan, 475001, China
| | - Yuqiong Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yadi Gao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yidong Qi
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiahao Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
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Redillas MCFR, Bang SW, Lee D, Kim YS, Jung H, Chung PJ, Suh J, Kim J. Allantoin accumulation through overexpression of ureide permease1 improves rice growth under limited nitrogen conditions. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1289-1301. [PMID: 30565833 PMCID: PMC6577366 DOI: 10.1111/pbi.13054] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 05/07/2023]
Abstract
In legumes, nitrogen (N) can be stored as ureide allantoin and transported by ureide permease (UPS) from nodules to leaves where it is catabolized to release ammonium and assimilation to amino acids. In non-leguminous plants especially rice, information on its roles in N metabolism is scarce. Here, we show that OsUPS1 is localized in plasma membranes and are highly expressed in vascular tissues of rice. We further evaluated an activation tagging rice overexpressing OsUPS1 (OsUPS1OX ) under several N regimes. Under normal field conditions, panicles from OsUPS1OX plants (14 days after flowering (DAF)) showed significant allantoin accumulation. Under hydroponic system at the vegetative stage, plants were exposed to N-starvation and measured the ammonium in roots after resupplying with ammonium sulphate. OsUPS1OX plants displayed higher ammonium uptake in roots compared to wild type (WT). When grown under low-N soil supplemented with different N-concentrations, OsUPS1OX exhibited better growth at 50% N showing higher chlorophyll, tiller number and at least 20% increase in shoot and root biomass relative to WT. To further confirm the effects of regulating the expression of OsUPS1, we evaluated whole-body-overexpressing plants driven by the GOS2 promoter (OsUPS1GOS2 ) as well as silencing plants (OsUPS1RNAi ). We found significant accumulation of allantoin in leaves, stems and roots of OsUPS1GOS2 while in OsUPS1RNAi allantoin was significantly accumulated in roots. We propose that OsUPS1 is responsible for allantoin partitioning in rice and its overexpression can support plant growth through accumulation of allantoin in sink tissues which can be utilized when N is limiting.
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Affiliation(s)
- Mark Christian Felipe R. Redillas
- Graduate School of International Agricultural Technology and Crop BiotechnologyInstitute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
- Present address:
Department of BiologyDe La Salle UniversityManilaPhilippines
| | - Seung Woon Bang
- Graduate School of International Agricultural Technology and Crop BiotechnologyInstitute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Dong‐Keun Lee
- Graduate School of International Agricultural Technology and Crop BiotechnologyInstitute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop BiotechnologyInstitute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Harin Jung
- Graduate School of International Agricultural Technology and Crop BiotechnologyInstitute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
- Present address:
NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Pil Joong Chung
- Graduate School of International Agricultural Technology and Crop BiotechnologyInstitute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
- Present address:
Temasek Life Science LaboratoryNational University of SingaporeSingaporeSingapore
| | - Joo‐Won Suh
- Center for Nutraceutical and Pharmaceutical MaterialsDivision of Bioscience and BioinformaticsMyongji UniversityYonginGyeonggiKorea
| | - Ju‐Kon Kim
- Graduate School of International Agricultural Technology and Crop BiotechnologyInstitute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
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Chun HJ, Baek D, Cho HM, Jung HS, Jeong MS, Jung WH, Choi CW, Lee SH, Jin BJ, Park MS, Kim HJ, Chung WS, Lee SY, Bohnert HJ, Bressan RA, Yun DJ, Hong YS, Kim MC. Metabolic Adjustment of Arabidopsis Root Suspension Cells During Adaptation to Salt Stress and Mitotic Stress Memory. PLANT & CELL PHYSIOLOGY 2019; 60:612-625. [PMID: 30496500 DOI: 10.1093/pcp/pcy231] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/22/2018] [Indexed: 05/14/2023]
Abstract
Sessile plants reprogram their metabolic and developmental processes during adaptation to prolonged environmental stresses. To understand the molecular mechanisms underlying adaptation of plant cells to saline stress, we established callus suspension cell cultures from Arabidopsis roots adapted to high salt for an extended period of time. Adapted cells exhibit enhanced salt tolerance compared with control cells. Moreover, acquired salt tolerance is maintained even after the stress is relieved, indicating the existence of a memory of acquired salt tolerance during mitotic cell divisions, known as mitotic stress memory. Metabolite profiling using 1H-nuclear magnetic resonance (NMR) spectroscopy revealed metabolic discrimination between control, salt-adapted and stress-memory cells. Compared with control cells, salt-adapted cells accumulated higher levels of sugars, amino acids and intermediary metabolites in the shikimate pathway, such as coniferin. Moreover, adapted cells acquired thicker cell walls with higher lignin contents, suggesting the importance of adjustments of physical properties during adaptation to elevated saline conditions. When stress-memory cells were reverted to normal growth conditions, the levels of metabolites again readjusted. Whereas most of the metabolic changes reverted to levels intermediate between salt-adapted and control cells, the amounts of sugars, alanine, γ-aminobutyric acid and acetate further increased in stress-memory cells, supporting a view of their roles in mitotic stress memory. Our results provide insights into the metabolic adjustment of plant root cells during adaptation to saline conditions as well as pointing to the function of mitotic memory in acquired salt tolerance.
