101
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Komatsu S, Kamal AHM, Hossain Z. Wheat proteomics: proteome modulation and abiotic stress acclimation. FRONTIERS IN PLANT SCIENCE 2014; 5:684. [PMID: 25538718 PMCID: PMC4259124 DOI: 10.3389/fpls.2014.00684] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 11/18/2014] [Indexed: 05/21/2023]
Abstract
Cellular mechanisms of stress sensing and signaling represent the initial plant responses to adverse conditions. The development of high-throughput "Omics" techniques has initiated a new era of the study of plant molecular strategies for adapting to environmental changes. However, the elucidation of stress adaptation mechanisms in plants requires the accurate isolation and characterization of stress-responsive proteins. Because the functional part of the genome, namely the proteins and their post-translational modifications, are critical for plant stress responses, proteomic studies provide comprehensive information about the fine-tuning of cellular pathways that primarily involved in stress mitigation. This review summarizes the major proteomic findings related to alterations in the wheat proteomic profile in response to abiotic stresses. Moreover, the strengths and weaknesses of different sample preparation techniques, including subcellular protein extraction protocols, are discussed in detail. The continued development of proteomic approaches in combination with rapidly evolving bioinformatics tools and interactive databases will facilitate understanding of the plant mechanisms underlying stress tolerance.
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Affiliation(s)
- Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Abu H. M. Kamal
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Zahed Hossain
- Plant Stress Biology Lab, Department of Botany, West Bengal State UniversityKolkata, India
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102
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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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103
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Li X, Huang L, Zhang Y, Ouyang Z, Hong Y, Zhang H, Li D, Song F. Tomato SR/CAMTA transcription factors SlSR1 and SlSR3L negatively regulate disease resistance response and SlSR1L positively modulates drought stress tolerance. BMC PLANT BIOLOGY 2014; 14:286. [PMID: 25348703 PMCID: PMC4219024 DOI: 10.1186/s12870-014-0286-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 10/15/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND The SR/CAMTA proteins represent a small family of transcription activators that play important roles in plant responses to biotic and abiotic stresses. Seven SlSR/CAMTA genes were identified in tomato as tomato counterparts of SR/CAMTA; however, the involvement of SlSRs/CAMTAs in biotic and abiotic stress responses is not clear. In this study, we performed functional analysis of the SlSR/CAMTA family for their possible functions in defense response against pathogens and tolerance to drought stress. RESULTS Expression of SlSRs was induced with distinct patterns by Botrytis cinerea and Pseudomonas syringae pv. tomato (Pst) DC3000. Virus-induced gene silencing (VIGS)-based knockdown of either SlSR1 or SlSR3L in tomato resulted in enhanced resistance to B. cinerea and Pst DC3000 and led to constitutive accumulation of H2O2, elevated expression of defense genes, marker genes for pathogen-associated molecular pattern-triggered immunity, and regulatory genes involved in the salicylic acid- and ethylene-mediated signaling pathways. Furthermore, the expression of SlSR1L and SlSR2L in detached leaves and whole plants was significantly induced by drought stress. Silencing of SlSR1L led to decreased drought stress tolerance, accelerated water loss in leaves, reduced root biomass and attenuated expression of drought stress responsive genes in tomato. The SlSR1 and SlSR3L proteins were localized in the nucleus of plant cells when transiently expressed in Nicotiana benthamiana and had transcriptional activation activity in yeast. CONCLUSIONS VIGS-based functional analyses demonstrate that both SlSR1 and SlSR3L in the tomato SlSR/CAMTA family are negative regulators of defense response against B. cinerea and Pst DC3000 while SlSR1L is a positive regulator of drought stress tolerance in tomato.
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Affiliation(s)
- Xiaohui Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Lei Huang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Yafen Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Zhigang Ouyang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Yongbo Hong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Huijuan Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
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104
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Wu J, Wang L, Li L, Wang S. De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes. PLoS One 2014; 9:e109262. [PMID: 25275443 PMCID: PMC4183588 DOI: 10.1371/journal.pone.0109262] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 09/04/2014] [Indexed: 12/01/2022] Open
Abstract
The common bean (Phaseolus vulgaris L.) is one of the most important food legumes, far ahead of other legumes. The average grain yield of the common bean worldwide is much lower than its potential yields, primarily due to drought in the field. However, the gene network that mediates plant responses to drought stress remains largely unknown in this species. The major goals of our study are to identify a large scale of genes involved in drought stress using RNA-seq. First, we assembled 270 million high-quality trimmed reads into a non-redundant set of 62,828 unigenes, representing approximately 49 Mb of unique transcriptome sequences. Of these unigenes, 26,501 (42.2%) common bean unigenes had significant similarity with unigenes/predicted proteins from other legumes or sequenced plants. All unigenes were functionally annotated within the GO, COG and KEGG pathways. The strategy for de novo assembly of transcriptome data generated here will be useful in other legume plant transcriptome studies. Second, we identified 10,482 SSRs and 4,099 SNPs in transcripts. The large number of genetic markers provides a resource for gene discovery and development of functional molecular markers. Finally, we found differential expression genes (DEGs) between terminal drought and optimal irrigation treatments and between the two different genotypes Long 22-0579 (drought tolerant) and Naihua (drought sensitive). DEGs were confirmed by quantitative real-time PCR assays, which indicated that these genes are functionally associated with the drought-stress response. These resources will be helpful for basic and applied research for genome analysis and crop drought resistance improvement in the common bean.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lanfen Wang
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shumin Wang
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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105
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Reddy SK, Liu S, Rudd JC, Xue Q, Payton P, Finlayson SA, Mahan J, Akhunova A, Holalu SV, Lu N. Physiology and transcriptomics of water-deficit stress responses in wheat cultivars TAM 111 and TAM 112. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1289-98. [PMID: 25014264 DOI: 10.1016/j.jplph.2014.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 05/05/2023]
Abstract
Hard red winter wheat crops on the U.S. Southern Great Plains often experience moderate to severe drought stress, especially during the grain filling stage, resulting in significant yield losses. Cultivars TAM 111 and TAM 112 are widely cultivated in the region, share parentage and showed superior but distinct adaption mechanisms under water-deficit (WD) conditions. Nevertheless, the physiological and molecular basis of their adaptation remains unknown. A greenhouse study was conducted to understand the differences in the physiological and transcriptomic responses of TAM 111 and TAM 112 to WD stress. Whole-plant data indicated that TAM 112 used more water, produced more biomass and grain yield under WD compared to TAM 111. Leaf-level data at the grain filling stage indicated that TAM 112 had elevated abscisic acid (ABA) content and reduced stomatal conductance and photosynthesis as compared to TAM 111. Sustained WD during the grain filling stage also resulted in greater flag leaf transcriptome changes in TAM 112 than TAM 111. Transcripts associated with photosynthesis, carbohydrate metabolism, phytohormone metabolism, and other dehydration responses were uniquely regulated between cultivars. These results suggested a differential role for ABA in regulating physiological and transcriptomic changes associated with WD stress and potential involvement in the superior adaptation and yield of TAM 112.
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Affiliation(s)
- Srirama Krishna Reddy
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, 6500 Amarillo Blvd W, Amarillo, TX 79106 USA
| | - Shuyu Liu
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, 6500 Amarillo Blvd W, Amarillo, TX 79106 USA.
| | - Jackie C Rudd
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, 6500 Amarillo Blvd W, Amarillo, TX 79106 USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, 6500 Amarillo Blvd W, Amarillo, TX 79106 USA
| | - Paxton Payton
- United States Department of Agriculture - Agriculture Research Services, Cropping Systems Research Laboratory, Lubbock, TX 79415 USA.
