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Quinet M, Vromman D, Clippe A, Bertin P, Lequeux H, Dufey I, Lutts S, Lefèvre I. Combined transcriptomic and physiological approaches reveal strong differences between short- and long-term response of rice (Oryza sativa) to iron toxicity. PLANT, CELL & ENVIRONMENT 2012; 35:1837-59. [PMID: 22506799 DOI: 10.1111/j.1365-3040.2012.02521.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Ferrous iron toxicity is a mineral disorder frequently occurring under waterlogged soils where rice is cultivated. To decipher the main metabolic pathways involved in rice response to iron excess, seedlings have been exposed to 125 mg L(-1) FeSO(4) for 3 weeks. A combined transcriptomic, biochemical and physiological study has been performed after short-term (3 d) or long-term (3 weeks) exposure to iron in order to elucidate the strategy of stress adaptation with time. Our results showed that short- and long-term exposure involved a very different response in gene expression regarding both the number and function. A larger number of genes were up- or down-regulated after 3 d than after 3 weeks of iron treatment; these changes also occurred in shoot even though no significant difference in iron concentration was recorded. Those modifications in gene expression after 3 d affected not only genes involved in hormonal signalling but also genes involved in C-compound and carbohydrate metabolism, oxygen and electron transfer, oxidative stress, and iron homeostasis and transport. Modification in some gene expression can be followed by modification in corresponding metabolic products and physiological properties, or differed in time for some others, underlying the importance of an integrated study.
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Affiliation(s)
- Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université catholique de Louvain, Louvain-la-Neuve, Belgium
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102
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Tuberosa R. Phenotyping for drought tolerance of crops in the genomics era. Front Physiol 2012; 3:347. [PMID: 23049510 PMCID: PMC3446691 DOI: 10.3389/fphys.2012.00347] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 08/09/2012] [Indexed: 12/11/2022] Open
Abstract
Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.
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Affiliation(s)
- Roberto Tuberosa
- Department of Agroenvironmental Science and Technology, University of BolognaBologna, Italy
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103
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Liu C, Wu Y, Wang X. bZIP transcription factor OsbZIP52/RISBZ5: a potential negative regulator of cold and drought stress response in rice. PLANTA 2012; 235:1157-69. [PMID: 22189955 DOI: 10.1007/s00425-011-1564-z] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/28/2011] [Indexed: 05/20/2023]
Abstract
OsbZIP52/RISBZ5 is a member of the basic leucine zipper (bZIP) transcription factor (TF) family in rice (Oryza sativa) isolated from rice (Zhonghua11) panicles. Expression of the OsbZIP52 gene was strongly induced by low temperature (4°C) but not by drought, PEG, salt, or ABA. The subcellular localization of OsbZIP52-GFP in onion (Allium cepa) epidermis cells revealed that OsbZIP52 is a nuclear localized protein. A transactivation assay in yeast demonstrated that OsbZIP52 functions as a transcriptional activator and can specifically bind to the G-box promoter motif. In a yeast two-hybrid (Y-2-H) experiment, OsbZIP52 was able to form homodimeric complexes. Rice plants overexpressing OsbZIP52 showed significantly increased sensitivity to cold and drought stress. Real-time PCR analysis revealed that some abiotic stress-related genes, such as OsLEA3, OsTPP1, Rab25, gp1 precursor, β-gal, LOC_Os05g11910 and LOC_Os05g39250, were down-regulated in OsbZIP52 overexpression lines. These results suggest that OsbZIP52/RISBZ5 could function as a negative regulator in cold and drought stress environments.
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Affiliation(s)
- Citao Liu
- Key Laboratory of Cell Proliferation and Regulation of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, People's Republic of China
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104
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Xiong H, Li Y, Yang J, Li Y. Comparative transcriptional profiling of two rice genotypes carrying SUB1A-1 but exhibiting differential tolerance to submergence. FUNCTIONAL PLANT BIOLOGY : FPB 2012; 39:449-461. [PMID: 32480796 DOI: 10.1071/fp11251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 04/04/2012] [Indexed: 06/11/2023]
Abstract
Submergence tolerance in rainfed lowland rice (Oryza sativa L.) is determined mainly by SUB1A-1, which confers the tolerance by regulating the ethylene- and gibberellin-mediated gene expression responsible for carbohydrate consumption, cell elongation and ethanolic fermentation. However, two indica rice genotypes, FR13A and Goda Heenati, both carrying this gene, exhibited differential tolerance to submergence. Comparative analysis of transcriptional profiling of the two genotypes revealed that many of antioxidant genes were more highly expressed in FR13A than in Goda Heenati under both submergence and control conditions, or only under submergence, whereas most of genes involved in biosynthesis and signalling of ethylene and GA and in anaerobic carbohydrate metabolism had comparable levels of expression between genotypes under the same conditions. H2O2 and malondialdehyde (MDA) assays demonstrated that Goda Heenati accumulated more H2O2 and had more MDA, a product of lipid peroxidation, than FR13A under submergence. These findings suggest that apart from SUB1A-mediated 'quiescence strategy', the detoxification of reactive oxygen species (ROS) is another important trait associated with submergence tolerance. The information obtained from this study helps in further understanding of the mechanism underlying submergence tolerance.
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Affiliation(s)
- Huaiyang Xiong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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105
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Berkman PJ, Lai K, Lorenc MT, Edwards D. Next-generation sequencing applications for wheat crop improvement. AMERICAN JOURNAL OF BOTANY 2012; 99:365-71. [PMID: 22268223 DOI: 10.3732/ajb.1100309] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Bread wheat (Triticum aestivum; Poaceae) is a crop plant of great importance. It provides nearly 20% of the world's daily food supply measured by calorie intake, similar to that provided by rice. The yield of wheat has doubled over the last 40 years due to a combination of advanced agronomic practice and improved germplasm through selective breeding. More recently, yield growth has been less dramatic, and a significant improvement in wheat production will be required if demand from the growing human population is to be met. Next-generation sequencing (NGS) technologies are revolutionizing biology and can be applied to address critical issues in plant biology. Technologies can produce draft sequences of genomes with a significant reduction to the cost and timeframe of traditional technologies. In addition, NGS technologies can be used to assess gene structure and expression, and importantly, to identify heritable genome variation underlying important agronomic traits. This review provides an overview of the wheat genome and NGS technologies, details some of the problems in applying NGS technology to wheat, and describes how NGS technologies are starting to impact wheat crop improvement.