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Affiliation(s)
- Hyun Jin Chun
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Korea
| | - Dongwon Baek
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Hyun Min Cho
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Korea
| | - Myeong Seon Jeong
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Korea
- Chuncheon Center, Korea Basic Science Institute (KBSI), Chuncheon, Korea
| | - Wook-Hun Jung
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Cheol Woo Choi
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Su Hyeon Lee
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Byung Jun Jin
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Mi Suk Park
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Hyun-Jin Kim
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Woo Sik Chung
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Hans J Bohnert
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ray A Bressan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Korea
| | - Young-Shick Hong
- Department of Food and Nutrition, Chonnam National University, Gwangju, Korea
| | - Min Chul Kim
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Korea
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
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Casartelli A, Melino VJ, Baumann U, Riboni M, Suchecki R, Jayasinghe NS, Mendis H, Watanabe M, Erban A, Zuther E, Hoefgen R, Roessner U, Okamoto M, Heuer S. Opposite fates of the purine metabolite allantoin under water and nitrogen limitations in bread wheat. PLANT MOLECULAR BIOLOGY 2019; 99:477-497. [PMID: 30721380 DOI: 10.1007/s11103-019-00831-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/24/2019] [Indexed: 05/06/2023]
Abstract
Degradation of nitrogen-rich purines is tightly and oppositely regulated under drought and low nitrogen supply in bread wheat. Allantoin is a key target metabolite for improving nitrogen homeostasis under stress. The metabolite allantoin is an intermediate of the catabolism of purines (components of nucleotides) and is known for its housekeeping role in nitrogen (N) recycling and also for its function in N transport and storage in nodulated legumes. Allantoin was also shown to differentially accumulate upon abiotic stress in a range of plant species but little is known about its role in cereals. To address this, purine catabolic pathway genes were identified in hexaploid bread wheat and their chromosomal location was experimentally validated. A comparative study of two Australian bread wheat genotypes revealed a highly significant increase of allantoin (up to 29-fold) under drought. In contrast, allantoin significantly decreased (up to 22-fold) in response to N deficiency. The observed changes were accompanied by transcriptional adjustment of key purine catabolic genes, suggesting that the recycling of purine-derived N is tightly regulated under stress. We propose opposite fates of allantoin in plants under stress: the accumulation of allantoin under drought circumvents its degradation to ammonium (NH4+) thereby preventing N losses. On the other hand, under N deficiency, increasing the NH4+ liberated via allantoin catabolism contributes towards the maintenance of N homeostasis.
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Affiliation(s)
- Alberto Casartelli
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- Strube Research GmbH & Co. KG, 38387, Söllingen, Germany
| | - Vanessa J Melino
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- School of Agriculture and Food, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ute Baumann
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Matteo Riboni
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Radoslaw Suchecki
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Nirupama S Jayasinghe
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Himasha Mendis
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mutsumi Watanabe
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Alexander Erban
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Ellen Zuther
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Rainer Hoefgen
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Ute Roessner
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mamoru Okamoto
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Sigrid Heuer
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia.
- Rothamsted Research, Plant Science Department, Harpenden, Hertfordshire, AL5 2JQ, UK.
