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Huang LZ, Zhou M, Ding YF, Zhu C. Gene Networks Involved in Plant Heat Stress Response and Tolerance. Int J Mol Sci 2022; 23:ijms231911970. [PMID: 36233272 PMCID: PMC9569452 DOI: 10.3390/ijms231911970] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 12/03/2022] Open
Abstract
Global warming is an environmental problem that cannot be ignored. High temperatures seriously affect the normal growth and development of plants, and threaten the development of agriculture and the distribution and survival of species at risk. Plants have evolved complex but efficient mechanisms for sensing and responding to high temperatures, which involve the activation of numerous functional proteins, regulatory proteins, and non-coding RNAs. These mechanisms consist of large regulatory networks that regulate protein and RNA structure and stability, induce Ca2+ and hormone signal transduction, mediate sucrose and water transport, activate antioxidant defense, and maintain other normal metabolic pathways. This article reviews recent research results on the molecular mechanisms of plant response to high temperatures, highlighting future directions or strategies for promoting plant heat tolerance, thereby helping to identify the regulatory mechanisms of heat stress responses in plants.
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Affiliation(s)
| | | | - Yan-Fei Ding
- Correspondence: (Y.-F.D.); (C.Z.); Tel.: +86-571-8683-6090 (C.Z.)
| | - Cheng Zhu
- Correspondence: (Y.-F.D.); (C.Z.); Tel.: +86-571-8683-6090 (C.Z.)
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2
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Norero NS, Rey Burusco MF, D’Ippólito S, Décima Oneto CA, Massa GA, Castellote MA, Feingold SE, Guevara MG. Genome-Wide Analyses of Aspartic Proteases on Potato Genome ( Solanum tuberosum): Generating New Tools to Improve the Resistance of Plants to Abiotic Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040544. [PMID: 35214878 PMCID: PMC8875628 DOI: 10.3390/plants11040544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/04/2021] [Accepted: 01/06/2022] [Indexed: 05/11/2023]
Abstract
Aspartic proteases are proteolytic enzymes widely distributed in living organisms and viruses. Although they have been extensively studied in many plant species, they are poorly described in potatoes. The present study aimed to identify and characterize S. tuberosum aspartic proteases. Gene structure, chromosome and protein domain organization, phylogeny, and subcellular predicted localization were analyzed and integrated with RNAseq data from different tissues, organs, and conditions focused on abiotic stress. Sixty-two aspartic protease genes were retrieved from the potato genome, distributed in 12 chromosomes. A high number of intronless genes and segmental and tandem duplications were detected. Phylogenetic analysis revealed eight StAP groups, named from StAPI to StAPVIII, that were differentiated into typical (StAPI), nucellin-like (StAPIIIa), and atypical aspartic proteases (StAPII, StAPIIIb to StAPVIII). RNAseq data analyses showed that gene expression was consistent with the presence of cis-acting regulatory elements on StAP promoter regions related to water deficit. The study presents the first identification and characterization of 62 aspartic protease genes and proteins on the potato genome and provides the baseline material for functional gene determinations and potato breeding programs, including gene editing mediated by CRISPR.