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Affiliation(s)
- Paul J Berkman
- University of Queensland, School of Agriculture and Food Sciences and Australian Centre for Plant Functional Genomics, Brisbane, QLD 4072, Australia
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106
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Manavalan LP, Chen X, Clarke J, Salmeron J, Nguyen HT. RNAi-mediated disruption of squalene synthase improves drought tolerance and yield in rice. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:163-75. [PMID: 21926092 PMCID: PMC3245457 DOI: 10.1093/jxb/err258] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
About one-third of the world's rice area is in rain-fed lowlands and most are prone to water shortage. The identification of genes imparting tolerance to drought in the model cereal plant, rice, is an attractive strategy to engineer improved drought tolerance not only rice but other cereals as well. It is demonstrated that RNAi-mediated disruption of a rice farnesyltransferase/squalene synthase (SQS) by maize squalene synthase improves drought tolerance at both the vegetative and reproductive stages. Twenty-day-old seedlings of wild type (Nipponbare) and seven independent events of transgenic RNAi lines showed no difference in morphology. When subjected to water stress for a period of 32 d under growth chamber conditions, transgenic positives showed delayed wilting, conserved more soil water, and improved recovery. When five independent events along with wild-type plants were subjected to drought at the reproductive stage under greenhouse conditions, the transgenic plants lost water more slowly compared with the wild type, through reduced stomatal conductance and the retention of high leaf relative water content (RWC). After 28 d of slow progressive soil drying, transgenic plants recovered better and flowered earlier than wild-type plants. The yield of water-stressed transgenic positive plants ranged from 14-39% higher than wild-type plants. When grown in plates with Yoshida's nutrient solution with 1.2% agar, transgenic positives from three independent events showed increased root length and an enhanced number of lateral roots. The RNAi-mediated inactivation produced reduced stomatal conductance and subsequent drought tolerance.
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Affiliation(s)
| | - Xi Chen
- Syngenta Biotechnology Inc, Research Triangle Park, NC-27709, USA
| | - Joseph Clarke
- Syngenta Biotechnology Inc, Research Triangle Park, NC-27709, USA
| | - John Salmeron
- Syngenta Biotechnology Inc, Research Triangle Park, NC-27709, USA
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO-65211, USA
- To whom correspondence should be addressed. E-mail:
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Schmidt R, Schippers JH, Welker A, Mieulet D, Guiderdoni E, Mueller-Roeber B. Transcription factor OsHsfC1b regulates salt tolerance and development in Oryza sativa ssp. japonica. AOB PLANTS 2012; 2012:pls011. [PMID: 22616023 PMCID: PMC3357053 DOI: 10.1093/aobpla/pls011] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 04/08/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Salt stress leads to attenuated growth and productivity in rice. Transcription factors like heat shock factors (HSFs) represent central regulators of stress adaptation. Heat shock factors of the classes A and B are well established as regulators of thermal and non-thermal stress responses in plants; however, the role of class C HSFs is unknown. Here we characterized the function of the OsHsfC1b (Os01g53220) transcription factor from rice. METHODOLOGY We analysed the expression of OsHsfC1b in the rice japonica cultivars Dongjin and Nipponbare exposed to salt stress as well as after mannitol, abscisic acid (ABA) and H(2)O(2) treatment. For functional characterization of OsHsfC1b, we analysed the physiological response of a T-DNA insertion line (hsfc1b) and two artificial micro-RNA (amiRNA) knock-down lines to salt, mannitol and ABA treatment. In addition, we quantified the expression of small Heat Shock Protein (sHSP) genes and those related to signalling and ion homeostasis by quantitative real-time polymerase chain reaction in roots exposed to salt. The subcellular localization of OsHsfC1b protein fused to green fluorescent protein (GFP) was determined in Arabidopsis mesophyll cell protoplasts. PRINCIPAL RESULTS Expression of OsHsfC1b was induced by salt, mannitol and ABA, but not by H(2)O(2). Impaired function of OsHsfC1b in the hsfc1b mutant and the amiRNA lines led to decreased salt and osmotic stress tolerance, increased sensitivity to ABA, and temporal misregulation of salt-responsive genes involved in signalling and ion homeostasis. Furthermore, sHSP genes showed enhanced expression in knock-down plants under salt stress. We observed retarded growth of hsfc1b and knock-down lines in comparison with control plants under non-stress conditions. Transient expression of OsHsfC1b fused to GFP in protoplasts revealed nuclear localization of the transcription factor. CONCLUSIONS OsHsfC1b plays a role in ABA-mediated salt stress tolerance in rice. Furthermore, OsHsfC1b is involved in the response to osmotic stress and is required for plant growth under non-stress conditions.