| | - Scott A Finlayson
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX 77843 USA
| | - James Mahan
- United States Department of Agriculture - Agriculture Research Services, Cropping Systems Research Laboratory, Lubbock, TX 79415 USA
| | - Alina Akhunova
- Integrated Genomics Facility, Kansas State University, 4024 Throckmorton, Manhattan, KS 66506 USA
| | - Srinidhi V Holalu
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX 77843 USA
| | - Nanyan Lu
- Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS 66506 USA
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106
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Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RCHJ, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JKC, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 2014. [PMID: 25064008 DOI: 10.1038/ng3046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
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Affiliation(s)
- Anthony Bolger
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany
| | - Federico Scossa
- 1] Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per l'Orticoltura, Pontecagnano, Italy
| | - Marie E Bolger
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Florian Maumus
- French National Institute for Agricultural Research (INRA), UR1164 Research Unit in Genomics Info (URGI), INRA de Versailles-Grignon, Versailles, France
| | - Takayuki Tohge
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Hadi Quesneville
- French National Institute for Agricultural Research (INRA), UR1164 Research Unit in Genomics Info (URGI), INRA de Versailles-Grignon, Versailles, France
| | - Saleh Alseekh
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Iben Sørensen
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Gabriel Lichtenstein
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - Eric A Fich
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Mariana Conte
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - Heike Keller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Korbinian Schneeberger
- 1] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. [2] Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rainer Schwacke
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Itai Ofner
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Julia Vrebalov
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Yimin Xu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Sonia Osorio
- 1] Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain
| | - Saulo Alves Aflitos
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Elio Schijlen
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - José M Jiménez-Goméz
- 1] Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany. [2] INRA, UMR 1318, Institut Jean-Pierre Bourgin, Versailles, France
| | - Malgorzata Ryngajllo
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Seisuke Kimura
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Ravi Kumar
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Daniel Koenig
- 1] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. [2] Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Lauren R Headland
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Roeland C H J van Ham
- 1] Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands. [2]
| | - René Klein Lankhorst
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Linyong Mao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Alexander Vogel
- Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany
| | - Borjana Arsova
- Entwicklungs und Molekularbiologie der Pflanzen, Heinrich Heine Universität, Düsseldorf, Germany
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen, Germany
| | - Zhangjun Fei
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA. [3] US Department of Agriculture Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA
| | - Jocelyn K C Rose
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Dani Zamir
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Fernando Carrari
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - James J Giovannoni
- 1] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA. [2] US Department of Agriculture Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Björn Usadel
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany. [3] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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107
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Ripoll J, Urban L, Staudt M, Lopez-Lauri F, Bidel LPR, Bertin N. Water shortage and quality of fleshy fruits--making the most of the unavoidable. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4097-117. [PMID: 24821951 DOI: 10.1093/jxb/eru197] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Extreme climatic events, including drought, are predicted to increase in intensity, frequency, and geographic extent as a consequence of global climate change. In general, to grow crops successfully in the future, growers will need to adapt to less available water and to take better advantage of the positive effects of drought. Fortunately, there are positive effects associated with drought. Drought stimulates the secondary metabolism, thereby potentially increasing plant defences and the concentrations of compounds involved in plant quality, particularly taste and health benefits. The role of drought on the production of secondary metabolites is of paramount importance for fruit crops. However, to manage crops effectively under conditions of limited water supply, for example by applying deficit irrigation, growers must consider not only the impact of drought on productivity but also on how plants manage the primary and secondary metabolisms. This question is obviously complex because during water deficit, trade-offs among productivity, defence, and quality depend upon the intensity, duration, and repetition of events of water deficit. The stage of plant development during the period of water deficit is also crucial, as are the effects of other stressors. In addition, growers must rely on relevant indicators of water status, i.e. parameters involved in the relevant metabolic processes, including those affecting quality. Although many reports on the effects of drought on plant function and crop productivity have been published, these issues have not been reviewed thus far. Here, we provide an up-to-date review of current knowledge of the effects of different forms of drought on fruit quality relative to the primary and secondary metabolisms and their interactions. We also review conventional and less conventional indicators of water status that could be used for monitoring purposes, such as volatile compounds. We focus on fruit crops owing to the importance of secondary metabolism in fruit quality and the importance of fruits in the human diet. The issue of defence is also briefly discussed.
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Affiliation(s)
- Julie Ripoll
- INRA - Centre d'Avignon, UR 1115 Plantes et Systèmes de culture Horticoles, Domaine Saint Paul - Site Agroparc, 228 route de l'Aérodrome, CS 40509, 84914 Avignon Cedex 9, France Laboratoire de Physiologie des Fruits et Légumes, Université d'Avignon et des Pays du Vaucluse, Bât. Agrosciences, 301 rue Baruch de Spinoza, B.p. 21239, F-84916 Avignon Cedex 9, France
| | - Laurent Urban
- Laboratoire de Physiologie des Fruits et Légumes, Université d'Avignon et des Pays du Vaucluse, Bât. Agrosciences, 301 rue Baruch de Spinoza, B.p. 21239, F-84916 Avignon Cedex 9, France
| | - Michael Staudt
- Centre d'Ecologie Fonctionnelle et Evolutive Montpellier, CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Félicie Lopez-Lauri
- Laboratoire de Physiologie des Fruits et Légumes, Université d'Avignon et des Pays du Vaucluse, Bât. Agrosciences, 301 rue Baruch de Spinoza, B.p. 21239, F-84916 Avignon Cedex 9, France
| | - Luc P R Bidel
- INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France
| | - Nadia Bertin
- INRA - Centre d'Avignon, UR 1115 Plantes et Systèmes de culture Horticoles, Domaine Saint Paul - Site Agroparc, 228 route de l'Aérodrome, CS 40509, 84914 Avignon Cedex 9, France
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108
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The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 2014; 46:1034-8. [PMID: 25064008 PMCID: PMC7036041 DOI: 10.1038/ng.3046] [Citation(s) in RCA: 265] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/30/2014] [Indexed: 11/12/2022]
Abstract
Björn Usadel and colleagues report the genome sequence of the wild tomato species Solanum pennellii. The authors identify genes important for stress tolerance, metabolism and fruit maturation and suggest that transposable elements have had an important role in the evolution of the S. penellii stress response. Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum1. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance2. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
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Liu B, Ouyang Z, Zhang Y, Li X, Hong Y, Huang L, Liu S, Zhang H, Li D, Song F. Tomato NAC transcription factor SlSRN1 positively regulates defense response against biotic stress but negatively regulates abiotic stress response. PLoS One 2014; 9:e102067. [PMID: 25010573 PMCID: PMC4092073 DOI: 10.1371/journal.pone.0102067] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/13/2014] [Indexed: 12/11/2022] Open
Abstract
Biotic and abiotic stresses are major unfavorable factors that affect crop productivity worldwide. NAC proteins comprise a large family of transcription factors that play important roles in plant growth and development as well as in responses to biotic and abiotic stresses. In a virus-induced gene silencing-based screening to identify genes that are involved in defense response against Botrytis cinerea, we identified a tomato NAC gene SlSRN1 (Solanum lycopersicumStress-related NAC1). SlSRN1 is a plasma membrane-localized protein with transactivation activity in yeast. Expression of SlSRN1 was significantly induced by infection with B. cinerea or Pseudomonas syringae pv. tomato (Pst) DC3000, leading to 6–8 folds higher than that in the mock-inoculated plants. Expression of SlSRN1 was also induced by salicylic acid, jasmonic acid and 1-amino cyclopropane-1-carboxylic acid and by drought stress. Silencing of SlSRN1 resulted in increased severity of diseases caused by B. cinerea and Pst DC3000. However, silencing of SlSRN1 resulted in increased tolerance against oxidative and drought stresses. Furthermore, silencing of SlSRN1 accelerated accumulation of reactive oxygen species but attenuated expression of defense genes after infection by B. cinerea. Our results demonstrate that SlSRN1 is a positive regulator of defense response against B. cinerea and Pst DC3000 but is a negative regulator for oxidative and drought stress response in tomato.
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Affiliation(s)
- Bo Liu
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhigang Ouyang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yafen Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaohui Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yongbo Hong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Lei Huang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shixia Liu
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Huijuan Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- * E-mail:
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Transcriptome expression profiling in response to drought stress in Paulownia australis. Int J Mol Sci 2014; 15:4583-607. [PMID: 24642880 PMCID: PMC3975415 DOI: 10.3390/ijms15034583] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/05/2014] [Accepted: 03/06/2014] [Indexed: 11/17/2022] Open
Abstract
The response and adaptation to drought remains poorly understood for Paulownia australis. To investigate this issue, transcriptome profiling of four P. australis accessions (two diploid and the other two autotetraploid) under water stress condition were studied using Illumina Genome Analyzer IIx analysis. The current study aimed to identify genes of P. australis metabolism pathways that might be involved in this plant's response to water deficit. Potted seedlings were subjected to well-watered conditions and drought stress, respectively. More than 290 million raw transcript reads were assembled into 111,660 unigenes, with a mean length of 1013 bp. Clusters of orthologous groups, gene ontology and the Kyoto Encyclopedia of Genes and Genomes annotations analyses were performed on the unigenes. Many differentially expressed genes and several metabolic pathways were identified. Quantitative real-time polymerase chain reaction was used to verify the expression patterns of 14 genes. Our study identified altered gene expression in P. australis induced by drought stress and provided a comprehensive map of drought-responsive genes and pathways in this species. To our knowledge, this is the first publicly available global transcriptome study of P. australis. This study provides a valuable genetic resource for this species.
