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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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Wellpott K, Jozefowicz AM, Meise P, Schum A, Seddig S, Mock HP, Winkelmann T, Bündig C. Combined nitrogen and drought stress leads to overlapping and unique proteomic responses in potato. PLANTA 2023; 257:58. [PMID: 36795167 PMCID: PMC9935667 DOI: 10.1007/s00425-023-04085-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Nitrogen deficient and drought-tolerant or sensitive potatoes differ in proteomic responses under combined (NWD) and individual stresses. The sensitive genotype 'Kiebitz' exhibits a higher abundance of proteases under NWD. Abiotic stresses such as N deficiency and drought affect the yield of Solanum tuberosum L. tremendously. Therefore, it is of importance to improve potato genotypes in terms of stress tolerance. In this study, we identified differentially abundant proteins (DAPs) in four starch potato genotypes under N deficiency (ND), drought stress (WD), or combined stress (NWD) in two rain-out shelter experiments. The gel-free LC-MS analysis generated a set of 1177 identified and quantified proteins. The incidence of common DAPs in tolerant and sensitive genotypes under NWD indicates general responses to this stress combination. Most of these proteins were part of the amino acid metabolism (13.9%). Three isoforms of S-adenosyl methionine synthase (SAMS) were found to be lower abundant in all genotypes. As SAMS were found upon application of single stresses as well, these proteins appear to be part of the general stress response in potato. Interestingly, the sensitive genotype 'Kiebitz' showed a higher abundance of three proteases (subtilase, carboxypeptidase, subtilase family protein) and a lower abundance of a protease inhibitor (stigma expressed protein) under NWD stress compared to control plants. The comparably tolerant genotype 'Tomba', however, displayed lower abundances of proteases. This indicates a better coping strategy for the tolerant genotype and a quicker reaction to WD when previously stressed with ND.
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Affiliation(s)
- Katharina Wellpott
- Department of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Anna M Jozefowicz
- Applied Biochemistry, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
| | - Philipp Meise
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn-Institute (JKI), Bundesforschungsinstitut Für Kulturpflanzen, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Annegret Schum
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn-Institute (JKI), Bundesforschungsinstitut Für Kulturpflanzen, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Sylvia Seddig
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn-Institute (JKI), Bundesforschungsinstitut Für Kulturpflanzen, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Hans-Peter Mock
- Applied Biochemistry, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
- Universidad de Costa Rica, CIGRAS, 11501-2060, San Pedro, Costa Rica
| | - Traud Winkelmann
- Department of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Christin Bündig
- Department of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany.
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Fei J, Wang YS, Cheng H, Sun FL, Sun CC. Comparative physiological and proteomic analyses of mangrove plant Kandelia obovata under cold stress. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1826-1840. [PMID: 34618290 DOI: 10.1007/s10646-021-02483-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Cold events had broadly affected the survival and geographic distribution of mangrove plants. Kandelia obovata, has an excellent cold tolerance as a true halophyte and widespread mangrove species. In this study, physiological characters and comparative proteomics of leaves of K. obovata were performed under cold treatment. The physiological analysis showed that K. obovata could alleviate its cold-stress injuries through increasing the levels of antioxidants, the activities of related enzymes, as well as osmotic regulation substances (proline). It was detected 184 differentially expressed protein spots, and of 129 (70.11%) spots were identified. These proteins have been involved in several pathways such as the stress and defense, photosynthesis and photorespiration, signal transduction, transcription factors, protein biosynthesis and degradation, molecular chaperones, ATP synthesis, the tricarboxylic acid (TCA) cycle and primary metabolisms. The protein post-translational modification may be a common phenomenon and plays a key role in cold-response process in K. obovata. According to our precious work, a schematic diagram was drawn for the resistance or adaptation strategy of mangrove plants under cold stress. This study provided valuable information to understand the mechanism of cold tolerance of K. obovata.
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Affiliation(s)
- Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China.