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Affiliation(s)
- Romy Schmidt
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Jos H.M. Schippers
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Annelie Welker
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
| | - Delphine Mieulet
- CIRAD, UMR AGAP, Avenue Agropolis, 34398 Montpellier, Cedex 5, France
| | | | - Bernd Mueller-Roeber
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
- Corresponding author's e-mail address:
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108
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Osakabe Y, Kawaoka A, Nishikubo N, Osakabe K. Responses to environmental stresses in woody plants: key to survive and longevity. JOURNAL OF PLANT RESEARCH 2012; 125:1-10. [PMID: 21874628 DOI: 10.1007/s10265-011-0446-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 07/13/2011] [Indexed: 05/08/2023]
Abstract
Environmental stresses have adverse effects on plant growth and productivity, and are predicted to become more severe and widespread in decades to come. Especially, prolonged and repeated severe stresses affecting growth and development would bring down long-lasting effects in woody plants as a result of its long-term growth period. To counteract these effects, trees have evolved specific mechanisms for acclimation and tolerance to environmental stresses. Plant growth and development are regulated by the integration of many environmental and endogenous signals including plant hormones. Acclimation of land plants to environmental stresses is controlled by molecular cascades, also involving cross-talk with other stresses and plant hormone signaling mechanisms. This review focuses on recent studies on molecular mechanisms of abiotic stress responses in woody plants, functions of plant hormones in wood formation, and the interconnection of cell wall biosynthesis and the mechanisms shown above. Understanding of these mechanisms in depth should shed light on the factors for improvement of woody plants to overcome severe environmental stress conditions.
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Affiliation(s)
- Yuriko Osakabe
- Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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109
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Moumeni A, Satoh K, Kondoh H, Asano T, Hosaka A, Venuprasad R, Serraj R, Kumar A, Leung H, Kikuchi S. Comparative analysis of root transcriptome profiles of two pairs of drought-tolerant and susceptible rice near-isogenic lines under different drought stress. BMC PLANT BIOLOGY 2011; 11:174. [PMID: 22136218 PMCID: PMC3268746 DOI: 10.1186/1471-2229-11-174] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 12/02/2011] [Indexed: 05/19/2023]
Abstract
BACKGROUND Plant roots are important organs to uptake soil water and nutrients, perceiving and transducing of soil water deficit signals to shoot. The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. We obtained gene expression profile in roots of rice NILs under different levels of drought stress help to identify genes and mechanisms involved in drought stress. RESULTS Global gene expression analysis showed that about 55% of genes differentially expressed in roots of rice in response to drought stress treatments. The number of differentially expressed genes (DEGs) increased in NILs as the level of water deficits, increased from mild to severe condition, suggesting that more genes were affected by increasing drought stress. Gene onthology (GO) test and biological pathway analysis indicated that activated genes in the drought tolerant NILs IR77298-14-1-2-B-10 and IR77298-5-6-B-18 were mostly involved in secondary metabolism, amino acid metabolism, response to stimulus, defence response, transcription and signal transduction, and down-regulated genes were involved in photosynthesis and cell wall growth. We also observed gibberellic acid (GA) and auxin crosstalk modulating lateral root formation in the tolerant NILs. CONCLUSIONS Transcriptome analysis on two pairs of NILs with a common genetic background (~97%) showed distinctive differences in gene expression profiles and could be effective to unravel genes involved in drought tolerance. In comparison with the moderately tolerant NIL IR77298-5-6-B-18 and other susceptible NILs, the tolerant NIL IR77298-14-1-2-B-10 showed a greater number of DEGs for cell growth, hormone biosynthesis, cellular transports, amino acid metabolism, signalling, transcription factors and carbohydrate metabolism in response to drought stress treatments. Thus, different mechanisms are achieving tolerance in the two tolerant lines.
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Affiliation(s)
- Ali Moumeni
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
- Rice Research Institute of Iran in Mazandaran, POBox 145, Postal-Code 46191-91951, Km8 Babol Rd., Amol, Mazandaran, Iran
| | - Kouji Satoh
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Hiroaki Kondoh
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Takayuki Asano
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Aeni Hosaka
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Ramiah Venuprasad
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
- Africa Rice Centre (AfricaRice), Ibadan station, c/o IITA, PmB 5320 Oyo road, Nigeria
| | - Rachid Serraj
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
- International Centre for Agricultural Research in the Dry Areas (ICARDA), POBox 5466, Aleppo, Syria
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Hei Leung
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Shoshi Kikuchi
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
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Sharoni AM, Nuruzzaman M, Satoh K, Moumeni A, Attia K, Venuprasad R, Serraj R, Kumar A, Leung H, Islam AKMR, Kikuchi S. Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. Mol Genet Genomics 2011; 287:1-19. [PMID: 22102215 PMCID: PMC3249189 DOI: 10.1007/s00438-011-0659-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 11/07/2011] [Indexed: 11/26/2022]
Abstract
The AP2/EREBP genes play various roles in developmental processes and in stress-related responses in plants. Genome-wide microarrays based on the gene expression profiles of the AP2/EREBP family were analyzed under conditions of normal growth and drought stress. The preferential expression of fifteen genes was observed in specific tissues, suggesting that these genes may play important roles in vegetative and reproductive stages of growth. A large number of redundant genes were differentially expressed following phytohormone treatments (NAA, GA3, KT, SA, JA, and ABA). To investigate the gene expression responses in the root, leaf, and panicle of three rice genotypes, two drought stress conditions were applied using the fraction of transpirable soil water (FTSW) under severe (0.2 FTSW), mild (0.5 FTSW), and control (1.0 FTSW) conditions. Following treatment, transcriptomic analysis using a 44-K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from two near-isogenic lines, IR77298-14-1-2-B-10 (drought tolerant) and IR77298-14-1-2-B-13 (drought susceptible), under drought stress conditions. The majority of the genes that were activated in the IR77298-14-1-2-B-10 line were members of the AP2/EREBP gene family. Non-redundant genes (sixteen) were found in the drought-tolerant line, and four genes were selected as candidate novel reference genes because of their higher expression levels in IR77298-14-1-2-B-10. Most of the genes in the AP2, B3, and B5 subgroups were involved in the panicle under severe stress conditions, but genes from the B1 and B2 subgroups were down-regulated in the root. Of the four subfamilies, RAV exhibited the highest number of up-regulated genes (80%) in the panicle under severe stress conditions in the drought-tolerant line compared to Minghui 63 under normal conditions, and the gene structures of the RAV subfamily may be involved in the response to drought stress in the flowering stage. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis.