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Qin Y, Song W, Xiao S, Yin G, Zhu Y, Yan Y, Hu Y. Stress-related genes distinctly expressed in unfertilized wheat ovaries under both normal and water deficit conditions whereas differed in fertilized ovaries. J Proteomics 2014; 102:11-27. [PMID: 24607492 DOI: 10.1016/j.jprot.2014.02.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/16/2014] [Accepted: 02/21/2014] [Indexed: 12/17/2022]
Abstract
UNLABELLED In this study, a proteomic approach was utilized to identify differentially accumulated proteins in developing wheat ovaries before and after fertilization and in response to water deficit. Proteins were extracted, quantified, and resolved by 2-DE at pH4-7. Statistical analysis of spot intensity was performed by using principal component analysis and samples were clustered by using Euclidean distance. In total, 136 differentially accumulated protein spots representing 88 unique proteins were successfully identified by MALDI-TOF/TOF MS. Under normal conditions, stress-related proteins were abundant in unfertilized ovaries while proteins involved in the metabolism of energy and matter were enriched in fertilized ovaries just 48h after fertilization. Similar trends were observed in unfertilized and fertilized wheat ovaries under water deficit conditions, except for increased accumulation of stress-related proteins in fertilized ovaries. Some proteins required for normal development were not present in ovaries subjected to water deficit. Our comprehensive results provide new insights into the biochemical mechanisms involved in ovary development before and after fertilization and in tolerance to water deficit. BIOLOGICAL SIGNIFICANCE Fertilization initiates the most dramatic changes that occur in the life cycle of higher plants; research into differences in gene expression before and after ovary pollination can make a substantial contribution to understanding the physiological and biochemical processes associated with fertilization. To date, a small number of studies have examined changes in transcriptional activity of the developing plant embryo sac before and after fertilization. However, comparative proteomic analysis of wheat ovary development before and after fertilization, and in response to water deficit, has not yet been reported. Our comprehensive results provide new insights into the biochemical mechanisms involved in ovary development before and after fertilization and in tolerance to water deficit.
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Affiliation(s)
- Yajuan Qin
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Wanlu Song
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Shuyang Xiao
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Guangjun Yin
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yan Zhu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
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Corrales AR, Nebauer SG, Carrillo L, Fernández-Nohales P, Marqués J, Renau-Morata B, Granell A, Pollmann S, Vicente-Carbajosa J, Molina RV, Medina J. Characterization of tomato Cycling Dof Factors reveals conserved and new functions in the control of flowering time and abiotic stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:995-1012. [PMID: 24399177 DOI: 10.1093/jxb/ert451] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA binding with One Finger (DOF) transcription factors are involved in multiple aspects of plant growth and development but their precise roles in abiotic stress tolerance are largely unknown. Here we report a group of five tomato DOF genes, homologous to Arabidopsis Cycling DOF Factors (CDFs), that function as transcriptional regulators involved in responses to drought and salt stress and flowering-time control in a gene-specific manner. SlCDF1-5 are nuclear proteins that display specific binding with different affinities to canonical DNA target sequences and present diverse transcriptional activation capacities in vivo. SlCDF1-5 genes exhibited distinct diurnal expression patterns and were differentially induced in response to osmotic, salt, heat, and low-temperature stresses. Arabidopsis plants overexpressing SlCDF1 or SlCDF3 showed increased drought and salt tolerance. In addition, the expression of various stress-responsive genes, such as COR15, RD29A, and RD10, were differentially activated in the overexpressing lines. Interestingly, overexpression in Arabidopsis of SlCDF3 but not SlCDF1 promotes late flowering through modulation of the expression of flowering control genes such as CO and FT. Overall, our data connect SlCDFs to undescribed functions related to abiotic stress tolerance and flowering time through the regulation of specific target genes and an increase in particular metabolites.
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Affiliation(s)
- Alba-Rocío Corrales
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus Montegancedo, Autopista M40 (km 38), 28223 Madrid, Spain
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Medina-Puche L, Cumplido-Laso G, Amil-Ruiz F, Hoffmann T, Ring L, Rodríguez-Franco A, Caballero JL, Schwab W, Muñoz-Blanco J, Blanco-Portales R. MYB10 plays a major role in the regulation of flavonoid/phenylpropanoid metabolism during ripening of Fragaria x ananassa fruits. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:401-17. [PMID: 24277278 DOI: 10.1093/jxb/ert377] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This work characterized the role of the R2R3-MYB10 transcription factor (TF) in strawberry fruit ripening. The expression of this TF takes place mainly in the fruit receptacle and is repressed by auxins and activated by abscisic acid (ABA), in parallel to the ripening process. Anthocyanin was not produced when FaMYB10 expression was transiently silenced in fruit receptacles. An increase in FaMYB10 expression was observed in water-stressed fruits, which was accompanied by an increase in both ABA and anthocyanin content. High-throughput transcriptomic analyses performed in fruits with downregulated FaMYB10 expression indicated that this TF regulates the expression of most of the Early-regulated Biosynthesis Genes (EBGs) and the Late-regulated Biosynthesis Genes (LBGs) genes involved in anthocyanin production in ripened fruit receptacles. Besides, the expression of FaMYB10 was not regulated by FaMYB1 and vice versa. Taken together, all these data clearly indicate that the Fragaria × ananassa MYB10 TF plays a general regulatory role in the flavonoid/phenylpropanoid pathway during the ripening of strawberry.
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Affiliation(s)
- Laura Medina-Puche
- Departamento de Bioquímica y Biología Molecular. Edificio Severo Ochoa, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, 14071 Córdoba, Spain
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Deeplanaik N, Kumaran RC, Venkatarangaiah K, Shivashankar SKH, Doddamani D, Telkar S. Expression of drought responsive genes in pigeonpea and in silico comparison with soybean cDNA library. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s12892-013-0069-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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115
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Manaa A, Faurobert M, Valot B, Bouchet JP, Grasselly D, Causse M, Ahmed HB. Effect of salinity and calcium on tomato fruit proteome. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:338-52. [PMID: 23692365 DOI: 10.1089/omi.2012.0108] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Salinity is a major abiotic stress that adversely affects plant growth and productivity. The physiology of the tomato in salty and nonsalty conditions has been extensively studied, providing an invaluable base to understand the responses of the plants to cultural practices. However few data are yet available at the proteomic level looking for the physiological basis of fruit development, under salt stress. Here, we report the effects of salinity and calcium on fruit proteome variations of two tomato genotypes (Cervil and Levovil). Tomato plants were irrigated with a control solution (3 dSm(-1)) or with saline solutions (Na or Ca+Na at 7.6 dSm(-1)). Tomato fruits were harvested at two ripening stages: green (14 days post-anthesis) and red ripe. Total proteins were extracted from pericarp tissue and separated by two-dimensional gel electrophoresis. Among the 600 protein spots reproducibly detected, 53 spots exhibited significant abundance variations between samples and were submitted to mass spectrometry for identification. Most of the identified proteins were involved in carbon and energy metabolism, salt stress, oxidative stress, and proteins associated with ripening process. Overall, there was a large variation on proteins abundance between the two genotypes that can be correlated to salt treatment or/and fruit ripening stage. The results showed a protective effect of calcium that limited the impact of salinization on metabolism, ripening process, and induced plant salt tolerance. Collectively, this work has improved our knowledge about salt and calcium effect on tomato fruit proteome.
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Affiliation(s)
- Arafet Manaa
- Unité d'Ecophysiologie et Nutrition des Plantes, Département de Biologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunisie.
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Li C, Yan JM, Li YZ, Zhang ZC, Wang QL, Liang Y. Silencing the SpMPK1, SpMPK2, and SpMPK3 genes in tomato reduces abscisic acid-mediated drought tolerance. Int J Mol Sci 2013; 14:21983-96. [PMID: 24201128 PMCID: PMC3856046 DOI: 10.3390/ijms141121983] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/28/2013] [Accepted: 10/28/2013] [Indexed: 11/16/2022] Open
Abstract
Drought is a major threat to agriculture production worldwide. Mitogen-activated protein kinases (MAPKs) play a pivotal role in sensing and converting stress signals into appropriate responses so that plants can adapt and survive. To examine the function of MAPKs in the drought tolerance of tomato plants, we silenced the SpMPK1, SpMPK2, and SpMPK3 genes in wild-type plants using the virus-induced gene silencing (VIGS) method. The results indicate that silencing the individual genes or co-silencing SpMPK1, SpMPK2, and SpMPK3 reduced the drought tolerance of tomato plants by varying degrees. Co-silencing SpMPK1 and SpMPK2 impaired abscisic acid (ABA)-induced and hydrogen peroxide (H2O2)-induced stomatal closure and enhanced ABA-induced H2O2 production. Similar results were observed when silencing SpMPK3 alone, but not when SpMPK1 and SpMPK2 were individually silenced. These data suggest that the functions of SpMPK1 and SpMPK2 are redundant, and they overlap with that of SpMPK3 in drought stress signaling pathways. In addition, we found that SpMPK3 may regulate H2O2 levels by mediating the expression of CAT1. Hence, SpMPK1, SpMPK2, and SpMPK3 may play crucial roles in enhancing tomato plants’ drought tolerance by influencing stomatal activity and H2O2 production via the ABA-H2O2 pathway.
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Affiliation(s)
- Cui Li
- State Key Laboratory of Crop Stress Biology in Arid Region, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (C.L.); (J.-M.Y.); (Y.-Z.L.); (Z.-C.Z.); (Q.-L.W.)