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Affiliation(s)
- Natalia Sigrid Norero
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - María Florencia Rey Burusco
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
- Faculty of Agricultural Sciences, University National of Mar del Plata, Balcarce B7620, Argentina
| | - Sebastián D’Ippólito
- Institute of Biological Research, University of Mar del Plata (IIB-UNMdP), Mar del Plata B7600, Argentina;
- National Scientific and Technical Research Council, Argentina (CONICET), Buenos Aires C1499, Argentina
| | - Cecilia Andrea Décima Oneto
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - Gabriela Alejandra Massa
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
- Faculty of Agricultural Sciences, University National of Mar del Plata, Balcarce B7620, Argentina
| | - Martín Alfredo Castellote
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - Sergio Enrique Feingold
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - María Gabriela Guevara
- Institute of Biological Research, University of Mar del Plata (IIB-UNMdP), Mar del Plata B7600, Argentina;
- National Scientific and Technical Research Council, Argentina (CONICET), Buenos Aires C1499, Argentina
- Correspondence: or
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3
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Cuesta-Seijo JA, De Porcellinis AJ, Valente AH, Striebeck A, Voss C, Marri L, Hansson A, Jansson AM, Dinesen MH, Fangel JU, Harholt J, Popovic M, Thieme M, Hochmuth A, Zeeman SC, Mikkelsen TN, J�rgensen RB, Roitsch TG, M�ller BL, Braumann I. Amylopectin Chain Length Dynamics and Activity Signatures of Key Carbon Metabolic Enzymes Highlight Early Maturation as Culprit for Yield Reduction of Barley Endosperm Starch after Heat Stress. PLANT & CELL PHYSIOLOGY 2019; 60:2692-2706. [PMID: 31397873 PMCID: PMC6896705 DOI: 10.1093/pcp/pcz155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/30/2019] [Indexed: 05/30/2023]
Abstract
Abiotic environmental stresses have a negative impact on the yield and quality of crops. Understanding these stresses is an essential enabler for mitigating breeding strategies and it becomes more important as the frequency of extreme weather conditions increases due to climate change. This study analyses the response of barley (Hordeum vulgare L.) to a heat wave during grain filling in three distinct stages: the heat wave itself, the return to a normal temperature regime, and the process of maturation and desiccation. The properties and structure of the starch produced were followed throughout the maturational stages. Furthermore, the key enzymes involved in the carbohydrate supply to the grain were monitored. We observed differences in starch structure with well-separated effects because of heat stress and during senescence. Heat stress produced marked effects on sucrolytic enzymes in source and sink tissues. Early cessation of plant development as an indirect consequence of the heat wave was identified as the major contributor to final yield loss from the stress, highlighting the importance for functional stay-green traits for the development of heat-resistant cereals.
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Affiliation(s)
| | | | | | - Alexander Striebeck
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Cynthia Voss
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Lucia Marri
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Andreas Hansson
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Anita M Jansson
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | | | - Jonatan Ulrik Fangel
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Jesper Harholt
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Milan Popovic
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Hojbakkegard Alle, 2630 Taastrup, Denmark
| | - Mercedes Thieme
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
- Institute of Molecular Plant Biology, ETH Zurich, Zurich 8092, Switzerland
| | - Anton Hochmuth
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
- Institute of Molecular Plant Biology, ETH Zurich, Zurich 8092, Switzerland
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Zurich 8092, Switzerland
| | - Teis N�rgaard Mikkelsen
- Atmospheric Environment, DTU Environmental engineering, Technical University of Denmark, Building 115, 2800 Kgs, Lyngby, Denmark
| | - Rikke Bagger J�rgensen
- Atmospheric Environment, DTU Environmental engineering, Technical University of Denmark, Building 115, 2800 Kgs, Lyngby, Denmark
| | - Thomas Georg Roitsch
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Hojbakkegard Alle, 2630 Taastrup, Denmark
| | - Birger Lindberg M�ller
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Ilka Braumann
- Carlsberg Research Laboratory, J.C, Jacobsens Gade 4, 1799 Copenhagen V, Denmark
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4
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Feng ZJ, Liu N, Zhang GW, Niu FG, Xu SC, Gong YM. Investigation of the AQP Family in Soybean and the Promoter Activity of TIP2;6 in Heat Stress and Hormone Responses. Int J Mol Sci 2019; 20:E262. [PMID: 30634702 PMCID: PMC6359280 DOI: 10.3390/ijms20020262] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/29/2018] [Accepted: 01/07/2019] [Indexed: 12/22/2022] Open
Abstract
Aquaporins (AQPs) are one diverse family of membrane channel proteins that play crucial regulatory roles in plant stress physiology. However, the heat stress responsiveness of AQP genes in soybean remains poorly understood. In this study, 75 non-redundant AQP encoding genes were identified in soybean. Multiple sequence alignments showed that all GmAQP proteins possessed the conserved regions, which contained 6 trans-membrane domains (TM1 to TM6). Different GmAQP members consisted of distinct Asn-Pro-Ala (NPA) motifs, aromatic/arginine (ar/R) selectivity filters and Froger's positions (FPs). Phylogenetic analyses distinguished five sub-families within these GmAQPs: 24 GmPIPs, 24 GmTIPs, 17 GmNIPs, 8 GmSIPs, and 2 GmXIPs. Promoter cis-acting elements analyses revealed that distinct number and composition of heat stress and hormone responsive elements existed in different promoter regions of GmAQPs. QRT-PCR assays demonstrated that 12 candidate GmAQPs with relatively extensive expression in various tissues or high expression levels in root or leaf exhibited different expression changes under heat stress and hormone cues (abscisic acid (ABA), l-aminocyclopropane-l-carboxylic acid (ACC), salicylic acid (SA) and methyl jasmonate (MeJA)). Furthermore, the promoter activity of one previously functionally unknown AQP gene-GmTIP2;6 was investigated in transgenic Arabidopsis plants. The beta-glucuronidase (GUS) activity driven by the promoter of GmTIP2;6 was strongly induced in the heat- and ACC-treated transgenic plants and tended to be accumulated in the hypocotyls, vascular bundles, and leaf trichomes. These results will contribute to uncovering the potential functions and molecular mechanisms of soybean GmAQPs in mediating heat stress and hormone signal responses.