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
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Dahal K, Li XQ, Tai H, Creelman A, Bizimungu B. Improving Potato Stress Tolerance and Tuber Yield Under a Climate Change Scenario - A Current Overview. FRONTIERS IN PLANT SCIENCE 2019; 10:563. [PMID: 31139199 PMCID: PMC6527881 DOI: 10.3389/fpls.2019.00563] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 04/12/2019] [Indexed: 05/06/2023]
Abstract
Global climate change in the form of extreme heat and drought poses a major challenge to sustainable crop production by negatively affecting plant performance and crop yield. Such negative impact on crop yield is likely to be aggravated in future because continued greenhouse gas emissions will cause further rise in temperature leading to increased evapo-transpiration and drought severity, soil salinity as well as insect and disease threats. This has raised a major challenge for plant scientists on securing global food demand, which urges an immediate need to enhance the current yield of major food crops by two-fold to feed the increasing population. As a fourth major food crop, enhancing potato productivity is important for food security of an increasing population. However, potato plant is highly prone to high temperature, drought, soil salinity, as well as insect and diseases. In order to maintain a sustainable potato production, we must adapt our cultivation practices and develop stress tolerant potato cultivars that are appropriately engineered for changing environment. Yet the lack of data on the underlying mechanisms of potato plant resistance to abiotic and biotic stress and the ability to predict future outcomes constitutes a major knowledge gap. It is a challenge for plant scientists to pinpoint means of improving tuber yield under increasing CO2, high temperature and drought stress including the changing patterns of pest and pathogen infestations. Understanding stress-related physiological, biochemical and molecular processes is crucial to develop screening procedures for selecting crop cultivars that can better adapt to changing growth conditions. Elucidation of such mechanism may offer new insights into the identification of specific characteristics that may be useful in breeding new cultivars aimed at maintaining or even enhancing potato yield under changing climate. This paper discusses the recent progress on the mechanism by which potato plants initially sense the changes in their surrounding CO2, temperature, water status, soil salinity and consequently respond to these changes at the molecular, biochemical and physiological levels. We suggest that future research needs to be concentrated on the identification and characterization of signaling molecules and target genes regulating stress tolerance and crop yield potential.
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Affiliation(s)
- Keshav Dahal
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
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Jaarsma R, de Boer AH. Salinity Tolerance of Two Potato Cultivars ( Solanum tuberosum) Correlates With Differences in Vacuolar Transport Activity. FRONTIERS IN PLANT SCIENCE 2018; 9:737. [PMID: 29922314 PMCID: PMC5996281 DOI: 10.3389/fpls.2018.00737] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/15/2018] [Indexed: 05/14/2023]
Abstract
Potato is an important cultivated crop species and since it is moderately salt sensitive there is a need to develop more salt tolerant cultivars. A high activity of Na+ transport across the tonoplast in exchange for H+ is essential to reduce Na+ toxicity. The proton motive force (PMF) generated by the V-H+-ATPase and the V-H+-PPase energizes the Na+(K+)/H+ antiport. We compared the activity, gene expression, and protein levels of the vacuolar proton pumps and the Na+/H+ antiporters in two potato cultivars (Solanum tuberosum) contrasting in their salt tolerance (cv. Desiree; tolerant and Mozart; sensitive) grown at 0 and 60 mM NaCl. Tonoplast-enriched vesicles were used to study the pump activity and protein levels of the V-H+-ATPase and the V-H+-PPase and the activity of the Na+/H+ antiporter. Although salt stress reduced the V-H+-ATPase and the V-H+-PPase activity in both cultivars, the decline in H+ pump activity was more severe in the salt-sensitive cultivar Mozart. After salt treatment, protein amounts of the vacuolar H+ pumps decreased in Mozart but remained unchanged in the cultivar Desiree. Decreased protein amounts of the V-H+-PPase found in Mozart may explain the reduced V-H+-PPase activity found for Mozart after salt stress. Under non-stress conditions, protein amounts of V-H+-PPase were equal in both cultivars while the V-H+-PPase activity was already twice as high and remained higher after salt treatment in the cultivar Desiree as compared to Mozart. This cultivar-dependent V-H+-PPase activity may explain the higher salt tolerance of Desiree. Moreover, combined with reduced vacuolar H+ pump activity, Mozart showed a lower Na+/H+ exchange activity and the Km for Na+ is at least twofold lower in tonoplast vesicles from Desiree, what suggests that NHXs from Desiree have a higher affinity for Na+ as compared to Mozart. From these results, we conclude that the higher capacity in combination with the higher affinity for Na+ uptake can be an important factor to explain the differences in salt tolerance of these two potato cultivars.