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jian-Min Yan
- State Key Laboratory of Crop Stress Biology in Arid Region, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (C.L.); (J.-M.Y.); (Y.-Z.L.); (Z.-C.Z.); (Q.-L.W.)
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yun-Zhou Li
- State Key Laboratory of Crop Stress Biology in Arid Region, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (C.L.); (J.-M.Y.); (Y.-Z.L.); (Z.-C.Z.); (Q.-L.W.)
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhen-Cai Zhang
- State Key Laboratory of Crop Stress Biology in Arid Region, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (C.L.); (J.-M.Y.); (Y.-Z.L.); (Z.-C.Z.); (Q.-L.W.)
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Qiao-Li Wang
- State Key Laboratory of Crop Stress Biology in Arid Region, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (C.L.); (J.-M.Y.); (Y.-Z.L.); (Z.-C.Z.); (Q.-L.W.)
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yan Liang
- State Key Laboratory of Crop Stress Biology in Arid Region, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (C.L.); (J.-M.Y.); (Y.-Z.L.); (Z.-C.Z.); (Q.-L.W.)
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +86-29-8708-2179
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Chen LM, Zhou XA, Li WB, Chang W, Zhou R, Wang C, Sha AH, Shan ZH, Zhang CJ, Qiu DZ, Yang ZL, Chen SL. Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions. BMC Genomics 2013; 14:687. [PMID: 24093224 PMCID: PMC3827939 DOI: 10.1186/1471-2164-14-687] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 09/25/2013] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Soybean is an important crop that provides valuable proteins and oils for human use. Because soybean growth and development is extremely sensitive to water deficit, quality and crop yields are severely impacted by drought stress. In the face of limited water resources, drought-responsive genes are therefore of interest. Identification and analysis of dehydration- and rehydration-inducible differentially expressed genes (DEGs) would not only aid elucidation of molecular mechanisms of stress response, but also enable improvement of crop stress tolerance via gene transfer. Using Digital Gene Expression Tag profiling (DGE), a new technique based on Illumina sequencing, we analyzed expression profiles between two soybean genotypes to identify drought-responsive genes. RESULTS Two soybean genotypes - drought-tolerant Jindou21 and drought-sensitive Zhongdou33 - were subjected to dehydration and rehydration conditions. For analysis of DEGs under dehydration conditions, 20 cDNA libraries were generated from roots and leaves at two different time points under well-watered and dehydration conditions. We also generated eight libraries for analysis under rehydration conditions. Sequencing of the 28 libraries produced 25,000-33,000 unambiguous tags, which were mapped to reference sequences for annotation of expressed genes. Many genes exhibited significant expression differences among the libraries. DEGs in the drought-tolerant genotype were identified by comparison of DEGs among treatments and genotypes. In Jindou21, 518 and 614 genes were differentially expressed under dehydration in leaves and roots, respectively, with 24 identified both in leaves and roots. The main functional categories enriched in these DEGs were metabolic process, response to stresses, plant hormone signal transduction, protein processing, and plant-pathogen interaction pathway; the associated genes primarily encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significantly expressed (|log2 ratio| ≥ 8) genes - Glyma15g03920, Glyma05g02470, Glyma15g15010, Glyma05g09070, Glyma06g35630, Glyma08g12590, and Glyma11g16000 - are more likely to determine drought stress tolerance. The expression patterns of eight randomly-selected genes were confirmed by quantitative RT-PCR; the results of QRT-PCR analysis agreed with transcriptional profile data for 96 out of 128 (75%) data points. CONCLUSIONS Many soybean genes were differentially expressed between drought-tolerant and drought-sensitive genotypes. Based on GO functional annotation and pathway enrichment analysis, some of these genes encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significant DEGs are candidates for improving soybean drought tolerance. These findings will be helpful for analysis and elucidation of molecular mechanisms of drought tolerance; they also provide a basis for cultivating new varieties of drought-tolerant soybean.
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Affiliation(s)
- Li M Chen
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Harbin 150030, China
| | - Xin A Zhou
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Wen B Li
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Harbin 150030, China
| | - Wei Chang
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Harbin 150030, China
| | - Rong Zhou
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Cheng Wang
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Ai H Sha
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Zhi H Shan
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Chan J Zhang
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - De Z Qiu
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Zhong L Yang
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
| | - Shui L Chen
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Key Laboratory of Oil Crop Biology Ministry of Agriculture, Wuhan 430062, China
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Xu Y, Gao S, Yang Y, Huang M, Cheng L, Wei Q, Fei Z, Gao J, Hong B. Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress. BMC Genomics 2013; 14:662. [PMID: 24074255 PMCID: PMC3849779 DOI: 10.1186/1471-2164-14-662] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 09/25/2013] [Indexed: 12/15/2022] Open
Abstract
Background Chrysanthemum is one of the most important ornamental crops in the world and drought stress seriously limits its production and distribution. In order to generate a functional genomics resource and obtain a deeper understanding of the molecular mechanisms regarding chrysanthemum responses to dehydration stress, we performed large-scale transcriptome sequencing of chrysanthemum plants under dehydration stress using the Illumina sequencing technology. Results Two cDNA libraries constructed from mRNAs of control and dehydration-treated seedlings were sequenced by Illumina technology. A total of more than 100 million reads were generated and de novo assembled into 98,180 unique transcripts which were further extensively annotated by comparing their sequencing to different protein databases. Biochemical pathways were predicted from these transcript sequences. Furthermore, we performed gene expression profiling analysis upon dehydration treatment in chrysanthemum and identified 8,558 dehydration-responsive unique transcripts, including 307 transcription factors and 229 protein kinases and many well-known stress responsive genes. Gene ontology (GO) term enrichment and biochemical pathway analyses showed that dehydration stress caused changes in hormone response, secondary and amino acid metabolism, and light and photoperiod response. These findings suggest that drought tolerance of chrysanthemum plants may be related to the regulation of hormone biosynthesis and signaling, reduction of oxidative damage, stabilization of cell proteins and structures, and maintenance of energy and carbon supply. Conclusions Our transcriptome sequences can provide a valuable resource for chrysanthemum breeding and research and novel insights into chrysanthemum responses to dehydration stress and offer candidate genes or markers that can be used to guide future studies attempting to breed drought tolerant chrysanthemum cultivars.
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Affiliation(s)
- Yanjie Xu
- Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China.
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Bhardwaj J, Chauhan R, Swarnkar MK, Chahota RK, Singh AK, Shankar R, Yadav SK. Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress. BMC Genomics 2013; 14:647. [PMID: 24059455 PMCID: PMC3853109 DOI: 10.1186/1471-2164-14-647] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 09/13/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drought tolerance is an attribute maintained in plants by cross-talk between multiple and cascading metabolic pathways. Without a sequenced genome available for horse gram, it is difficult to comprehend such complex networks and intercalated genes associated with drought tolerance of horse gram (Macrotyloma uniflorum). Therefore, de novo transcriptome discovery and associated analyses was done for this highly drought tolerant yet under exploited legume to decipher its genetic makeup. RESULTS Eight samples comprising of shoot and root tissues of two horse gram genotypes (drought-sensitive; M-191 and drought-tolerant; M-249) were used for comparison under control and polyethylene glycol-induced drought stress conditions. Using Illumina sequencing technology, a total of 229,297,896 paired end read pairs were generated and utilized for de novo assembly of horse gram. Significant BLAST hits were obtained for 26,045 transcripts while, 3,558 transcripts had no hits but contained important conserved domains. A total of 21,887 unigenes were identified. SSRs containing sequences covered 16.25% of the transcriptome with predominant tri- and mono-nucleotides (43%). The total GC content of the transcriptome was found to be 43.44%. Under Gene Ontology response to stimulus, DNA binding and catalytic activity was highly expressed during drought stress conditions. Serine/threonine protein kinase was found to dominate in Enzyme Classification while pathways belonging to ribosome metabolism followed by plant pathogen interaction and plant hormone signal transduction were predominant in Kyoto Encyclopedia of Genes and Genomes analysis. Independent search on plant metabolic network pathways suggested valine degradation, gluconeogenesis and purine nucleotide degradation to be highly influenced under drought stress in horse gram. Transcription factors belonging to NAC, MYB-related, and WRKY families were found highly represented under drought stress. qRT-PCR validated the expression profile for 9 out of 10 genes analyzed in response to drought stress. CONCLUSIONS De novo transcriptome discovery and analysis has generated enormous information over horse gram genomics. The genes and pathways identified suggest efficient regulation leading to active adaptation as a basal defense response against drought stress by horse gram. The knowledge generated can be further utilized for exploring other underexploited plants for stress responsive genes and improving plant tolerance.
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Affiliation(s)
- Jyoti Bhardwaj
- Plant Metabolic Engineering Laboratory, Council of Scientific and Industrial Research-Institute of Himalayan Bioresource Technology, Palampur 176061, HP, India.