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Affiliation(s)
- Zhi-Juan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Gu-Wen Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Fu-Ge Niu
- Food Safety Key Lab of Zhejiang Province, The School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China.
| | - Sheng-Chun Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Ya-Ming Gong
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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5
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Cao J, Gulyás Z, Kalapos B, Boldizsár Á, Liu X, Pál M, Yao Y, Galiba G, Kocsy G. Identification of a redox-dependent regulatory network of miRNAs and their targets in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:85-99. [PMID: 30260414 DOI: 10.1093/jxb/ery339] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
Reactive oxygen species and antioxidants have an important role in the regulation of plant growth and development under both optimal and stress conditions. In this study, we investigate a possible redox control of miRNAs in wheat (Triticum aestivum ssp. aestivum). Treatment of seedlings with 10 mM H2O2 via the roots for 24 h resulted in decreased glutathione content, increased half-cell reduction potential of the glutathione disulphide/glutathione redox pair, and greater ascorbate peroxidase activity compared to the control plants. These changes were accompanied by alterations in the miRNA transcript profile, with 70 miRNAs being identified with at least 1.5-fold difference in their expression between control and treated (0, 3, 6 h) seedlings. Degradome sequencing identified 86 target genes of these miRNAs, and 6722 possible additional target genes were identified using bioinformatics tools. The H2O2-responsiveness of 1647 target genes over 24 h of treatment was also confirmed by transcriptome analysis, and they were mainly found to be related to the control of redox processes, transcription, and protein phosphorylation and degradation. In a time-course experiment (0-24 h of treatment) a correlation was found between the levels of glutathione, other antioxidants, and the transcript levels of the H2O2-responsive miRNAs and their target mRNAs. This relationship together with bioinformatics modelling of the regulatory network indicated glutathione-related redox control of miRNAs and their targets, which allows the adjustment of the metabolism to changing environmental conditions.
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Affiliation(s)
- Jie Cao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
| | - Zsolt Gulyás
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Balázs Kalapos
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
- Festetics Doctoral School, Georgikon Faculty, University of Pannonia, Keszthely, Deák Ferenc str. 16., Hungary
| | - Ákos Boldizsár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
| | - Magda Pál
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
| | - Gábor Galiba
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
- Festetics Doctoral School, Georgikon Faculty, University of Pannonia, Keszthely, Deák Ferenc str. 16., Hungary
| | - Gábor Kocsy
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
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6
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Lawas LMF, Zuther E, Jagadish SK, Hincha DK. Molecular mechanisms of combined heat and drought stress resilience in cereals. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:212-217. [PMID: 29673612 DOI: 10.1016/j.pbi.2018.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/26/2018] [Accepted: 04/04/2018] [Indexed: 05/22/2023]
Abstract
Global climate change leads to increased temperatures and decreased precipitation in many parts of the world. The simultaneous occurrence of high temperature and water deficit results in heat stress damage in plants. Cereals provide the majority of calories for human consumption, making this stress scenario particularly threatening for global food security. Several studies in both dicots and cereals indicate that the molecular reactions of plants to combined stresses cannot be predicted from reactions to single stresses. Recent results indicate that the regulation of heat shock proteins and of sugar transport and accumulation in flowers are crucial factors determining resilience of tolerant genotypes to combined heat and drought stress.