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Piasecka A, Kachlicki P, Stobiecki M. Analytical Methods for Detection of Plant Metabolomes Changes in Response to Biotic and Abiotic Stresses. Int J Mol Sci 2019; 20:E379. [PMID: 30658398 PMCID: PMC6358739 DOI: 10.3390/ijms20020379] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/08/2019] [Accepted: 01/15/2019] [Indexed: 11/17/2022] Open
Abstract
Abiotic and biotic stresses are the main reasons of substantial crop yield losses worldwide. Research devoted to reveal mechanisms of plant reactions during their interactions with the environment are conducted on the level of genome, transcriptome, proteome, and metabolome. Data obtained during these studies would permit to define biochemical and physiological mechanisms of plant resistance or susceptibility to affecting factors/stresses. Metabolomics based on mass spectrometric techniques is an important part of research conducted in the direction of breeding new varieties of crop plants tolerant to the affecting stresses and possessing good agronomical features. Studies of this kind are carried out on model, crop and resurrection plants. Metabolites profiling yields large sets of data and due to this fact numerous advanced statistical and bioinformatic methods permitting to obtain qualitative and quantitative evaluation of the results have been developed. Moreover, advanced integration of metabolomics data with these obtained on other omics levels: genome, transcriptome and proteome should be carried out. Such a holistic approach would bring us closer to understanding biochemical and physiological processes of the cell and whole plant interacting with the environment and further apply these observations in successful breeding of stress tolerant or resistant crop plants.
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Affiliation(s)
- Anna Piasecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznań, Poland.
| | - Piotr Kachlicki
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznań, Poland.
| | - Maciej Stobiecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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Kim KS, Bang E. Metabolomics Profiling of the Effects of Taurine Supplementation on Dyslipidemia in a High-Fat-Diet-Induced Rat Model by 1H NMR Spectroscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 975 Pt 1:329-336. [PMID: 28849467 DOI: 10.1007/978-94-024-1079-2_29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Metabolomics, the comprehensive study of metabolites, has merged as a potent tool for analyzing complex phenotypes and identifying biomarkers of specific physiological responses and has the potential to lead to innovative therapeutic and diagnostic schemes for many diseases. In a former report, we showed that taurine supplementation considerably ameliorated dyslipidemia in rats fed a high-caloric diet. In this work, we examined the metabolic changes that occur in rat serum after they were fed a normal diet, a high-fat diet, and a high-fat diet containing 2% taurine (tau) by NMR spectroscopy combined with a multivariate statistical analysis containing PCA, PLS-DA, and OPLS-DA. We obtained 1H-NMR spectra of rat serum and used pattern recognition to identify key metabolites related to taurine supplementation. We found significant changes in creatine, methionine, glutamine, and threonine as well as in lipids, all of which decreased in the Tau group. To use these changes in metabolites as novel therapeutic and diagnostic markers, it should first be investigated whether these results are reproducible in future experiments. Next, researchers should determine how these changes affect serum lipid changes. This study identified some changes in serum metabolites and demonstrated the possibility of using an NMR-based metabolomics method to explore the effects of a taurine supplement on dyslipidemia in a high-fat-diet-induced rat model.
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Affiliation(s)
- Kyoung Soo Kim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, South Korea.
- East-West Bone and Joint Disease Research Institute, Kyung Hee University Hospital at Gangdong, 149 Sangil-dong, Gangdong-gu, Seoul, South Korea.
| | - Eunjung Bang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, South Korea.
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Global analysis of threonine metabolism genes unravel key players in rice to improve the abiotic stress tolerance. Sci Rep 2018; 8:9270. [PMID: 29915249 PMCID: PMC6006157 DOI: 10.1038/s41598-018-27703-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/08/2018] [Indexed: 12/13/2022] Open
Abstract
The diversity in plant metabolites with improved phytonutrients is essential to achieve global food security and sustainable crop yield. Our study using computational metabolomics genome wide association study (cmGWAS) reports on a comprehensive profiling of threonine (Thr) metabolite in rice. Sixteen abiotic stress responsive (AbSR) – Thr metabolite producing genes (ThrMPG), modulate metabolite levels and play a significant role determining both physiological and nutritional importance of rice. These AbSR-ThrMPG were computationally analysed for their protein properties using OryzaCyc through plant metabolic network analyser. A total of 1373 and 1028 SNPs were involved in complex traits and genomic variations. Comparative mapping of AbSR-ThrMPG revealed the chromosomal colinearity with C4 grass species. Further, computational expression pattern of these genes predicted a differential expression profiling in diverse developmental tissues. Protein interaction of protein coding gene sequences revealed that the abiotic stresses (AbS) are multigenic in nature. In silico expression of AbSR-ThrMPG determined the putative involvement in response to individual AbS. This is the first comprehensive genome wide study reporting on AbSR –ThrMPG analysis in rice. The results of this study provide a pivotal resource for further functional investigation of these key genes in the vital areas of manipulating AbS signaling in rice improvement.