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Filippis I, Lopez-Cobollo R, Abbott J, Butcher S, Bishop GJ. Using a periclinal chimera to unravel layer-specific gene expression in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:1039-1049. [PMID: 23725542 PMCID: PMC4223383 DOI: 10.1111/tpj.12250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/18/2013] [Accepted: 05/24/2013] [Indexed: 05/29/2023]
Abstract
Plant organs are made from multiple cell types, and defining the expression level of a gene in any one cell or group of cells from a complex mixture is difficult. Dicotyledonous plants normally have three distinct layers of cells, L1, L2 and L3. Layer L1 is the single layer of cells making up the epidermis, layer L2 the single cell sub-epidermal layer and layer L3 constitutes the rest of the internal cells. Here we show how it is possible to harvest an organ and characterise the level of layer-specific expression by using a periclinal chimera that has its L1 layer from Solanum pennellii and its L2 and L3 layers from Solanum lycopersicum. This is possible by measuring the level of the frequency of species-specific transcripts. RNA-seq analysis enabled the genome-wide assessment of whether a gene is expressed in the L1 or L2/L3 layers. From 13 277 genes that are expressed in both the chimera and the parental lines and with at least one polymorphism between the parental alleles, we identified 382 genes that are preferentially expressed in L1 in contrast to 1159 genes in L2/L3. Gene ontology analysis shows that many genes preferentially expressed in L1 are involved in cutin and wax biosynthesis, whereas numerous genes that are preferentially expressed in L2/L3 tissue are associated with chloroplastic processes. These data indicate the use of such chimeras and provide detailed information on the level of layer-specific expression of genes.
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Affiliation(s)
- Ioannis Filippis
- Imperial College London, South Kensington CampusLondon, SW7 2AZ, UK
| | | | - James Abbott
- Imperial College London, South Kensington CampusLondon, SW7 2AZ, UK
| | - Sarah Butcher
- Imperial College London, South Kensington CampusLondon, SW7 2AZ, UK
| | - Gerard J Bishop
- Imperial College London, South Kensington CampusLondon, SW7 2AZ, UK
- East Malling ResearchEast Malling, Kent, ME19 6BJ, UK
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Wang R, Gao F, Guo BQ, Huang JC, Wang L, Zhou YJ. Short-term chromium-stress-induced alterations in the maize leaf proteome. Int J Mol Sci 2013; 14:11125-44. [PMID: 23712354 PMCID: PMC3709723 DOI: 10.3390/ijms140611125] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/25/2013] [Accepted: 05/15/2013] [Indexed: 11/16/2022] Open
Abstract
Soil contamination by chromium (Cr) has become an increasing problem worldwide as a result of extensive industrial activities. Chromium, especially hexavalent Cr, impairs the growth and productivity of plants. Although it has been proposed that plants could modify their metabolism to adapt to Cr stress by reprogramming the expression of genes, especially those related to the antioxidant system, damage response, and electron transport chain, evidence at the protein expression level is lacking. To better understand the precise mechanisms underlying Cr phytoxicity and the plant response to Cr exposure, the time-course of changes in the protein expression profile induced by short-term hexavalent Cr exposure (1, 6 and 24 h) were analyzed in maize leaves. Among the over 1200 protein spots detected reproducibly by two-dimensional electrophoresis (2-DE), 60 were found to be differentially accumulated during Cr stress treatment. Of the Cr-regulated proteins, 58 were identified using tandem mass spectrometry (MS/MS). The Cr-regulated proteins identified were mainly involved in ROS detoxification and defense responses (26%), photosynthesis and chloroplast organization (22%), post-transcriptional processing of mRNA and rRNA (12%), protein synthesis and folding (10%), the DNA damage response (5%), and the cytoskeleton (3%). The possible involvement of these Cr stress-responsive proteins in Cr phytoxicity and the plant response to Cr exposure in maize is discussed, taking into consideration the information available from other plant models. Our results provide preliminary evidence that will facilitate understanding the molecular mechanisms underlying Cr toxicity in maize.
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Affiliation(s)
- Rong Wang
- College of Life Science, Fuyang Teachers College, Fuyang 236037, China; E-Mails: (R.W.); (J.-C.H.)
| | - Fei Gao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; E-Mails: (F.G.); (B.-Q.G.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bing-Qian Guo
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; E-Mails: (F.G.); (B.-Q.G.)
| | - Ji-Chang Huang
- College of Life Science, Fuyang Teachers College, Fuyang 236037, China; E-Mails: (R.W.); (J.-C.H.)
| | - Lei Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Authors to whom correspondence should be addressed; E-Mails: (L.W.); (Y.-J.Z.); Tel./Fax: +86-10-8210-6134 (L.W.); +86-10-6893-2922 (Y.-J.Z.)
| | - Yi-Jun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; E-Mails: (F.G.); (B.-Q.G.)
- Authors to whom correspondence should be addressed; E-Mails: (L.W.); (Y.-J.Z.); Tel./Fax: +86-10-8210-6134 (L.W.); +86-10-6893-2922 (Y.-J.Z.)
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122
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Gao R, Duan K, Guo G, Du Z, Chen Z, Li L, He T, Lu R, Huang J. Comparative Transcriptional Profiling of Two Contrasting Barley Genotypes under Salinity Stress during the Seedling Stage. Int J Genomics 2013; 2013:972852. [PMID: 23762821 PMCID: PMC3671521 DOI: 10.1155/2013/972852] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 03/31/2013] [Accepted: 04/03/2013] [Indexed: 11/22/2022] Open
Abstract
Salinity is one of the major abiotic stresses that affect crop productivity. Identification of the potential novel genes responsible for salt tolerance in barley will contribute to understanding the molecular mechanism of barley responses to salt stress. We compared changes in transcriptome between Hua 11 (a salt-tolerant genotype) and Hua 30 (a salt sensitive genotype) in response to salt stress at the seedling stage using barley cDNA microarrays. In total, 557 and 247 salt-responsive genes were expressed exclusively in the shoot and root tissue of the salt-tolerant genotype, respectively. Among these genes, a number of signal-related genes, transcription factors and compatible solutes were identified and some of these genes were carefully discussed. Notably, a LysM RLK was firstly found involved in salt stress response. Moreover, key enzymes in the pathways of jasmonic acid biosynthesis, lipid metabolism and indole-3-acetic acid homeostasis were specifically affected by salt stress in salt tolerance genotype. These salt-responsive genes and biochemical pathways identified in this study could provide further information for understanding the mechanisms of salt tolerance in barley.
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Affiliation(s)
- Runhong Gao
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Beidi Road 2901, Minhang District, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Ke Duan
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Beidi Road 2901, Minhang District, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Guimei Guo
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Beidi Road 2901, Minhang District, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
- College of Fishery and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Zhizhao Du
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Beidi Road 2901, Minhang District, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Zhiwei Chen
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Beidi Road 2901, Minhang District, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Liang Li
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Beidi Road 2901, Minhang District, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
- College of Fishery and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Ting He
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Beidi Road 2901, Minhang District, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Ruiju Lu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Beidi Road 2901, Minhang District, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Jianhua Huang
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Beidi Road 2901, Minhang District, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
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123
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Pujar A, Menda N, Bombarely A, Edwards JD, Strickler SR, Mueller LA. From manual curation to visualization of gene families and networks across Solanaceae plant species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat028. [PMID: 23681907 PMCID: PMC3655285 DOI: 10.1093/database/bat028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants. Database URL:http://solgenomics.net/
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Affiliation(s)
- Anuradha Pujar
- Boyce Thompson Institute for Plant Research, 533, Tower Road, Ithaca, NY 14853, USA
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Turyagyenda LF, Kizito EB, Ferguson M, Baguma Y, Agaba M, Harvey JJW, Osiru DSO. Physiological and molecular characterization of drought responses and identification of candidate tolerance genes in cassava. AOB PLANTS 2013; 5:plt007. [PMID: 23519782 PMCID: PMC3604649 DOI: 10.1093/aobpla/plt007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/22/2013] [Indexed: 05/08/2023]
Abstract
Cassava is an important root crop to resource-poor farmers in marginal areas, where its production faces drought stress constraints. Given the difficulties associated with cassava breeding, a molecular understanding of drought tolerance in cassava will help in the identification of markers for use in marker-assisted selection and genes for transgenic improvement of drought tolerance. This study was carried out to identify candidate drought-tolerance genes and expression-based markers of drought stress in cassava. One drought-tolerant (improved variety) and one drought-susceptible (farmer-preferred) cassava landrace were grown in the glasshouse under well-watered and water-stressed conditions. Their morphological, physiological and molecular responses to drought were characterized. Morphological and physiological measurements indicate that the tolerance of the improved variety is based on drought avoidance, through reduction of water loss via partial stomatal closure. Ten genes that have previously been biologically validated as conferring or being associated with drought tolerance in other plant species were confirmed as being drought responsive in cassava. Four genes (MeALDH, MeZFP, MeMSD and MeRD28) were identified as candidate cassava drought-tolerance genes, as they were exclusively up-regulated in the drought-tolerant genotype to comparable levels known to confer drought tolerance in other species. Based on these genes, we hypothesize that the basis of the tolerance at the cellular level is probably through mitigation of the oxidative burst and osmotic adjustment. This study provides an initial characterization of the molecular response of cassava to drought stress resembling field conditions. The drought-responsive genes can now be used as expression-based markers of drought stress tolerance in cassava, and the candidate tolerance genes tested in the context of breeding (as possible quantitative trait loci) and engineering drought tolerance in transgenics.