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Affiliation(s)
- Lovely Mae F Lawas
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Ellen Zuther
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | | | - Dirk K Hincha
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany.
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7
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Gupta S, Mishra VK, Kumari S, Raavi, Chand R, Varadwaj PK. Deciphering genome-wide WRKY gene family of Triticum aestivum L. and their functional role in response to Abiotic stress. Genes Genomics 2018; 41:79-94. [PMID: 30238225 DOI: 10.1007/s13258-018-0742-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/11/2018] [Indexed: 12/18/2022]
Abstract
WRKY transcription factors (TFs) act in regulating plant growth and development as well as in response to different stress. Some earlier studies done by individual researchers reported different wheat WRKY TFs. Although, the recently released wheat genome has opened an avenue to investigate wheat WRKYs (TaWRKY) TFs. Prime objective of this study to performed genome-wide classifications of TaWRKYs and their functional annotation. The classification of 107 individual identified characterized sequences of TaWRKY (IICS-TaWRKY) and 160 uncharacterized draft sequences of TaWRKY (UDS-TaWRKY), along with their gene structures and motifs analysis was performed. Along with comparative sequence analysis and microarray analysis was performed to mimic out TaWRKYs functions in response to different abiotic stresses, accompanied by in-vitro validation. The comparative phylogenetic analysis and estimation of Ka/Ks ratio with Triticum urartu, illustrate group based clasifications of TaWRKYs and evolutionary divergences. Furthermore, motif-based and protein-DNA interaction analysis of TaWRKYs helps to identify, their putative function in target DNA recognition sites. Subsequently, results of microarray and comparative sequence analysis provides the evidence of TaWRKYs involved in heat and/or drought stress. Further, in-vitro results validates that TaWRKY014, TaWRKY090 are found to participate in response of drought stress, whereas TaWRKY008, TaWRKY122, and WRKY45 are involved in response of heat and drought stress. These findings can be utilized in developing novel heat and drought-tolerant wheat cultivars using marker-assisted breeding and transgenic development.
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Affiliation(s)
- Saurabh Gupta
- Department of Applied Sciences, Indian Institute of Information Technology, Deoghat, Jhalwa, Allahabad, 211015, India.,AgriGenome Labs Pvt. Ltd., Hyderabad, 500078, India
| | - Vinod Kumar Mishra
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sunita Kumari
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Raavi
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, 02215, USA
| | - Ramesh Chand
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Deoghat, Jhalwa, Allahabad, 211015, India.
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Liu Z, Qin J, Tian X, Xu S, Wang Y, Li H, Wang X, Peng H, Yao Y, Hu Z, Ni Z, Xin M, Sun Q. Global profiling of alternative splicing landscape responsive to drought, heat and their combination in wheat (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2018; 16:714-726. [PMID: 28834352 PMCID: PMC5814593 DOI: 10.1111/pbi.12822] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/17/2017] [Accepted: 08/10/2017] [Indexed: 05/13/2023]
Abstract
Plant can acquire tolerance to environmental stresses via transcriptome reprogramming at transcriptional and alternative splicing (AS) levels. However, how AS coordinates with transcriptional regulation to contribute to abiotic stresses responses is still ambiguous. In this study, we performed genome-wide analyses of AS responses to drought stress (DS), heat stress (HS) and their combination (HD) in wheat seedlings, and further compared them with transcriptional responses. In total, we found 200, 3576 and 4056 genes exhibiting significant AS pattern changes in response to DS, HS and HD, respectively, and combined drought and heat stress can induce specific AS compared with individual one. In addition, wheat homeologous genes exhibited differential AS responses under stress conditions that more AS events occurred on B subgenome than on A and D genomes. Comparison of genes regulated at AS and transcriptional levels showed that only 12% of DS-induced AS genes were subjected to transcriptional regulation, whereas the proportion increased to ~40% under HS and HD. Functional enrichment analysis revealed that abiotic stress-responsive pathways tended to be highly overrepresented among these overlapped genes under HS and HD. Thus, we proposed that transcriptional regulation may play a major role in response to DS, which coordinates with AS regulation to contribute to HS and HD tolerance in wheat.