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Affiliation(s)
- Akhter Most Sharoni
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
- Department of Botany, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Mohammed Nuruzzaman
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
| | - Kouji Satoh
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
| | - Ali Moumeni
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
| | - Kotb Attia
- Graduate School of Science and Technology, Niigata University, Ikarashi-2, Niigata, 950-2181 Japan
- Centre of Excellence in Biotechnology Research, King Saud University, Riyadh, 11451 Kingdom of Saudi Arabia
| | - Ramiah Venuprasad
- Africa Rice Center (AfricaRice), Ibadan Station, c/o IITA, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Rachid Serraj
- Diversification and Sustainable Intensification of Production Systems Program (DSIPSP), International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5466, Aleppo, Syria
| | - Arvind Kumar
- Plant Breeding, Genetics and Biotechnology Division (PBGB), International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines
| | - Hei Leung
- Plant Breeding, Genetics and Biotechnology Division (PBGB), International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines
| | | | - Shoshi Kikuchi
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
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Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species. Proc Natl Acad Sci U S A 2011; 108:19276-81. [PMID: 22084086 DOI: 10.1073/pnas.1107680108] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Large-scale transcription profiling via direct cDNA sequencing provides important insights as to how foundation species cope with increasing climatic extremes predicted under global warming. Species distributed along a thermal cline, such as the ecologically important seagrass Zostera marina, provide an opportunity to assess temperature effects on gene expression as a function of their long-term adaptation to heat stress. We exposed a southern and northern European population of Zostera marina from contrasting thermal environments to a realistic heat wave in a common-stress garden. In a fully crossed experiment, eight cDNA libraries, each comprising ~125 000 reads, were obtained during and after a simulated heat wave, along with nonstressed control treatments. Although gene-expression patterns during stress were similar in both populations and were dominated by classical heat-shock proteins, transcription profiles diverged after the heat wave. Gene-expression patterns in southern genotypes returned to control values immediately, but genotypes from the northern site failed to recover and revealed the induction of genes involved in protein degradation, indicating failed metabolic compensation to high sea-surface temperature. We conclude that the return of gene-expression patterns during recovery provides critical information on thermal adaptation in aquatic habitats under climatic stress. As a unifying concept for ecological genomics, we propose transcriptomic resilience, analogous to ecological resilience, as an important measure to predict the tolerance of individuals and hence the fate of local populations in the face of global warming.
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Dugas DV, Monaco MK, Olsen A, Klein RR, Kumari S, Ware D, Klein PE. Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics 2011; 12:514. [PMID: 22008187 PMCID: PMC3219791 DOI: 10.1186/1471-2164-12-514] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 10/18/2011] [Indexed: 12/31/2022] Open
Abstract
Background Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought. Results RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed. Conclusions The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought.
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Affiliation(s)
- Diana V Dugas
- Department of Horticulture, Texas A&M University, College Station, TX 77843, USA
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Mosolov VV, Valueva TA. Inhibitors of proteolytic enzymes under abiotic stresses in plants (review). APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683811050097] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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114
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Akinwale M, Gregorio G, Nwilene F, Akinyele B, Ogunbayo S, Odiyi A, Shittu A. Comparative Performance of Lowland Hybrids and Inbred Rice Varieties in Nigeria. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/ijpbg.2011.224.234] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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115
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Lenka SK, Katiyar A, Chinnusamy V, Bansal KC. Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:315-27. [PMID: 20809928 DOI: 10.1111/j.1467-7652.2010.00560.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Genetic improvement in drought tolerance in rice is the key to save water for sustainable agriculture. Drought tolerance is a complex trait and involves interplay of a vast array of genes. Several genotypes of rice have evolved features that impart tolerance to drought and other abiotic stresses. Comparative analysis of drought stress-responsive transcriptome between drought-tolerant (DT) landraces/genotypes and drought-sensitive modern rice cultivars will unravel novel genetic regulatory mechanisms involved in stress tolerance. Here, we report transcriptome analysis in a highly DT rice landrace, Nagina 22 (N22), versus a high-yielding but drought-susceptible rice variety IR64. Both genotypes exhibited a diverse global transcriptional response under normal and drought conditions. Gene ontology (GO) analysis suggested that drought tolerance of N22 was attributable to the enhanced expression of several enzyme-encoding genes. Drought susceptibility of IR64 was attributable to significant down-regulation of regulatory components that confer drought tolerance. Pathway analysis unravelled significant up-regulation of several components of carbon fixation, glycolysis/gluconeogenesis and flavonoid biosynthesis and down-regulation of starch and sucrose metabolism in both the cultivars under drought. However, significant up-regulation of α-linolenic acid metabolic pathway observed in N22 under drought appears to be in good agreement with high drought tolerance of this genotype. Consensus cis-motif profiling of drought-induced co-expressed genes led to the identification of novel cis-motifs. Taken together, the results of the comparative transcriptome analysis led to the identification of specific genotype-dependent genes responsible for drought tolerance in the rice landrace N22.
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Affiliation(s)
- Sangram K Lenka
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
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116
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Hadiarto T, Tran LSP. Progress studies of drought-responsive genes in rice. PLANT CELL REPORTS 2011; 30:297-310. [PMID: 21132431 DOI: 10.1007/s00299-010-0956-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 11/22/2010] [Accepted: 11/22/2010] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa L.), one of the most agronomically important crops, supplies staple food for more than half of the world's population, especially those living in developing countries. The intensively increasing world population has put a great burden on rice production. Drought as one of the major limiting factors for rice productivity has challenged researchers to improve both the water management system and rice characteristics. Biotechnology has assisted researchers to identify genes that are responsive toward drought. This review consolidates the recent studies that expose a number of drought-responsive genes in rice, which are potential candidates for development of improved drought-tolerant transgenic rice cultivars. In addition, examples are provided of how various drought-responsive genes, such as transcription factor and protein kinase encoding genes, were explored to engineer rice plants for enhanced drought tolerance using transgenic approach. Furthermore, the involvement of various phytohormones in regulation of drought response as well as the complexity of drought-responsive networks, which is indicated by the crosstalks with other stress-responsive networks such as cold and salt stresses, will be discussed. It is hoped that by understanding how rice responds to drought, crop performance can be stabilized and protected under water deficit conditions.