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Affiliation(s)
- Rinse Jaarsma
- Faculty of Earth and Life Sciences, Vrije Universiteit AmsterdamAmsterdam, Netherlands
| | - Albertus H. de Boer
- Faculty of Earth and Life Sciences, Vrije Universiteit AmsterdamAmsterdam, Netherlands
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Mohanta TK, Bashir T, Hashem A, Abd Allah EF. Systems biology approach in plant abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 121:58-73. [PMID: 29096174 DOI: 10.1016/j.plaphy.2017.10.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/28/2017] [Accepted: 10/20/2017] [Indexed: 05/05/2023]
Abstract
Plant abiotic stresses are the major constraint on plant growth and development, causing enormous crop losses across the world. Plants have unique features to defend themselves against these challenging adverse stress conditions. They modulate their phenotypes upon changes in physiological, biochemical, molecular and genetic information, thus making them tolerant against abiotic stresses. It is of paramount importance to determine the stress-tolerant traits of a diverse range of genotypes of plant species and integrate those traits for crop improvement. Stress-tolerant traits can be identified by conducting genome-wide analysis of stress-tolerant genotypes through the highly advanced structural and functional genomics approach. Specifically, whole-genome sequencing, development of molecular markers, genome-wide association studies and comparative analysis of interaction networks between tolerant and susceptible crop varieties grown under stress conditions can greatly facilitate discovery of novel agronomic traits that protect plants against abiotic stresses.
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Affiliation(s)
- Tapan Kumar Mohanta
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
| | - Tufail Bashir
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Science, King Saud University, P.O. Box 24160, Riyadh, 11451, Saudi Arabia
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Guerriero G, Behr M, Hausman JF, Legay S. Textile Hemp vs. Salinity: Insights from a Targeted Gene Expression Analysis. Genes (Basel) 2017; 8:E242. [PMID: 28954403 PMCID: PMC5664092 DOI: 10.3390/genes8100242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 12/15/2022] Open
Abstract
Soil salinity is a serious threat to agriculture, because it compromises biomass production and plant productivity, by negatively affecting the vegetative growth and development of plants. Fiber crops like textile hemp (Cannabis sativa L.) are important natural resources that provide, sustainably, both cellulosic and woody fibers for industry. In this work, the response to salinity (200 mM NaCl) of a fiber variety of hemp (Santhica 27) was studied using quantitative real-time PCR. The responses of plantlets aged 15 days were analyzed by microscopy and by measuring the changes in expression of cell wall-related genes, as well as in the general response to exogenous constraints. The results presented here show that a different response is present in the hemp hypocotyls and leaves. In the leaves, genes coding for heat shock proteins were significantly upregulated, together with a phytohormone-related transcript (ethylene-responsive factor 1 ERF1) and genes involved in secondary cell wall biosynthesis (cellulose synthase CesA4, fasciclin-like arabinogalactan proteins FLA10 and FLA8). Moreover, a tendency towards upregulation was also observed in the leaves for genes involved in lignification (4CL, CAD, PAL); a finding that suggests growth arrest. In the hypocotyl, the genes involved in lignification did not show changes in expression, while a gene related to expansion (expansin EXPA8), as well as transcripts coding for calcium-dependent lipid-binding family proteins (CALB), were upregulated. Microscopic analyses on the hypocotyl cross sections revealed changes in the vascular tissues of salt-exposed plantlets, where the lumen of xylem vessels was reduced. The gene expression results show that a different response is present in the hemp hypocotyls and leaves. The data presented contribute to our understanding of the regulatory gene network in response to salinity in different tissues of an important fiber crop.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg.
| | - Marc Behr
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg.
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg.
| | - Sylvain Legay
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg.