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Affiliation(s)
- Laban F. Turyagyenda
- Makerere University-Uganda, PO Box 7062, Kampala, Uganda
- National Agriculture Research Organization (NARO)-Uganda, PO Box 295, Entebbe, Uganda
| | - Elizabeth B. Kizito
- National Agriculture Research Organization (NARO)-Uganda, PO Box 295, Entebbe, Uganda
| | - Morag Ferguson
- International Institute of Tropical Agriculture (IITA), c/o International Livestock Research Institute (ILRI), PO Box 30709, Nairobi 00100,Kenya
| | - Yona Baguma
- National Agriculture Research Organization (NARO)-Uganda, PO Box 295, Entebbe, Uganda
| | - Morris Agaba
- The Nelson Mandela Institute of Science and Technology, PO Box 447, Arusha, Tanzania
- Biosciences Eastern and Central Africa–International Livestock Research Institute (BecA–ILRI) Hub, PO Box 30709, Nairobi 00100, Kenya
| | - Jagger J. W. Harvey
- Biosciences Eastern and Central Africa–International Livestock Research Institute (BecA–ILRI) Hub, PO Box 30709, Nairobi 00100, Kenya
- Corresponding authors' e-mail addresses: ,
| | - David S. O. Osiru
- Makerere University-Uganda, PO Box 7062, Kampala, Uganda
- Corresponding authors' e-mail addresses: ,
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125
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Kamthan A, Kamthan M, Azam M, Chakraborty N, Chakraborty S, Datta A. Expression of a fungal sterol desaturase improves tomato drought tolerance, pathogen resistance and nutritional quality. Sci Rep 2012; 2:951. [PMID: 23230516 PMCID: PMC3517979 DOI: 10.1038/srep00951] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/24/2012] [Indexed: 12/03/2022] Open
Abstract
Crop genetic engineering mostly aims at improving environmental stress (biotic and abiotic) tolerance as well as nutritional quality. Empowering a single crop with multiple traits is highly demanding and requires manipulation of more than one gene. However, we report improved drought tolerance and fungal resistance along with the increased iron and polyunsaturated fatty acid content in tomato by expressing a single gene encoding C-5 sterol desaturase (FvC5SD) from an edible fungus Flammulina velutipes. FvC5SD is an iron binding protein involved in ergosterol biosynthesis. Morphological and biochemical analyses indicated ≈23% more epicuticular wax deposition in leaves of transgenic plants that provides an effective waterproof barrier resulting in improved protection from drought and infection by phytopathogenic fungus Sclerotiniasclerotiorum. Furthermore, the transgenic fruits have improved nutritional value attributed to enhanced level of beneficial PUFA and 2-3 fold increase in total iron content. This strategy can be extended to other economically important crops.
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Affiliation(s)
- Ayushi Kamthan
- National Institute of Plant Genome Research, New Delhi, India
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126
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Dai F, Zhang C, Jiang X, Kang M, Yin X, Lü P, Zhang X, Zheng Y, Gao J. RhNAC2 and RhEXPA4 are involved in the regulation of dehydration tolerance during the expansion of rose petals. PLANT PHYSIOLOGY 2012; 160:2064-82. [PMID: 23093360 PMCID: PMC3510132 DOI: 10.1104/pp.112.207720] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Dehydration inhibits petal expansion resulting in abnormal flower opening and results in quality loss during the marketing of cut flowers. We constructed a suppression subtractive hybridization library from rose (Rosa hybrida) flowers containing 3,513 unique expressed sequence tags and analyzed their expression profiles during cycles of dehydration. We found that 54 genes were up-regulated by the first dehydration, restored or even down-regulated by rehydration, and once again up-regulated by the second dehydration. Among them, we identified a putative NAC family transcription factor (RhNAC2). With transactivation activity of its carboxyl-terminal domain in yeast (Saccharomyces cerevisiae) cell and Arabidopsis (Arabidopsis thaliana) protoplast, RhNAC2 belongs to the NAC transcription factor clade related to plant development in Arabidopsis. A putative expansin gene named RhEXPA4 was also dramatically up-regulated by dehydration. Silencing RhNAC2 or RhEXPA4 in rose petals by virus-induced gene silencing significantly decreased the recovery of intact petals and petal discs during rehydration. Overexpression of RhNAC2 or RhEXPA4 in Arabidopsis conferred strong drought tolerance in the transgenic plants. RhEXPA4 expression was repressed in RhNAC2-silenced rose petals, and the amino-terminal binding domain of RhNAC2 bound to the RhEXPA4 promoter. Twenty cell wall-related genes, including seven expansin family members, were up-regulated in Arabidopsis plants overexpressing RhNAC2. These data indicate that RhNAC2 and RhEXPA4 are involved in the regulation of dehydration tolerance during the expansion of rose petals and that RhEXPA4 expression may be regulated by RhNAC2.
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127
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Liu H, Ouyang B, Zhang J, Wang T, Li H, Zhang Y, Yu C, Ye Z. Differential modulation of photosynthesis, signaling, and transcriptional regulation between tolerant and sensitive tomato genotypes under cold stress. PLoS One 2012; 7:e50785. [PMID: 23226384 PMCID: PMC3511270 DOI: 10.1371/journal.pone.0050785] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/24/2012] [Indexed: 11/25/2022] Open
Abstract
The wild species Solanum habrochaites is more cold tolerant than the cultivated tomato (S. lycopersicum). To explore the mechanisms underlying cold tolerance of S. habrochaites, seedlings of S. habrochaites LA1777 introgression lines (ILs), as well as the two parents, were evaluated under low temperature (4°C). The IL LA3969 and its donor parent LA1777 were found to be more cold tolerant than the recurrent parent S. lycopersicum LA4024. The differences in physiology and global gene expression between cold-tolerant (LA1777 and LA3969) and -sensitive (LA4024) genotypes under cold stress were further investigated. Comparative transcriptome analysis identified 1613, 1456, and 1523 cold-responsive genes in LA1777, LA3969, and LA4024, respectively. Gene ontology (GO) term enrichment analysis revealed that more GO biological process terms were significantly enriched among the up-regulated genes in the two tolerant genotypes, whereas more biological processes were significantly repressed by cold stress in the sensitive one. A total of 92 genes with significant differential expression between tolerant and sensitive genotypes under cold stress were identified. Among these, many stress-related GO terms were significantly enriched, such as 'response to stimulus' and 'response to stress'. Moreover, GO terms 'response to hormone stimulus', 'response to reactive oxygen species (ROS)', and 'calcium-mediated signaling' were also overrepresented. Several transcripts involved in hormone or ROS homeostasis were also differentially expressed. ROS, hormones, and calcium as signaling molecules may play important roles in regulating gene expression in response to cold stress. Moreover, the expression of various transcription factors, post-translational proteins, metabolic enzymes, and photosynthesis-related genes was also specifically modulated. These specific modifications may play pivotal roles in conferring cold tolerance in tomato. These results not only provide new insights into the molecular mechanisms of cold tolerance in tomato, but also provide potential candidate genes for genetic improvement.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yuyang Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Chuying Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
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128
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Ali Z, Zhang DY, Xu ZL, Xu L, Yi JX, He XL, Huang YH, Liu XQ, Khan AA, Trethowan RM, Ma HX. Uncovering the salt response of soybean by unraveling its wild and cultivated functional genomes using tag sequencing. PLoS One 2012; 7:e48819. [PMID: 23209559 PMCID: PMC3509101 DOI: 10.1371/journal.pone.0048819] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 10/01/2012] [Indexed: 11/19/2022] Open
Abstract
Soil salinity has very adverse effects on growth and yield of crop plants. Several salt tolerant wild accessions and cultivars are reported in soybean. Functional genomes of salt tolerant Glycine soja and a salt sensitive genotype of Glycine max were investigated to understand the mechanism of salt tolerance in soybean. For this purpose, four libraries were constructed for Tag sequencing on Illumina platform. We identify around 490 salt responsive genes which included a number of transcription factors, signaling proteins, translation factors and structural genes like transporters, multidrug resistance proteins, antiporters, chaperons, aquaporins etc. The gene expression levels and ratio of up/down-regulated genes was greater in tolerant plants. Translation related genes remained stable or showed slightly higher expression in tolerant plants under salinity stress. Further analyses of sequenced data and the annotations for gene ontology and pathways indicated that soybean adapts to salt stress through ABA biosynthesis and regulation of translation and signal transduction of structural genes. Manipulation of these pathways may mitigate the effect of salt stress thus enhancing salt tolerance.