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Affiliation(s)
- Toto Hadiarto
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jl Tentara Pelajar 3a, Bogor, Indonesia
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117
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Ahuja I, de Vos RCH, Bones AM, Hall RD. Plant molecular stress responses face climate change. TRENDS IN PLANT SCIENCE 2010; 15:664-74. [PMID: 20846898 DOI: 10.1016/j.tplants.2010.08.002] [Citation(s) in RCA: 465] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 08/06/2010] [Accepted: 08/11/2010] [Indexed: 05/18/2023]
Abstract
Environmental stress factors such as drought, elevated temperature, salinity and rising CO₂ affect plant growth and pose a growing threat to sustainable agriculture. This has become a hot issue due to concerns about the effects of climate change on plant resources, biodiversity and global food security. Plant adaptation to stress involves key changes in the '-omic' architecture. Here, we present an overview of the physiological and molecular programs in stress adaptation focusing on how genes, proteins and metabolites change after individual and multiple environmental stresses. We address the role which '-omics' research, coupled to systems biology approaches, can play in future research on plants seemingly unable to adapt as well as those which can tolerate climatic change.
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Affiliation(s)
- Ishita Ahuja
- Department of Biology, Norwegian University of Science and Technology, Realfagbygget, NO-7491 Trondheim, Norway
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118
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Grudkowska M, Zagdańska B. Acclimation to frost alters proteolytic response of wheat seedlings to drought. JOURNAL OF PLANT PHYSIOLOGY 2010; 167:1321-1327. [PMID: 20674076 DOI: 10.1016/j.jplph.2010.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 05/17/2010] [Accepted: 05/17/2010] [Indexed: 05/29/2023]
Abstract
A comparative examination of cysteine proteinases in winter wheat (Triticum aestivum L.) seedlings differing in sensitivity to frost and drought revealed many similarities and differences in response to water deprivation. Azocaseinolytic activity was enhanced under water deficiency, but the enhancement was significantly lower in the tolerant genotype (Kobra cultivar). On the contrary, acclimation of wheat seedlings at low temperature had no effect on the proteolytic activity of the tolerant cultivar and depressed the azocaseinolytic activity of the sensitive cultivar (Tortija). However, the observed depression of enzyme activity was fully reversible under dehydration. The content of soluble proteins was reduced in dehydrated non-acclimated and in acclimated seedlings of the frost-sensitive cultivar, but increased in acclimated seedlings of the tolerant cultivar. The cysteine proteinases were preferentially induced under water deficiency when assessment was based on the inhibitory effect of iodoacetate on azocasein hydrolysis. Separation of cysteine proteinases by SDS-PAGE containing gelatin as a substrate showed two bands with apparent molecular masses of 36 and 38 kDa in the sensitive cultivar, and a third band was detected (42 kDa) in the resistant cultivar. Water deficit and low temperature induced the new cysteine proteinases of molecular masses about 29, 33 and 42 kDa in sensitive non-acclimated seedlings. Polyclonal antibodies raised against Arabidopsis proteinase responsive to drought (RD21) cross-reacted with the protein in the 33 kDa region, and a slight signal was obtained in the 42 kDa region, but only in dehydrated seedlings acclimated to frost. Several polypeptides of molecular masses of 30, 22, 20 and 18 kDa were recognized by the Arabidopsis aleurain-like proteinase (AtALEU) antibodies. The results presented indicate that cysteine proteinases are potentially responsible for both low temperature and drought tolerance.
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Affiliation(s)
- Małgorzata Grudkowska
- Institute of Plant Breeding and Acclimatization, Department of Plant Physiology and Biochemistry, Radzików, POB 1019, 00-950 Warsaw, Poland
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119
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Sečenji M, Lendvai Á, Miskolczi P, Kocsy G, Gallé Á, Szucs A, Hoffmann B, Sárvári É, Schweizer P, Stein N, Dudits D, Györgyey J. Differences in root functions during long-term drought adaptation: comparison of active gene sets of two wheat genotypes. PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12:871-82. [PMID: 21040302 DOI: 10.1111/j.1438-8677.2009.00295.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In an attempt to shed light on the role of root systems in differential responses of wheat genotypes to long-term water limitation, transcriptional differences between two wheat genotypes (Triticum aestivum L., cv. Plainsman V and landrace Kobomugi) were identified during adaptation to moderate water stress at the tillering stage. Differences in organ sizes, water-use efficiency and seed production were detected in plants grown in soil, and root functions were characterised by expression profiling. The molecular genetic background of the behaviour of the two genotypes during this stress was revealed using a cDNA macroarray for transcript profiling of the roots. During a 4-week period of moderate water deficit, a set of up-regulated genes displaying transiently increased expression was identified in young plantlets, mostly in the second week in the roots of Kobomugi, while transcript levels remained constantly high in roots of Plainsman V. These genes encode proteins with various functions, such as transport, protein metabolism, osmoprotectant biosynthesis, cell wall biogenesis and detoxification, and also regulatory proteins. Oxidoreductases, peroxidases and cell wall-related genes were induced significantly only in Plainsman V, while induction of stress- and defence-related genes was more pronounced in Kobomugi. Real-time qPCR analysis of selected members of the glutathione S-transferase gene family revealed differences in regulation of family members in the two genotypes and confirmed the macroarray results. The TaGSTZ gene was stress-activated only in the roots of Kobomugi.