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Irani S, Todd CD. Exogenous allantoin increases Arabidopsis seedlings tolerance to NaCl stress and regulates expression of oxidative stress response genes. JOURNAL OF PLANT PHYSIOLOGY 2018; 221:43-50. [PMID: 29245127 DOI: 10.1016/j.jplph.2017.11.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 05/21/2023]
Abstract
Allantoin is a nitrogenous compound derived from purine catabolism that contributes to nitrogen recycling in plants. Accumulation of allantoin in plant tissues and a potential role in protection of plants from abiotic stress conditions has been identified. The present work shows that application of exogenous allantoin increased stress tolerance of Arabidopsis seedlings when germinated on, or subjected to the media containing NaCl. Allantoin-induced tolerance to NaCl stress was associated with decreased production of superoxide and hydrogen peroxide in seedlings. To understand the molecular mechanism, the effect of exogenous allantoin treatment on expression of several stress-related genes was investigated. Exogenous allantoin altered the expression of several antioxidant encoding genes and upregulated the expression of two genes involved in oxidative stress tolerance, SOS1 and RCD1, in the presence or absence of NaCl. Allantoin increased the NaCl tolerance of abscisic acid insensitive mutants, suggesting that it can function independently of abscisic acid signaling. These results provide additional evidence for the role of allantoin in enhancing plants tolerance to oxidative stress.
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Affiliation(s)
- Solmaz Irani
- University of Saskatchewan, Department of Biology, 112 Science Place, Saskatoon, SK, S7N5E2, Canada
| | - Christopher D Todd
- University of Saskatchewan, Department of Biology, 112 Science Place, Saskatoon, SK, S7N5E2, Canada.
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38
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Cui F, Sui N, Duan G, Liu Y, Han Y, Liu S, Wan S, Li G. Identification of Metabolites and Transcripts Involved in Salt Stress and Recovery in Peanut. FRONTIERS IN PLANT SCIENCE 2018; 9:217. [PMID: 29520289 PMCID: PMC5827294 DOI: 10.3389/fpls.2018.00217] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/05/2018] [Indexed: 05/18/2023]
Abstract
HIGHLIGHTS Metabolites and transcripts related to plant physiology in salt stress conditions, especially to the recovery process were disclosed in peanut. Peanut (Arachis hypogaea L.) is considered as a moderately salt-sensitive species and thus soil salinity can be a limiting factor for peanut cultivation. To gain insights into peanut plant physiology in response to salt stress and alleviation, we comprehensively characterized leaf relative electrolyte leakage (REC), photosynthesis, leaf transpiration, and metabolism of plants under salt stress and plants that were subjected to salt stress followed by salt alleviation period. As expected, we found that REC levels were higher when plants were subjected to salt stress compared with the untreated plants. However, in contrast to expectations, REC was even higher compared with salt treated plants when plants were transferred from salt stress to standard conditions. To decipher REC variation in response to salt stress, especial during the recovery, metabolite, and transcript variations were analyzed by GC/MS and RNA-seq method, respectively. Ninety two metabolites, among total 391 metabolites identified, varied in response to salt and 42 metabolites responded to recovery specially. Transcriptomics data showed 1,742 in shoots and 3,281 in roots transcript varied in response to salt stress and 372 in shoots and 1,386 transcripts in roots responded specifically to recovery, but not salt stress. Finally, 95 transcripts and 1 metabolite are indicated as candidates involved in REC, photosynthesis, transpiration, and Na+ accumulation variation were revealed by using the principal component analysis (PCA) and correlation analysis. This study provides valuable information on peanut response to salt stress and recovery and may inspire further study to improve salt tolerance in peanut germplasm innovation.