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Karam MA, Abd-Elgawad ME, Ali RM. Differential gene expression of salt-stressed Peganum harmala L. J Genet Eng Biotechnol 2016; 14:319-326. [PMID: 30647630 PMCID: PMC6299858 DOI: 10.1016/j.jgeb.2016.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/26/2016] [Accepted: 10/17/2016] [Indexed: 11/26/2022]
Abstract
The response of Peganum harmala L. seedlings subjected to salinity was investigated through the observation of germination at the 4th, 6th and 8th days under normal and two salinity levels (150 and 200 mM NaCl). Genetic response of P. harmala was examined by quantitative estimation and electrophoretic separation of catalase and salt-soluble proteins. The gene expression of catalase and osmotin were investigated using RT-PCR. Final percentage of germination at the eighth day of germination was reduced from 85% in the control to 70 and 30% under the concentration of 150 and 200 mM. The catalase activity and protein content increased as the salinity increased compared to control seedlings. The electrophoretic separation of catalase and salt-soluble proteins exhibited stress-related isozymes and protein bands. RT-PCR of cat1, cat2-3 and cat3 and osmotin genes exhibited up-regulation and down-regulation of genes subsequent to salinity. The reduced germination percentage of salt stressed seedlings was attributed to oxidative damage and osmotic imbalance. The increased catalase activity and protein content were concluded as protective response of P. harmala seedlings to salinity induced oxidative stress and osmoregulation. The additional isozyme bands in the salt-stressed seedlings indicated modulation of CAT gene expression in response to elevated H2O2 subsequent to salinity. The stress specific gene expression was interpreted as molecular mechanism by which plants can tolerate salinity stress. The up-regulation of cat2-3 gene in relation to stress suggests it crucial role in salinity tolerance in P. harmala and further studies are needed for its sequence identification.
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Affiliation(s)
- Mohamed A. Karam
- Botany Department, Faculty of Science, Fayoum University, 63514 Fayoum, Egypt
| | - Magda E. Abd-Elgawad
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Refaat M. Ali
- Botany Department, Faculty of Science, Fayoum University, 63514 Fayoum, Egypt
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Ambrosone A, Batelli G, Bostan H, D'Agostino N, Chiusano ML, Perrotta G, Leone A, Grillo S, Costa A. Distinct gene networks drive differential response to abrupt or gradual water deficit in potato. Gene 2016; 597:30-39. [PMID: 27771448 DOI: 10.1016/j.gene.2016.10.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/08/2016] [Accepted: 10/18/2016] [Indexed: 02/08/2023]
Abstract
Water-limiting conditions affect dramatically plant growth and development and, ultimately, yield of potato plants (Solanum tuberosum L.). Therefore, understanding the mechanisms underlying the response to water deficit is of paramount interest to obtain drought tolerant potato varieties. Herein, potato 10K cDNA array slides were used to profile transcriptomic changes of two potato cell populations under abrupt (shocked cells) or gradual exposure (adapted cells) to polyethylene glycol (PEG)-mediated water stress. Data analysis identified >1000 differentially expressed genes (DEGs) in our experimental conditions. Noteworthy, our microarray study also suggests that distinct gene networks underlie the cellular response to shock or gradual water stress. On the basis of our experimental findings, it is possible to speculate that DEGs identified in shocked cells participate in early protective and sensing mechanisms to environmental insults, while the genes whose expression was modulated in adapted cells are directly involved in the acquisition of a new cellular homeostasis to cope with water stress conditions. To validate microarray data obtained for potato cells, the expression analysis of 21 selected genes of interest was performed by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR). Intriguingly, the expression levels of these transcripts in 4-week old potato plants exposed to long-term water-deficit. qRT-PCR analysis showed that several genes were regulated similarly in potato cells cultures and tissues exposed to drought, thus confirming the efficacy of our simple experimental system to capture important genes involved in osmotic stress response. Highlighting the differences in gene expression between shock-like and adaptive response, our findings could contribute to the discussion on the biological function of distinct gene networks involved in the response to abrupt and gradual adaptation to water deficit.
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Affiliation(s)
- Alfredo Ambrosone
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici (NA), Italy
| | - Giorgia Batelli
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici (NA), Italy
| | - Hamed Bostan
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (NA), Italy
| | - Nunzio D'Agostino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per l'orticoltura (CREA-ORT), Pontecagnano Faiano (SA), Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (NA), Italy
| | - Gaetano Perrotta
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), TRISAIA Research Center, Rotondella, MT, Italy
| | - Antonietta Leone
- Department of Pharmacy, University of Salerno, Fisciano SA, Italy
| | - Stefania Grillo
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici (NA), Italy
| | - Antonello Costa
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), Portici (NA), Italy.