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Affiliation(s)
- M Sečenji
- Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
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120
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Ray S, Dansana PK, Giri J, Deveshwar P, Arora R, Agarwal P, Khurana JP, Kapoor S, Tyagi AK. Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Funct Integr Genomics 2010; 11:157-78. [PMID: 20821243 DOI: 10.1007/s10142-010-0187-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2010] [Revised: 08/10/2010] [Accepted: 08/16/2010] [Indexed: 01/04/2023]
Abstract
Water-deficit stress is detrimental for rice growth, development, and yield. Transcriptome analysis of 1-week-old rice (Oryza sativa L. var. IR64) seedling under water-deficit stress condition using Affymetrix 57 K GeneChip® has revealed 1,563 and 1,746 genes to be up- and downregulated, respectively. In an effort to amalgamate data across laboratories, we identified 5,611 differentially expressing genes under varying extrinsic water-deficit stress conditions in six vegetative and one reproductive stage of development in rice. Transcription factors (TFs) involved in ABA-dependent and ABA-independent pathways have been found to be upregulated during water-deficit stress. Members of zinc-finger TFs namely, C₂H₂, C₂C₂, C₃H, LIM, PHD, WRKY, ZF-HD, and ZIM, along with TF families like GeBP, jumonji, MBF1 and ULT express differentially under water-deficit conditions. NAC (NAM, ATAF and CUC) TF family emerges to be a potential key regulator of multiple abiotic stresses. Among the 12 TF genes that are co-upregulated under water-deficit, salt and cold stress conditions, five belong to the NAC TF family. We identified water-deficit stress-responsive genes encoding key enzymes involved in biosynthesis of osmoprotectants like polyols and sugars; amino acid and quaternary ammonium compounds; cell wall loosening and structural components; cholesterol and very long chain fatty acid; cytokinin and secondary metabolites. Comparison of genes responsive to water-deficit stress conditions with genes preferentially expressed during panicle and seed development revealed a significant overlap of transcriptome alteration and pathways.
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Affiliation(s)
- Swatismita Ray
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
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121
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Wilkins O, Bräutigam K, Campbell MM. Time of day shapes Arabidopsis drought transcriptomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:715-27. [PMID: 20553421 DOI: 10.1111/j.1365-313x.2010.04274.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Under natural conditions, it is common for plants to experience water deprivation (drought) for periods of days or longer. Plants respond to drought stress by reconfiguring their transcriptome activity. Transcriptome changes in response to drought are dynamic, and are shaped by mitigating factors like time during the diurnal cycle. To date, analyses of drought-induced transcriptome remodelling have concentrated on dynamic changes induced by rapid desiccation, or changes at a single time point following gradual water stress. To gain insights into the dynamics of transcriptome reconfiguration in response to gradual drying of the soil, the drought-induced transcriptomes of Arabidopsis thaliana were examined at four time points over a single diel period - midday, late day, midnight, and pre-dawn. Transcriptome reconfigurations were induced by drought in advance of changes to relative water content, leaf water loss, and chlorophyll content. Comparative analyses support the hypothesis that the drought-responsive transcriptomes were shaped by invocation of distinct hormonal and stress response pathways at different times of the day. While a core set of genes were drought responsive at multiple time points throughout the day, the magnitude of the response varied in a manner dependent on the time of day. Moreover, analysis of a single time point would fail to identify suites of drought-responsive genes that can only be detected through assessment of the dynamics of diurnal changes, emphasising the value of characterising multiple time-of-day-specific drought transcriptomes.
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Affiliation(s)
- Olivia Wilkins
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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122
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Parent B, Suard B, Serraj R, Tardieu F. Rice leaf growth and water potential are resilient to evaporative demand and soil water deficit once the effects of root system are neutralized. PLANT, CELL & ENVIRONMENT 2010; 33:1256-67. [PMID: 20302604 DOI: 10.1111/j.1365-3040.2010.02145.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Rice is known to be sensitive to soil water deficit and evaporative demand, with a greatest sensitivity of lowland-adapted genotypes. We have analysed the responses of plant water relations and of leaf elongation rate (LER) to soil water status and evaporative demand in seven rice genotypes belonging to different species, subspecies, either upland- or lowland-adapted. In the considered range of soil water potential (0 to -0.6 MPa), stomatal conductance was controlled in such a way that the daytime leaf water potential was similar in well-watered, droughted or flooded conditions (isohydric behaviour). A low sensitivity of LER to evaporative demand was observed in the same three conditions, with small differences between genotypes and lower sensitivity than in maize. The sensitivity of LER to soil water deficit was similar to that of maize. A tendency towards lower sensitivities was observed in upland than lowland genotypes but with smaller differences than expected. We conclude that leaf water status and leaf elongation of rice are not particularly sensitive to water deficit. The main origin of drought sensitivity in rice may be its poor root system, whose effect was alleviated in the study presented here by growing plants in pots whose soil was entirely colonized by roots of all genotypes.
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Affiliation(s)
- Boris Parent
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060 Montpellier, France
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123
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Yoon UH, Kim YK, Kim CK, Hahn JH, Kim DH, Lee TH, Lee GS, Park SC, Nahm BH. Current status on expression profiling using rice microarray. ACTA ACUST UNITED AC 2010. [DOI: 10.5010/jpb.2010.37.3.144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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124
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Krugman T, Chagué V, Peleg Z, Balzergue S, Just J, Korol AB, Nevo E, Saranga Y, Chalhoub B, Fahima T. Multilevel regulation and signalling processes associated with adaptation to terminal drought in wild emmer wheat. Funct Integr Genomics 2010; 10:167-86. [PMID: 20333536 DOI: 10.1007/s10142-010-0166-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 02/07/2010] [Accepted: 02/09/2010] [Indexed: 12/13/2022]
Abstract
Low water availability is the major environmental factor limiting crop productivity. Transcriptome analysis was used to study terminal drought response in wild emmer wheat, Triticum dicoccoides, genotypes contrasting in their productivity and yield stability under drought stress. A total of 5,892 differentially regulated transcripts were identified between drought and well-watered control and/or between drought resistant (R) and drought susceptible (S) genotypes. Functional enrichment analyses revealed that multilevel regulatory and signalling processes were significantly enriched among the drought-induced transcripts, in particular in the R genotype. Therefore, further analyses were focused on selected 221 uniquely expressed or highly abundant transcripts in the R genotype, as potential candidates for drought resistance genes. Annotation of the 221 genes revealed that 26% of them are involved in multilevel regulation, including: transcriptional regulation, RNA binding, kinase activity and calcium and abscisic acid signalling implicated in stomatal closure. Differential expression patterns were also identified in genes known to be involved in drought adaptation pathways, such as: cell wall adjustment, cuticular wax deposition, lignification, osmoregulation, redox homeostasis, dehydration protection and drought-induced senescence. These results demonstrate the potential of wild emmer wheat as a source for candidate genes for improving drought resistance.