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Affiliation(s)
- Zhenshan Liu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Jinxia Qin
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Xuejun Tian
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Yu Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Hongxia Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Huiru Peng
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Yingyin Yao
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zhaorong Hu
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zhongfu Ni
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Mingming Xin
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Qixin Sun
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
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9
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Kalapos B, Dobrev P, Nagy T, Vítámvás P, Györgyey J, Kocsy G, Marincs F, Galiba G. Transcript and hormone analyses reveal the involvement of ABA-signalling, hormone crosstalk and genotype-specific biological processes in cold-shock response in wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 253:86-97. [PMID: 27969000 DOI: 10.1016/j.plantsci.2016.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
The effect of one-day cold-shock on the transcriptome and phytohormones (auxin, cytokinins, abscisic, jasmonic and salicylic acids) was characterised in freezing-sensitive (Chinese Spring), highly freezing-tolerant (Cheyenne) and moderately freezing-tolerant (Chinese Spring substituted with Cheyenne's 5A chromosome) wheat genotypes. Altogether, 636 differentially expressed genes responding to cold-shock were identified. Defence genes encoding LEA proteins, dehydrins, chaperons and other temperature-stress responsive proteins were up-regulated in a genotype-independent manner. Abscisic acid was up-regulated by cold accompanied by adherent expression of its metabolic genes. Data revealed the involvement of particular routes within ABA-dependent signalling in response to cold-shock in the examined genotypes. Cold-shock affected gene expression along carbohydrate metabolic pathways. In photosynthesis, cold-shock changed the expression of a number of genes in the same way as it was previously reported for ABA. Overrepresentation analysis of the differentially expressed genes supported the ABA-signalling and carbohydrate metabolism results, and revealed some pronounced biological process GO categories associated with the cold-shock response of the genotypes. Protein network analysis indicated differences between the genotypes in the information flow along their signal perception and transduction, suggesting different biochemical and cellular strategies in their reaction to cold-shock.
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Affiliation(s)
- Balázs Kalapos
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, 2462 Martonvásár, Brunszvik u. 2, Hungary; Festetics Doctoral School, Georgikon Faculty, University of Pannonia, 8360, Keszthely, Festetics u. 7, Hungary.
| | - Petre Dobrev
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 165 02 Praha 6, Czech Republic.
| | - Tibor Nagy
- Agricultural Biotechnology Institute, NAIK, 2100 Gödöllő, Szent-Györgyi Albert u. 4, Hungary.
| | - Pavel Vítámvás
- Department of Genetics and Plant Breeding, Crop Research Institute, Drnovska 507/73 16106 Prague 6, Czech Republic.
| | - János Györgyey
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, 6726, Szeged, Temesvári krt. 62, Hungary.
| | - Gábor Kocsy
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, 2462 Martonvásár, Brunszvik u. 2, Hungary.
| | - Ferenc Marincs
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, 2462 Martonvásár, Brunszvik u. 2, Hungary; Agricultural Biotechnology Institute, NAIK, 2100 Gödöllő, Szent-Györgyi Albert u. 4, Hungary.
| | - Gábor Galiba
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, 2462 Martonvásár, Brunszvik u. 2, Hungary; Festetics Doctoral School, Georgikon Faculty, University of Pannonia, 8360, Keszthely, Festetics u. 7, Hungary.