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Liu J, Qiao Q, Cheng X, Du G, Deng G, Zhao M, Liu F. Transcriptome differences between fiber-type and seed-type Cannabis sativa variety exposed to salinity. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:429-443. [PMID: 27924117 PMCID: PMC5120038 DOI: 10.1007/s12298-016-0381-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 05/08/2023]
Abstract
The industrial hemp varieties 'Yunma 5' and 'Bamahuoma,' which demonstrate growth vigor and environmental adaptability, have been primarily cultivated in Yunnan and Guangxi, China, respectively, for fiber and seeds. The results of physiological measurements showed the phenotypic differences between the two varieties in response to salt stress. RNA-Seq analysis was first performed on leaves of both varieties sampled at four time intervals (0, 2, 4, 6 days) after treatment with salt (500 mM NaCl) We identified 220 co-up-regulated differentially expressed genes (DEGs) in the two varieties, while 26 up-regulated DEGs and 24 down-regulated DEGs were identified exclusively in the single varieties after 2 days of salt stress. Among the 220 DEGs, we identified 22 transcription factors, including key transcription factors involved in salt stress, such as MYB, NAC, GATA, and HSF. We applied gene expression profile analysis and found that 'Yunma 5' and 'Bamahuoma' have variety-specific pathways for resisting salt stress. The DEGs of 'Yunma 5' were enriched in spliceosome and amino acid metabolism genes, while the DEGs of 'Bamahuoma' were enriched in fatty acid metabolism, amino acid metabolism, and endoplasmic reticulum protein processing pathway. Although there were common DEGs, such as genes encoding cysteine protease and alpha/beta-hydrolase superfamily, the two varieties' responses to salt stress impacted different metabolic pathways. The DEGs that were co-expressed in both varieties under stress may provide useful insights into the tolerance of cultivated hemp and other bast fiber crops to saline soil conditions. These transcriptomes also represent reference sequences for industrial hemp.
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Affiliation(s)
- Jiajia Liu
- Plant Improvement and Utilization Lab, Yunnan University, Kunming, 650091 Yunnan China
| | - Qin Qiao
- Plant Improvement and Utilization Lab, Yunnan University, Kunming, 650091 Yunnan China
| | - Xia Cheng
- Plant Improvement and Utilization Lab, Yunnan University, Kunming, 650091 Yunnan China
| | - Guanghui Du
- Plant Improvement and Utilization Lab, Yunnan University, Kunming, 650091 Yunnan China
| | - Gang Deng
- Plant Improvement and Utilization Lab, Yunnan University, Kunming, 650091 Yunnan China
| | - Mingzhi Zhao
- Kunming Medical University Haiyuan College, Kunming, 650106 Yunnan China
| | - Feihu Liu
- Plant Improvement and Utilization Lab, Yunnan University, Kunming, 650091 Yunnan China
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Yoon SK, Park EJ, Choi YI, Bae EK, Kim JH, Park SY, Kang KS, Lee H. Response to drought and salt stress in leaves of poplar (Populus alba × Populus glandulosa): expression profiling by oligonucleotide microarray analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 84:158-168. [PMID: 25285889 DOI: 10.1016/j.plaphy.2014.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 09/21/2014] [Indexed: 05/24/2023]
Abstract
Drought and salt stresses are major environmental constraints on forest productivity. To identify genes responsible for stress tolerance, we conducted a genome-wide analysis in poplar (Populus alba × Populus glandulosa) leaves exposed to drought and salt (NaCl) stresses. We investigated gene expression at the mRNA level using oligonucleotide microarrays containing 44,718 genes from Populus trichocarpa. A total of 1604 and 1042 genes were up-regulated (≥2-fold; P value < 0.05) by drought and salt stresses, respectively, and 765 genes were up-regulated by both stresses. In addition, 2742 and 1685 genes were down-regulated by drought and salt stresses, respectively, and 1564 genes were down-regulated by both stresses. The large number of genes regulated by both stresses suggests that crosstalk occurs between the drought and salt stress responses. Most up-regulated genes were involved in functions such as subcellular localization, signal transduction, metabolism, and transcription. Among the up-regulated genes, we identified 47 signaling proteins, 65 transcription factors, and 43 abiotic stress-related genes. Several genes were modulated by only one of the two stresses. About 25% of the genes significantly regulated by these stresses are of unknown function, suggesting that poplar may provide an opportunity to discover novel stress-related genes.