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Affiliation(s)
- Tamar Krugman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Mt. Carmel, Haifa, 31905, Israel
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125
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Larrainzar E, Wienkoop S, Scherling C, Kempa S, Ladrera R, Arrese-Igor C, Weckwerth W, González EM. Carbon metabolism and bacteroid functioning are involved in the regulation of nitrogen fixation in Medicago truncatula under drought and recovery. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:1565-76. [PMID: 19888822 DOI: 10.1094/mpmi-22-12-1565] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Regulation of symbiotic nitrogen fixation (SNF) during drought stress is complex and not yet fully understood. In the present work, the involvement of nodule C and N metabolism in the regulation of SNF in Medicago truncatula under drought and a subsequent rewatering treatment was analyzed using a combination of metabolomic and proteomic approaches. Drought induced a reduction of SNF rates and major changes in the metabolic profile of nodules, mostly an accumulation of amino acids (Pro, His, and Trp) and carbohydrates (sucrose, galactinol, raffinose, and trehalose). This accumulation was coincidental with a decline in the levels of bacteroid proteins involved in SNF and C metabolism, along with a partial reduction of the levels of plant sucrose synthase 1 (SuSy1). In contrast, the variations in enzymes related to N assimilation were found not to correlate with the reduction in SNF, suggesting that these enzymes do not have a role in the regulation of SNF. Unlike the situation in other legumes such as pea and soybean, the drought-induced inhibition of SNF in M. truncatula appears to be caused by impairment of bacteroid metabolism and N(2)-fixing capacity rather than a limitation of respiratory substrate.
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Affiliation(s)
- Estíbaliz Larrainzar
- Departamento Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Spain
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126
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Wilkins O, Waldron L, Nahal H, Provart NJ, Campbell MM. Genotype and time of day shape the Populus drought response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:703-15. [PMID: 19682285 DOI: 10.1111/j.1365-313x.2009.03993.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
As exposure to episodic drought can impinge significantly on forest health and the establishment of productive tree plantations, there is great interest in understanding the mechanisms of drought response in trees. The ecologically dominant and economically important genus Populus, with its sequenced genome, provides an ideal opportunity to examine transcriptome level changes in trees in response to a drought stimulus. The transcriptome level drought response of two commercially important Populus clones (P. deltoides x P. nigra, DN34, and P. nigra x P. maximowiczii, NM6) was characterized over a diurnal period using a 4 x 2 x 2 complete randomized factorial anova experimental design (four time points, two genotypes and two treatment conditions), using Affymetrix Poplar GeneChip microarrays. Notably, the specific genes that exhibited changes in transcript abundance in response to drought differed between the genotypes and/or the time of day that they exhibited their greatest differences. This study emphasizes the fact that it is not possible to draw simple, generalized conclusions about the drought response of the genus Populus on the basis of one species, nor on the basis of results collected at a single time point. The data derived from our studies provide insights into the variety of genetic mechanisms underpinning the Populus drought response, and provide candidates for future experiments aimed at understanding this response across this economically and ecologically important genus.
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Affiliation(s)
- Olivia Wilkins
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
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127
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Hayano-Kanashiro C, Calderón-Vázquez C, Ibarra-Laclette E, Herrera-Estrella L, Simpson J. Analysis of gene expression and physiological responses in three Mexican maize landraces under drought stress and recovery irrigation. PLoS One 2009; 4:e7531. [PMID: 19888455 PMCID: PMC2766256 DOI: 10.1371/journal.pone.0007531] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 09/18/2009] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Drought is one of the major constraints for plant productivity worldwide. Different mechanisms of drought-tolerance have been reported for several plant species including maize. However, the differences in global gene expression between drought-tolerant and susceptible genotypes and their relationship to physiological adaptations to drought are largely unknown. The study of the differences in global gene expression between tolerant and susceptible genotypes could provide important information to design more efficient breeding programs to produce maize varieties better adapted to water limiting conditions. METHODOLOGY/PRINCIPAL FINDINGS Changes in physiological responses and gene expression patterns were studied under drought stress and recovery in three Mexican maize landraces which included two drought tolerant (Cajete criollo and Michoacán 21) and one susceptible (85-2) genotypes. Photosynthesis, stomatal conductance, soil and leaf water potentials were monitored throughout the experiment and microarray analysis was carried out on transcripts obtained at 10 and 17 days following application of stress and after recovery irrigation. The two tolerant genotypes show more drastic changes in global gene expression which correlate with different physiological mechanisms of adaptation to drought. Differences in the kinetics and number of up- and down-regulated genes were observed between the tolerant and susceptible maize genotypes, as well as differences between the two tolerant genotypes. Interestingly, the most dramatic differences between the tolerant and susceptible genotypes were observed during recovery irrigation, suggesting that the tolerant genotypes activate mechanisms that allow more efficient recovery after a severe drought. CONCLUSIONS/SIGNIFICANCE A correlation between levels of photosynthesis and transcription under stress was observed and differences in the number, type and expression levels of transcription factor families were also identified under drought and recovery between the three maize landraces. Gene expression analysis suggests that the drought tolerant landraces have a greater capacity to rapidly modulate more genes under drought and recovery in comparison to the susceptible landrace. Modulation of a greater number of differentially expressed genes of different TF gene families is an important characteristic of the tolerant genotypes. Finally, important differences were also noted between the tolerant landraces that underlie different mechanisms of achieving tolerance.