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Affiliation(s)
- Feng Cui
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Na Sui
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guangyou Duan
- School of Life Sciences, Qilu Normal University, Jinan, China
| | - Yiyang Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Yan Han
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Shanshan Liu
- College of Life Science, Shandong Normal University, Jinan, China
| | - Shubo Wan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- *Correspondence: Shubo Wan
| | - Guowei Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- Guowei Li
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Escandón M, Meijón M, Valledor L, Pascual J, Pinto G, Cañal MJ. Metabolome Integrated Analysis of High-Temperature Response in Pinus radiata. FRONTIERS IN PLANT SCIENCE 2018; 9:485. [PMID: 29719546 PMCID: PMC5914196 DOI: 10.3389/fpls.2018.00485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/29/2018] [Indexed: 05/19/2023]
Abstract
The integrative omics approach is crucial to identify the molecular mechanisms underlying high-temperature response in non-model species. Based on future scenarios of heat increase, Pinus radiata plants were exposed to a temperature of 40°C for a period of 5 days, including recovered plants (30 days after last exposure to 40°C) in the analysis. The analysis of the metabolome using complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) allowed the reliable quantification of 2,287 metabolites. The analysis of identified metabolites and highlighter metabolic pathways across heat time exposure reveal the dynamism of the metabolome in relation to high-temperature response in P. radiata, identifying the existence of a turning point (on day 3) at which P. radiata plants changed from an initial stress response program (shorter-term response) to an acclimation one (longer-term response). Furthermore, the integration of metabolome and physiological measurements, which cover from the photosynthetic state to hormonal profile, suggests a complex metabolic pathway interaction network related to heat-stress response. Cytokinins (CKs), fatty acid metabolism and flavonoid and terpenoid biosynthesis were revealed as the most important pathways involved in heat-stress response in P. radiata, with zeatin riboside (ZR) and isopentenyl adenosine (iPA) as the key hormones coordinating these multiple and complex interactions. On the other hand, the integrative approach allowed elucidation of crucial metabolic mechanisms involved in heat response in P. radiata, as well as the identification of thermotolerance metabolic biomarkers (L-phenylalanine, hexadecanoic acid, and dihydromyricetin), crucial metabolites which can reschedule the metabolic strategy to adapt to high temperature.
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Affiliation(s)
- Mónica Escandón
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- *Correspondence: Mónica Escandón, ; María Jesús Cañal,
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- Plant Biotechnology Unit, University Institute of Biotechnology of Asturias (IUBA), Oviedo, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- Plant Biotechnology Unit, University Institute of Biotechnology of Asturias (IUBA), Oviedo, Spain
| | - Jesús Pascual
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Gloria Pinto
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- Plant Biotechnology Unit, University Institute of Biotechnology of Asturias (IUBA), Oviedo, Spain
- *Correspondence: Mónica Escandón, ; María Jesús Cañal,
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40
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Gupta P, De B. Metabolomics analysis of rice responses to salinity stress revealed elevation of serotonin, and gentisic acid levels in leaves of tolerant varieties. PLANT SIGNALING & BEHAVIOR 2017; 12:e1335845. [PMID: 28594277 PMCID: PMC5586353 DOI: 10.1080/15592324.2017.1335845] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 05/18/2023]
Abstract
A GC-MS based analytical approach was undertaken to understand the metabolomic responses of seedlings of 2 salt sensitive (Sujala and MTU 7029) and 2 tolerant varieties (Bhutnath, and Nonabokra) of indica rice (Oryza sativa L.) to NaCl induced stress. The 4 varieties responded differently to NaCl treatment with respect to the conserved primary metabolites (sugars, polyols, amino acids, organic acids and certain purine derivatives) of the leaf of rice seedlings. However, there were significant differences in salt induced production of chorismic acid derivatives. Serotonin level was increased in both the salt tolerant varieties in response to NaCl induced stress. In both the salt tolerant varieties, increased production of the signaling molecule gentisic acid in response to NaCl treatment was noticed. Salt tolerant varieties also produced increased level of ferulic acid and vanillic acid. In the salt sensitive varieties, cinnamic acid derivatives, 4-hydroxycinnamic acid (in Sujala) and 4-hydroxybenzoic acid (in MTU 7029), were elevated in the leaves. So increased production of the 2 signaling molecules serotonin and gentisic acid may be considered as 2 important biomarker compounds produced in tolerant varieties contributing toward NaCl tolerance.