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Affiliation(s)
- Seo-Kyung Yoon
- Department of Forest Genetic Resources, Korea Forest Research Institute, 39 Onjeong-ro, Suwon 441-847, Republic of Korea; Department of Forest Sciences, Seoul National University, 1 Gwanak-ro, Seoul 151-742, Republic of Korea
| | - Eung-Jun Park
- Department of Forest Genetic Resources, Korea Forest Research Institute, 39 Onjeong-ro, Suwon 441-847, Republic of Korea
| | - Young-Im Choi
- Department of Forest Genetic Resources, Korea Forest Research Institute, 39 Onjeong-ro, Suwon 441-847, Republic of Korea
| | - Eun-Kyung Bae
- Department of Forest Genetic Resources, Korea Forest Research Institute, 39 Onjeong-ro, Suwon 441-847, Republic of Korea
| | - Joon-Hyeok Kim
- Department of Forest Genetic Resources, Korea Forest Research Institute, 39 Onjeong-ro, Suwon 441-847, Republic of Korea
| | - So-Young Park
- Department of Horticultural Science, Chungbuk National University, 52 Naesudong-ro, Cheongju 361-763, Republic of Korea
| | - Kyu-Suk Kang
- Department of Forest Sciences, Seoul National University, 1 Gwanak-ro, Seoul 151-742, Republic of Korea
| | - Hyoshin Lee
- Department of Forest Genetic Resources, Korea Forest Research Institute, 39 Onjeong-ro, Suwon 441-847, Republic of Korea.
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Kim CK, Lim HM, Na JK, Choi JW, Sohn SH, Park SC, Kim YH, Kim YK, Kim DY. A multistep screening method to identify genes using evolutionary transcriptome of plants. Evol Bioinform Online 2014; 10:69-78. [PMID: 24812480 PMCID: PMC3999899 DOI: 10.4137/ebo.s14823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 11/17/2022] Open
Abstract
We introduced a multistep screening method to identify the genes in plants using microarrays and ribonucleic acid (RNA)-seq transcriptome data. Our method describes the process for identifying genes using the salt-tolerance response pathways of the potato (Solanum tuberosum) plant. Gene expression was analyzed using microarrays and RNA-seq experiments that examined three potato lines (high, intermediate, and low salt tolerance) under conditions of salt stress. We screened the orthologous genes and pathway genes involved in salinity-related biosynthetic pathways, and identified nine potato genes that were candidates for salinity-tolerance pathways. The nine genes were selected to characterize their phylogenetic reconstruction with homologous genes of Arabidopsis thaliana, and a Circos diagram was generated to understand the relationships among the selected genes. The involvement of the selected genes in salt-tolerance pathways was verified by reverse transcription polymerase chain reaction analysis. One candidate potato gene was selected for physiological validation by generating dehydration-responsive element-binding 1 (DREB1)-overexpressing transgenic potato plants. The DREB1 overexpression lines exhibited increased salt tolerance and plant growth when compared to that of the control. Although the nine genes identified by our multistep screening method require further characterization and validation, this study demonstrates the power of our screening strategy after the initial identification of genes using microarrays and RNA-seq experiments.