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Affiliation(s)
- Corina Hayano-Kanashiro
- Centro de Investigación y Estudios Avanzados, Departamento de Ingeniería Genética de Plantas, Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| | - Carlos Calderón-Vázquez
- Centro de Investigación y Estudios Avanzados, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| | - Enrique Ibarra-Laclette
- Centro de Investigación y Estudios Avanzados, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Centro de Investigación y Estudios Avanzados, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| | - June Simpson
- Centro de Investigación y Estudios Avanzados, Departamento de Ingeniería Genética de Plantas, Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
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128
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Edwards CE, Haselhorst MSH, McKnite AM, Ewers BE, Williams DG, Weinig C. Genotypes of Brassica rapa respond differently to plant-induced variation in air CO2 concentration in growth chambers with standard and enhanced venting. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:991-1004. [PMID: 19603146 DOI: 10.1007/s00122-009-1103-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 06/25/2009] [Indexed: 05/16/2023]
Abstract
Growth chambers allow measurement of phenotypic differences among genotypes under controlled environment conditions. However, unintended variation in growth chamber air CO2 concentration ([CO2]) may affect the expression of diverse phenotypic traits, and genotypes may differ in their response to variation in [CO2]. We monitored [CO2] and quantified phenotypic responses of 22 Brassica rapa genotypes in growth chambers with either standard or enhanced venting. [CO2] in chambers with standard venting dropped to 280 micromol mol(-1) during the period of maximum canopy development, approximately 80 micromol mol(-1) lower than in chambers with enhanced venting. The stable carbon isotope ratio of CO2 in chamber air (delta13C(air)) was negatively correlated with [CO2], suggesting that photosynthesis caused observed [CO2] decreases. Significant genotype x chamber-venting interactions were detected for 12 of 20 traits, likely due to differences in the extent to which [CO2] changed in relation to genotypes' phenology or differential sensitivity of genotypes to low [CO2]. One trait, 13C discrimination (delta13C), was particularly influenced by unaccounted-for fluctuations in delta13C(air) and [CO2]. Observed responses to [CO2] suggest that genetic variance components estimated in poorly vented growth chambers may be influenced by the expression of genes involved in CO2 stress responses; genotypic values estimated in these chambers may likewise be misleading such that some mapped quantitative trait loci may regulate responses to CO2 stress rather than a response to the environmental factor of interest. These results underscore the importance of monitoring, and where possible, controlling [CO2].
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129
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Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M. A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. PLANT, CELL & ENVIRONMENT 2009; 32:1211-29. [PMID: 19389052 DOI: 10.1111/j.1365-3040.2009.01978.x] [Citation(s) in RCA: 382] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MapMan is a software tool that supports the visualization of profiling data sets in the context of existing knowledge. Scavenger modules generate hierarchical and essentially non-redundant gene ontologies ('mapping files'). An ImageAnnotator module visualizes the data on a gene-by-gene basis on schematic diagrams ('maps') of biological processes. The PageMan module uses the same ontologies to statistically evaluate responses at the pathway or processes level. The generic structure of MapMan also allows it to be used for transcripts, proteins, enzymes and metabolites. MapMan was developed for use with Arabidopsis, but has already been extended for use with several other species. These tools are available as downloadable and web-based versions. After providing an introduction to the scope and use of MapMan, we present a case study where MapMan is used to analyse the transcriptional response of the crop plant maize to diurnal changes and an extension of the night. We then explain how MapMan can be customized to visually and systematically compare responses in maize and Arabidopsis. These analyses illustrate how MapMan can be used to analyse and compare global transcriptional responses between phylogenetically distant species, and show that analyses at the level of functional categories are especially useful in cross-species comparisons.
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Affiliation(s)
- Björn Usadel
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany.
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Centritto M, Lauteri M, Monteverdi MC, Serraj R. Leaf gas exchange, carbon isotope discrimination, and grain yield in contrasting rice genotypes subjected to water deficits during the reproductive stage. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:2325-39. [PMID: 19443613 DOI: 10.1093/jxb/erp123] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Genotypic variations in leaf gas exchange and yield were analysed in five upland-adapted and three lowland rice cultivars subjected to a differential soil moisture gradient, varying from well-watered to severely water-stressed conditions. A reduction in the amount of water applied resulted in a significant decrease in leaf gas exchange and, subsequently, in above-ground dry mass and grain yield, that varied among genotypes and distance from the line source. The comparison between the variable J and the Delta values in recently synthesized sugars methods, yielded congruent estimations of mesophyll conductance (g(m)), confirming the reliability of these two techniques. Our data demonstrate that g(m) is a major determinant of photosynthesis (A), because rice genotypes with inherently higher g(m) were capable of keeping higher A in stressed conditions. Furthermore, A, g(s), and g(m) of water-stressed genotypes rapidly recovered to the well-watered values upon the relief of water stress, indicating that drought did not cause any lasting metabolic limitation to photosynthesis. The comparisons between the A/C(i) and corresponding A/C(c) curves, measured in the genotypes that showed intrinsically higher and lower instantaneous A, confirmed this finding. Moreover, the effect of drought stress on grain yield was correlated with the effects on both A and total diffusional limitations to photosynthesis. Overall, these data indicate that genotypes which showed higher photosynthesis and conductances were also generally more productive across the entire soil moisture gradient. The analysis of Delta revealed a substantial variation of water use efficiency among the genotypes, both on the long-term (leaf pellet analysis) and short-term scale (leaf soluble sugars analysis).
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Affiliation(s)
- Mauro Centritto
- Institute of Agro-Environmental and Forest Biology, National Research Council, Monterotondo Scalo, RM, Italy.
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