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Affiliation(s)
- Zulfiqar Ali
- Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Da Yong Zhang
- Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Zhao Long Xu
- Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Ling Xu
- Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Jin Xin Yi
- Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xiao Lan He
- Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Yi Hong Huang
- Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xiao Qing Liu
- Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Asif Ali Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Richard M. Trethowan
- Plant Breeding Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Hong Xiang Ma
- Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
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129
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Li J, Sima W, Ouyang B, Wang T, Ziaf K, Luo Z, Liu L, Li H, Chen M, Huang Y, Feng Y, Hao Y, Ye Z. Tomato SlDREB gene restricts leaf expansion and internode elongation by downregulating key genes for gibberellin biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:6407-20. [PMID: 23077200 PMCID: PMC3504492 DOI: 10.1093/jxb/ers295] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants have evolved and adapted to different environments. Dwarfism is an adaptive trait of plants that helps them avoid high-energy costs under unfavourable conditions. The role of gibberellin (GA) in plant development has been well established. Several plant dehydration-responsive element-binding proteins (DREBs) have been identified and reported to be induced under abiotic and biotic stress conditions. A tomato DREB gene named SlDREB, which is a transcription factor and was cloned from cultivated tomato M82, was found to play a negative role in tomato plant architecture and enhances drought tolerance. Tissue expression profiles indicated that SlDREB was expressed mainly in the stem and leaf and could be induced by abscisic acid (ABA) but suppressed by GA and ethylene. SlDREB altered plant morphology by restricting leaf expansion and internode elongation when overexpressed, and the resulting dwarfism of tomato plants could be recovered by application of exogenous gibberellic acid (GA(3)). Transcriptional analysis of transgenic plants revealed that overexpression of SlDREB caused the dwarf phenotype by downregulating key genes involved in GA biosynthesis such as ent-copalyl diphosphate synthase (SlCPS) and GA 20-oxidases (SlGA20ox1, -2, and -4), thereby decreasing endogenous GA levels in transgenic plants. A yeast activity assay demonstrated that SlDREB specifically bound to dehydration-responsive element/C-repeat (DRE/CRT) elements of the SlCPS promoter region. Taken together, these data demonstrated that SlDREB can downregulate the expression of key genes required for GA biosynthesis and that it acts as a positive regulator in drought stress responses by restricting leaf expansion and internode elongation.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wei Sima
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Khurram Ziaf
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zhidan Luo
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lifeng Liu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mingluan Chen
- 2 Key Laboratory of Analytical Chemistry for Biology and Medicine (MOE), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yunqing Huang
- 2 Key Laboratory of Analytical Chemistry for Biology and Medicine (MOE), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yuqi Feng
- 2 Key Laboratory of Analytical Chemistry for Biology and Medicine (MOE), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yanhong Hao
- 2 Key Laboratory of Analytical Chemistry for Biology and Medicine (MOE), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, PR China
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130
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Loukehaich R, Wang T, Ouyang B, Ziaf K, Li H, Zhang J, Lu Y, Ye Z. SpUSP, an annexin-interacting universal stress protein, enhances drought tolerance in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5593-606. [PMID: 22915741 PMCID: PMC3444279 DOI: 10.1093/jxb/ers220] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Universal stress protein (USP) appears to play an active role in the abiotic stress response, but their functions remain largely unknown in plants. A USP gene (SpUSP) was cloned from wild tomato (Solanum pennellii) and functionally characterized in cultivated tomato in the present study. The SpUSP transcript is abundantly accumulated in leaf stomata and its expression varied with the circadian rhythm. SpUSP was remarkably induced by dehydration, salt stress, oxidative stress, and the phytohormone abscisic acid (ABA) etc. This protein was predominantly localized in the nucleus and cell membrane. Overexpressing SpUSP increased drought tolerance of tomato in the seedling and adult stages. Under drought stress, the ABA content significantly increased in the SpUSP-overexpressing plants, which induced stomatal closure and reduced water loss, leading to the enhancement of drought tolerance. Based on the microarray data, a large number of chlorophyll a/b-binding proteins and photosystem-related genes were up-regulated in the SpUSP-overexpressing plants under drought conditions, which possibly enhanced the stomatal sensivitity to ABA and maintained the photosynthetic function. SpUSP overexpression also alleviated the oxidative damage accompanied by oxidative stress-responsive gene activation and osmolyte accumulation. Annexin (SGN-U314161) was found to interacte with SpUSP in the yeast two-hybrid method. This interaction was further confirmed by the bimolecular fluorescence complementation assay. The present study demonstrated that the annexin-interacting SpUSP plays important roles in the drought tolerance of tomato by influencing ABA-induced stomatal movement, increasing photosynthesis, and alleviating oxidative stress.
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Affiliation(s)
| | - Taotao Wang
- These authors contributed equally to the article
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, and National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan 430070China
| | - Khurram Ziaf
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, and National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan 430070China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, and National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan 430070China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, and National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan 430070China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, and National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan 430070China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, and National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan 430070China
- To whom correspondence should be addressed: E-mail:
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131
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Soares-Cavalcanti NM, Belarmino LC, Kido EA, Wanderley-Nogueira AC, Bezerra-Neto JP, Cavalcanti-Lira R, Pandolfi V, Nepomuceno AL, Abdelnoor RV, Nascimento LC, Benko-Iseppon AM. In silico identification of known osmotic stress responsive genes from Arabidopsis in soybean and Medicago. Genet Mol Biol 2012; 35:315-21. [PMID: 22802716 PMCID: PMC3392883 DOI: 10.1590/s1415-47572012000200012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Plants experience various environmental stresses, but tolerance to these adverse conditions is a very complex phenomenon. The present research aimed to evaluate a set of genes involved in osmotic response, comparing soybean and medicago with the well-described Arabidopsis thaliana model plant. Based on 103 Arabidopsis proteins from 27 categories of osmotic stress response, comparative analyses against Genosoja and Medicago truncatula databases allowed the identification of 1,088 soybean and 1,210 Medicago sequences. The analysis showed a high number of sequences and high diversity, comprising genes from all categories in both organisms. Genes with unknown function were among the most representative, followed by transcription factors, ion transport proteins, water channel, plant defense, protein degradation, cellular structure, organization & biogenesis and senescence. An analysis of sequences with unknown function allowed the annotation of 174 soybean and 217 Medicago sequences, most of them concerning transcription factors. However, for about 30% of the sequences no function could be attributed using in silico procedures. The establishment of a gene set involved in osmotic stress responses in soybean and barrel medic will help to better understand the survival mechanisms for this type of stress condition in legumes.
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Affiliation(s)
- Nina M Soares-Cavalcanti
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, PE, Brazil
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132
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Moon SJ, Shin DJ, Kim BG, Byun MO. Putative fructose-1,6-bisphosphate aldolase 1 (AtFBA1) affects stress tolerance in yeast and Arabidopsis. ACTA ACUST UNITED AC 2012. [DOI: 10.5010/jpb.2012.39.2.106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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133
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Benešová M, Holá D, Fischer L, Jedelský PL, Hnilička F, Wilhelmová N, Rothová O, Kočová M, Procházková D, Honnerová J, Fridrichová L, Hniličková H. The physiology and proteomics of drought tolerance in maize: early stomatal closure as a cause of lower tolerance to short-term dehydration? PLoS One 2012; 7:e38017. [PMID: 22719860 PMCID: PMC3374823 DOI: 10.1371/journal.pone.0038017] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 05/02/2012] [Indexed: 01/05/2023] Open
Abstract
Understanding the response of a crop to drought is the first step in the breeding of tolerant genotypes. In our study, two maize (Zea mays L.) genotypes with contrasting sensitivity to dehydration were subjected to moderate drought conditions. The subsequent analysis of their physiological parameters revealed a decreased stomatal conductance accompanied by a slighter decrease in the relative water content in the sensitive genotype. In contrast, the tolerant genotype maintained open stomata and active photosynthesis, even under dehydration conditions. Drought-induced changes in the leaf proteome were analyzed by two independent approaches, 2D gel electrophoresis and iTRAQ analysis, which provided compatible but only partially overlapping results. Drought caused the up-regulation of protective and stress-related proteins (mainly chaperones and dehydrins) in both genotypes. The differences in the levels of various detoxification proteins corresponded well with the observed changes in the activities of antioxidant enzymes. The number and levels of up-regulated protective proteins were generally lower in the sensitive genotype, implying a reduced level of proteosynthesis, which was also indicated by specific changes in the components of the translation machinery. Based on these results, we propose that the hypersensitive early stomatal closure in the sensitive genotype leads to the inhibition of photosynthesis and, subsequently, to a less efficient synthesis of the protective/detoxification proteins that are associated with drought tolerance.