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Affiliation(s)
- Chang-Kug Kim
- Genomics Division, National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon, Korea
| | - Hye-Min Lim
- Genomics Division, National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon, Korea
| | - Jong-Kuk Na
- Molecular Breeding Division, NAAS, RDA, Suwon, Korea
| | - Ji-Weon Choi
- Vegetable Science Division, National Institute of Horticultural and Herbal Science, Suwon, Korea
| | - Seong-Han Sohn
- Genomics Division, National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon, Korea
| | | | - Young-Hwan Kim
- Policy Development Office, Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries, Anyang, Korea
| | - Yong-Kab Kim
- School of Electrical Information Communication Engineering, Wonkwang University, Iksan, Korea
| | - Dool-Yi Kim
- Molecular Breeding Division, NAAS, RDA, Suwon, Korea
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Folgado R, Panis B, Sergeant K, Renaut J, Swennen R, Hausman JF. Differential Protein Expression in Response to Abiotic Stress in Two Potato Species: Solanum commersonii Dun and Solanum tuberosum L. Int J Mol Sci 2013; 14:4912-33. [PMID: 23455465 PMCID: PMC3634427 DOI: 10.3390/ijms14034912] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 02/08/2013] [Accepted: 02/13/2013] [Indexed: 01/05/2023] Open
Abstract
Better knowledge on responses to dehydration stress could help to improve the existing cryopreservation protocols for potato, since plant tissues processed for cryopreservation are often submitted to similar in vitro stress conditions. Cryopreservation (the best method of conservation for vegetatively propagated plants) of potato still needs to be standardized to make it available and to conserve the wide diversity of this crop. In the present work, the response to osmotic stress and chilling temperature was investigated in two potato species, Solanum tuberosum and its relative, frost-tolerant S. commersonii. After 14 days of exposure, different growth parameters, such as shoot length and number of leaves, were measured. Furthermore, differentially abundant proteins were identified after performing 2-fluorescence difference gel electrophoresis (2-DIGE) experiments, and soluble carbohydrates were analyzed by High Performance Anion Exchange Chromatography with Pulsed Amperometric Detection (HPAEC-PAD). The results show different responses in both species depending on the stress treatment. Focusing on the differences in growth parameters during the treatments, Solanum commersonii seems to be more affected than S. tuberosum cv. Désirée. At the molecular level, there are some differences and similarities between the two potato species studied that are dependent on the type of stressor.
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Affiliation(s)
- Raquel Folgado
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public—Gabriel Lippmann, 41, rue du Brill, L-4422 Belvaux, Luxembourg; E-Mails: (R.F.); (K.S.); (J.R.)
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan, 42 bus 2455, B-3001 Leuven, Belgium; E-Mails: (B.P.); (R.S.)
| | - Bart Panis
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan, 42 bus 2455, B-3001 Leuven, Belgium; E-Mails: (B.P.); (R.S.)
| | - Kjell Sergeant
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public—Gabriel Lippmann, 41, rue du Brill, L-4422 Belvaux, Luxembourg; E-Mails: (R.F.); (K.S.); (J.R.)
| | - Jenny Renaut
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public—Gabriel Lippmann, 41, rue du Brill, L-4422 Belvaux, Luxembourg; E-Mails: (R.F.); (K.S.); (J.R.)
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan, 42 bus 2455, B-3001 Leuven, Belgium; E-Mails: (B.P.); (R.S.)
- Bioversity International, Willem de Croylaan, 42 bus 2455, B-3001 Leuven, Belgium
| | - Jean-Francois Hausman
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public—Gabriel Lippmann, 41, rue du Brill, L-4422 Belvaux, Luxembourg; E-Mails: (R.F.); (K.S.); (J.R.)
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Evers D, Legay S, Lamoureux D, Hausman JF, Hoffmann L, Renaut J. Towards a synthetic view of potato cold and salt stress response by transcriptomic and proteomic analyses. PLANT MOLECULAR BIOLOGY 2012; 78:503-514. [PMID: 22258187 DOI: 10.1007/s11103-012-9879-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 01/07/2012] [Indexed: 05/31/2023]
Abstract
Potato can suffer from several abiotic stresses such as cold temperature, high soil salinity, lack of water or heavy metal exposure, to name a few. They are known to affect plant growth as well as productivity, with differential regulations at several levels. Potato response to cold and salt exposure was investigated at both transcriptomic and proteomic levels in a growth chamber experiment. Cold exposure in potato resulted in a higher number of significantly differentially regulated genes compared to salt exposure, whereas there were nearly three times more differentially regulated proteins after salt exposure when compared to cold exposure. The allocation of up and down-regulated genes at the functional category level also differed between salt and cold exposure although common trends, previously described in various abiotic stresses, were observed. In both stresses, the majority of photosynthesis-related genes were down-regulated whereas cell rescue and transcription factor-related genes were mostly up-regulated. In the other functional categories no common trend was observed; salt exposure results displayed a strong down-regulation of genes implicated in primary metabolism, detoxication apparatus and signal transduction, whereas upon cold exposure, up and down-regulated genes were similar in number. At the proteomic level, the abundance of the majority of identified proteins was increased except for the photosynthesis-related proteins, which were mostly less abundant after both salt and cold exposure. Common responses between salt and cold stress and specific responses inherent to these abiotic stresses are described.