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Affiliation(s)
- Poulami Gupta
- Department of Botany, University of Calcutta, Kolkata, India
| | - Bratati De
- Department of Botany, University of Calcutta, Kolkata, India
- CONTACT Bratati De Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
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Huo Y, Kamal GM, Wang J, Liu H, Zhang G, Hu Z, Anwar F, Du H. 1 H NMR-based metabolomics for discrimination of rice from different geographical origins of China. J Cereal Sci 2017. [DOI: 10.1016/j.jcs.2017.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Fernandez O, Urrutia M, Bernillon S, Giauffret C, Tardieu F, Le Gouis J, Langlade N, Charcosset A, Moing A, Gibon Y. Fortune telling: metabolic markers of plant performance. Metabolomics 2016; 12:158. [PMID: 27729832 PMCID: PMC5025497 DOI: 10.1007/s11306-016-1099-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/16/2016] [Indexed: 02/01/2023]
Abstract
BACKGROUND In the last decade, metabolomics has emerged as a powerful diagnostic and predictive tool in many branches of science. Researchers in microbes, animal, food, medical and plant science have generated a large number of targeted or non-targeted metabolic profiles by using a vast array of analytical methods (GC-MS, LC-MS, 1H-NMR….). Comprehensive analysis of such profiles using adapted statistical methods and modeling has opened up the possibility of using single or combinations of metabolites as markers. Metabolic markers have been proposed as proxy, diagnostic or predictors of key traits in a range of model species and accurate predictions of disease outbreak frequency, developmental stages, food sensory evaluation and crop yield have been obtained. AIM OF REVIEW (i) To provide a definition of plant performance and metabolic markers, (ii) to highlight recent key applications involving metabolic markers as tools for monitoring or predicting plant performance, and (iii) to propose a workable and cost-efficient pipeline to generate and use metabolic markers with a special focus on plant breeding. KEY MESSAGE Using examples in other models and domains, the review proposes that metabolic markers are tending to complement and possibly replace traditional molecular markers in plant science as efficient estimators of performance.
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Affiliation(s)
- Olivier Fernandez
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Maria Urrutia
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Stéphane Bernillon
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
| | | | | | | | - Nicolas Langlade
- UMR LIPM, INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Alain Charcosset
- UMR GQE, INRA, CNRS, Université Paris Sud, AgroParisTech, Ferme du Moulon, 91190 Gif-Sur-Yvette, France
| | - Annick Moing
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
| | - Yves Gibon
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
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Irani S, Todd CD. Ureide metabolism under abiotic stress in Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2016; 199:87-95. [PMID: 27302009 DOI: 10.1016/j.jplph.2016.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 05/21/2023]
Abstract
Ureides are nitrogenous compounds derived from purine catabolism which contribute to nitrogen recycling in plants. Accumulation of ureide compounds has been reported in a number of plant species under stress conditions, suggesting their involvement in plants' response to stress. In this research a biochemical and molecular approach was applied to address the ureide accumulation under abiotic stress conditions in Arabidopsis thaliana. Ureide concentration and changes in expression of ureide metabolic genes were examined in response to drought, NaCl and mannitol treatments. Additionally, an Arabidopsis allantoinase (ALN) mutant with constitutive accumulation of a ureide compound, allantoin, was used to investigate the impact of high levels of this compound on drought and NaCl stress responses. In the leaf tissue of adult plants allantoin accumulated in response to soil drying. Transcription of urate oxidase (UO), involved in allantoin production, was highly up-regulated under the same conditions. Allantoin and allantoate also accumulated in seedlings following treatment with NaCl or mannitol. aln mutants with enhanced levels of allantoin exhibited higher tolerance to drought and NaCl. Hydrogen peroxide and superoxide did not accumulate in the aln mutant leaves to the same degree in response to drought when compared to the wild-type. Our results suggest that ureide metabolism and accumulation contribute to the abiotic stress response which is regulated, at least in part, at the transcriptional level. Higher concentrations of allantoin in the mutant elevates abiotic stress tolerance, possibly by reducing oxidative damage.
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Affiliation(s)
- Solmaz Irani
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Christopher D Todd
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada.
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