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Affiliation(s)
- Monika Benešová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Dana Holá
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Lukáš Fischer
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Petr L. Jedelský
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Laboratory of Mass Spectrometry, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - František Hnilička
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Naďa Wilhelmová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Olga Rothová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Marie Kočová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Dagmar Procházková
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jana Honnerová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Lenka Fridrichová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Helena Hniličková
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
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134
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Gu J, Weber K, Klemp E, Winters G, Franssen SU, Wienpahl I, Huylmans AK, Zecher K, Reusch TBH, Bornberg-Bauer E, Weber APM. Identifying core features of adaptive metabolic mechanisms for chronic heat stress attenuation contributing to systems robustness. Integr Biol (Camb) 2012; 4:480-93. [PMID: 22402787 DOI: 10.1039/c2ib00109h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The contribution of metabolism to heat stress may play a significant role in defining robustness and recovery of systems; either by providing the energy and metabolites required for cellular homeostasis, or through the generation of protective osmolytes. However, the mechanisms by which heat stress attenuation could be adapted through metabolic processes as a stabilizing strategy against thermal stress are still largely unclear. We address this issue through metabolomic and transcriptomic profiles for populations along a thermal cline where two seagrass species, Zostera marina and Zostera noltii, were found in close proximity. Significant changes captured by these profile comparisons could be detected, with a larger response magnitude observed in northern populations to heat stress. Sucrose, fructose, and myo-inositol were identified to be the most responsive of the 29 analyzed organic metabolites. Many key enzymes in the Calvin cycle, glycolysis and pentose phosphate pathways also showed significant differential expression. The reported comparison suggests that adaptive mechanisms are involved through metabolic pathways to dampen the impacts of heat stress, and interactions between the metabolome and proteome should be further investigated in systems biology to understand robust design features against abiotic stress.
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Affiliation(s)
- Jenny Gu
- Institute for Evolution and Biodiversity, University of Muenster, Germany.
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135
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Padmalatha KV, Dhandapani G, Kanakachari M, Kumar S, Dass A, Patil DP, Rajamani V, Kumar K, Pathak R, Rawat B, Leelavathi S, Reddy PS, Jain N, Powar KN, Hiremath V, Katageri IS, Reddy MK, Solanke AU, Reddy VS, Kumar PA. Genome-wide transcriptomic analysis of cotton under drought stress reveal significant down-regulation of genes and pathways involved in fibre elongation and up-regulation of defense responsive genes. PLANT MOLECULAR BIOLOGY 2012; 78:223-46. [PMID: 22143977 DOI: 10.1007/s11103-011-9857-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 11/08/2011] [Indexed: 05/06/2023]
Abstract
Cotton is an important source of natural fibre used in the textile industry and the productivity of the crop is adversely affected by drought stress. High throughput transcriptomic analyses were used to identify genes involved in fibre development. However, not much information is available on cotton genome response in developing fibres under drought stress. In the present study a genome wide transcriptome analysis was carried out to identify differentially expressed genes at various stages of fibre growth under drought stress. Our study identified a number of genes differentially expressed during fibre elongation as compared to other stages. High level up-regulation of genes encoding for enzymes involved in pectin modification and cytoskeleton proteins was observed at fibre initiation stage. While a large number of genes encoding transcription factors (AP2-EREBP, WRKY, NAC and C2H2), osmoprotectants, ion transporters and heat shock proteins and pathways involved in hormone (ABA, ethylene and JA) biosynthesis and signal transduction were up-regulated and genes involved in phenylpropanoid and flavonoid biosynthesis, pentose and glucuronate interconversions and starch and sucrose metabolism pathways were down-regulated during fibre elongation. This study showed that drought has relatively less impact on fibre initiation but has profound effect on fibre elongation by down-regulating important genes involved in cell wall loosening and expansion process. The comprehensive transcriptome analysis under drought stress has provided valuable information on differentially expressed genes and pathways during fibre development that will be useful in developing drought tolerant cotton cultivars without compromising fibre quality.
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136
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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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137
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Ziaf K, Loukehaich R, Gong P, Liu H, Han Q, Wang T, Li H, Ye Z. A multiple stress-responsive gene ERD15 from Solanum pennellii confers stress tolerance in tobacco. PLANT & CELL PHYSIOLOGY 2011; 52:1055-67. [PMID: 21576192 DOI: 10.1093/pcp/pcr057] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Wild species often show more tolerance to environmental stress factors than their cultivated counterparts. An early responsive-to-dehydration gene was cloned from a drought- and salt-tolerant wild tomato Solanum pennellii (SpERD15). SpERD15 transcript accumulated differentially in different organs, and was remarkably induced by dehydration, salinity, cold and treatment with plant growth regulators. The protein encoded by SpERD15 was predominantly localized in the nucleus. Interestingly, we found that the majority of the transgenic tobacco plants were co-suppressed along with the overexpressing line. Overexpressing plants manifested stress tolerance accompanied by the accumulation of more soluble sugars and proline, and limited lipid peroxidation compared with co-suppression lines, which were more sensitive than the wild type. The differential contents of these compatible solutes in different transgenic lines were related to the changes in the expression of the genes involved in the production of some important osmolytes (P5CS and Sucrose synthase). Reduced lipid peroxidation over a broad range of stress factors was in agreement with increased expression of stress-responsive genes (ADH and GAPDH). Overexpression of SpERD15 increased the efficiency of PSII (F(v)/F(m)) in transgenic tobacco plants by maintaining PSII quinone acceptors in a partially oxidized form. The results show that SpERD15 augments stress tolerance by enhancing the efficiency of PSII through the protection of cellular membranes, as conferred by the accumulation of compatible solutes and limited lipid peroxidation.
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MESH Headings
- Acclimatization
- Cells, Cultured
- Chlorophyll/analysis
- Cloning, Molecular
- Cold Temperature
- Droughts
- Gene Expression Regulation, Plant
- Genes, Plant
- Germination
- Lipid Peroxidation
- Malondialdehyde/analysis
- Oxidation-Reduction
- Phenotype
- Photosynthesis
- Photosystem II Protein Complex/physiology
- Phylogeny
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Plants, Genetically Modified/physiology
- Proline/analysis
- RNA Interference
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Salinity
- Seeds/physiology
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Solanum/genetics
- Solanum/metabolism
- Solanum/physiology
- Stress, Physiological
- Nicotiana/genetics
- Nicotiana/metabolism
- Nicotiana/physiology
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Affiliation(s)
- Khurram Ziaf
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
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138
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Deokar AA, Kondawar V, Jain PK, Karuppayil SM, Raju NL, Vadez V, Varshney RK, Srinivasan R. Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress. BMC PLANT BIOLOGY 2011; 11:70. [PMID: 21513527 PMCID: PMC3110109 DOI: 10.1186/1471-2229-11-70] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 04/22/2011] [Indexed: 05/19/2023]
Abstract
BACKGROUND Chickpea (Cicer arietinum L.) is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs) by suppression subtraction hybridization (SSH) to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea. RESULTS EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant) and ICC 1882 (drought resistant) exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs) (10 each) for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons), 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71%) unigenes showed significant BLASTX similarity (<1E-06) in the NCBI non-redundant (nr) database. Gene ontology functional classification terms (BLASTX results and GO term), were retrieved for 2006 (92.0%) sequences, and 656 sequences were further annotated with 812 Enzyme Commission (EC) codes and were mapped to 108 different KEGG pathways. In addition, expression status of 830 unigenes in response to terminal drought stress was evaluated using macro-array (dot blots). The expression of few selected genes was validated by northern blotting and quantitative real-time PCR assay. CONCLUSION Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide a better insight into the selection of candidate genes (both up- and downregulated) associated with drought tolerance. These results can be used to identify suitable targets for manipulating the drought-tolerance trait in chickpea.
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Affiliation(s)
- Amit A Deokar
- National Research Center on Plant Biotechnology, IARI Campus, New Delhi 110012, India
- School of Life Sciences, S.R.T.M. University, "Dnyanteerth", Vishnupuri, Nanded - 431 606, India
| | - Vishwajith Kondawar
- National Research Center on Plant Biotechnology, IARI Campus, New Delhi 110012, India
- School of Life Sciences, S.R.T.M. University, "Dnyanteerth", Vishnupuri, Nanded - 431 606, India
| | - Pradeep K Jain
- National Research Center on Plant Biotechnology, IARI Campus, New Delhi 110012, India
| | - S Mohan Karuppayil
- School of Life Sciences, S.R.T.M. University, "Dnyanteerth", Vishnupuri, Nanded - 431 606, India
| | - N L Raju
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, AP, India
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, AP, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, AP, India
- Genomics towards Gene Discovery Sub Programme, Generation Challenge Programme (GCP) c/o CIMMYT, Int. Apartado Postal 6-641, 06600, Mexico, DF Mexico
| | - R Srinivasan
- National Research Center on Plant Biotechnology, IARI Campus, New Delhi 110012, India
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139
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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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