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Affiliation(s)
- D Evers
- Department of Environment and Agrobiotechnologies, Centre de Recherche Public-Gabriel Lippmann, 41, rue du Brill, 4422 Belvaux, Luxembourg.
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15
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Carbohydrate metabolism and cell protection mechanisms differentiate drought tolerance and sensitivity in advanced potato clones (Solanum tuberosum L.). Funct Integr Genomics 2011; 11:275-91. [PMID: 21274588 DOI: 10.1007/s10142-010-0206-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 12/01/2010] [Accepted: 12/18/2010] [Indexed: 12/25/2022]
Abstract
In potatoes and many other crops, drought is one of the most important environmental constraints leading to yield loss. Development of drought-tolerant cultivars is therefore required for maintaining yields under climate change conditions and for the extension of agriculture to sub-optimal cropping areas. Drought tolerance mechanisms have been well described for many crop plants including Native Andean potato. However, knowledge on tolerance traits suitable for commercial potato varieties is scarce. In order to describe drought tolerance mechanisms that sustain potato yield under water stress, we have designed a growth-chamber experiment with two Solanum tuberosum L. cultivars, the more drought tolerant accession 397077.16, and the sensitive variety Canchan. After 21 days of drought exposure, gene expression was studied in leaves using cDNA microarrays. The results showed that the tolerant clone presented more differentially expressed genes than the sensitive one, suggesting greater stress response and adaptation. Moreover, it exhibited a large pool of upregulated genes belonging to cell rescue and detoxication such as LEAs, dehydrins, HSPs, and metallothioneins. Transcription factors related to abiotic stresses and genes belonging to raffinose family oligosaccharide synthesis, involved in desiccation tolerance, were upregulated to a greater extent in the tolerant clone. This latter result was corroborated by biochemical analyses performed at 32 and 49 days after drought that showed an increase in galactinol and raffinose especially in clone 397077.16. The results depict key components for the drought tolerance of this advanced potato clone.
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Evers D, Lefèvre I, Legay S, Lamoureux D, Hausman JF, Rosales ROG, Marca LRT, Hoffmann L, Bonierbale M, Schafleitner R. Identification of drought-responsive compounds in potato through a combined transcriptomic and targeted metabolite approach. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:2327-43. [PMID: 20406784 DOI: 10.1093/jxb/erq060] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two potato clones (Solanum tuberosum L.) of the Andean cultivar group, called Sullu and SS2613, with different drought-tolerance phenotypes were exposed to a continuously increasing drought stress in a field trial. At the physiological level, while relative leaf water contents were similar in both clones, osmotic potential was lower in Sullu and declined more strongly during drought compared with SS2613. In the drought-stressed plants, tuber yield was reduced by about 70% compared with control plants in both clones. Potato cDNA microarrays and target metabolite analysis were performed on leaves sampled at several time-points after the onset of drought. At the transcriptomic level, photosynthesis-related genes were already strongly repressed in Sullu after 28 d of withholding irrigation and even more strongly after a longer stress duration, whereas, in SS2613, repression occurred only after 49 d of soil drying; similarly, a strong perturbation of carbohydrate-related genes was observed in Sullu. At the metabolite level, differential accumulation of osmotically active solutes was observed between the two cultivars; indeed, in Sullu, contents of galactose, inositol, galactinol, proline, and proline analogues were higher upon drought stress compared with SS2613. These results point to different drought responses in the cultivars at the leaf level, with, however, similar tuber yield reductions. The previously shown tolerant clone Sullu lost part of its tolerance under the experimental conditions used here; it was, however, able to maintain an absolute yield three times higher than SS2613.
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Affiliation(s)
- Danièle Evers
- Centre de Recherche Public-Gabriel Lippmann, Department EVA, 41, rue du Brill, L-4422 Belvaux, Luxembourg.
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