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10
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Pandey P, Ramegowda V, Senthil-Kumar M. Shared and unique responses of plants to multiple individual stresses and stress combinations: physiological and molecular mechanisms. FRONTIERS IN PLANT SCIENCE 2015; 6:723. [PMID: 26442037 PMCID: PMC4584981 DOI: 10.3389/fpls.2015.00723] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/28/2015] [Indexed: 05/18/2023]
Abstract
In field conditions, plants are often simultaneously exposed to multiple biotic and abiotic stresses resulting in substantial yield loss. Plants have evolved various physiological and molecular adaptations to protect themselves under stress combinations. Emerging evidences suggest that plant responses to a combination of stresses are unique from individual stress responses. In addition, plants exhibit shared responses which are common to individual stresses and stress combination. In this review, we provide an update on the current understanding of both unique and shared responses. Specific focus of this review is on heat-drought stress as a major abiotic stress combination and, drought-pathogen and heat-pathogen as examples of abiotic-biotic stress combinations. We also comprehend the current understanding of molecular mechanisms of cross talk in relation to shared and unique molecular responses for plant survival under stress combinations. Thus, the knowledge of shared responses of plants from individual stress studies and stress combinations can be utilized to develop varieties with broad spectrum stress tolerance.
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Affiliation(s)
- Prachi Pandey
- National Institute of Plant Genome ResearchNew Delhi, India
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Liu Z, Xin M, Qin J, Peng H, Ni Z, Yao Y, Sun Q. Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2015; 15:152. [PMID: 26092253 PMCID: PMC4474349 DOI: 10.1186/s12870-015-0511-8] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/28/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Hexaploid wheat (Triticum aestivum) is a globally important crop. Heat, drought and their combination dramatically reduce wheat yield and quality, but the molecular mechanisms underlying wheat tolerance to extreme environments, especially stress combination, are largely unknown. As an allohexaploid, wheat consists of three closely related subgenomes (A, B, and D), and was reported to show improved tolerance to stress conditions compared to tetraploid. But so far very little is known about how wheat coordinates the expression of homeologous genes to cope with various environmental constraints on the whole-genome level. RESULTS To explore the transcriptional response of wheat to the individual and combined stress, we performed high-throughput transcriptome sequencing of seedlings under normal condition and subjected to drought stress (DS), heat stress (HS) and their combination (HD) for 1 h and 6 h, and presented global gene expression reprograms in response to these three stresses. Gene Ontology (GO) enrichment analysis of DS, HS and HD responsive genes revealed an overlap and complexity of functional pathways between each other. Moreover, 4,375 wheat transcription factors were identified on a whole-genome scale based on the released scaffold information by IWGSC, and 1,328 were responsive to stress treatments. Then, the regulatory network analysis of HSFs and DREBs implicated they were both involved in the regulation of DS, HS and HD response and indicated a cross-talk between heat and drought stress. Finally, approximately 68.4 % of homeologous genes were found to exhibit expression partitioning in response to DS, HS or HD, which was further confirmed by using quantitative RT-PCR and Nullisomic-Tetrasomic lines. CONCLUSIONS A large proportion of wheat homeologs exhibited expression partitioning under normal and abiotic stresses, which possibly contributes to the wide adaptability and distribution of hexaploid wheat in response to various environmental constraints.
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Affiliation(s)
- Zhenshan Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Jinxia Qin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
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Wang ZM, Li HX, Liu XF, He Y, Zeng HL. Reduction of pyruvate orthophosphate dikinase activity is associated with high temperature-induced chalkiness in rice grains. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 89:76-84. [PMID: 25725409 DOI: 10.1016/j.plaphy.2015.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/18/2015] [Indexed: 05/01/2023]
Abstract
Global warming affects both rice (Oryza sativa) yields and grain quality. Rice chalkiness due to high temperature during grain filling would lower the grain quality. The biochemical and molecular mechanisms responsible for the increased occurrence of chalkiness under high temperature are not fully understood. Previous research suggested that cytosolic pyruvate orthophosphate dikinase (cyPPDK, EC 2.7.9.1) in rice modulates carbon metabolism. The objective of this study was to determine the relationship between cyPPDK and high temperature-induced chalkiness. High temperature treatments were applied during the grain filling of two rice cultivars (9311 and TXZ-25) which had different sensitivity of chalkiness to high temperature. Chalkiness was increased significantly under high temperature treatment, especially for TXZ-25. A shortened grain filling duration and a decreased grain weight in both cultivars were caused by high temperature treatment. A reduction in PPDK activities due to high temperature was observed during the middle and late grain filling periods, accompanied by down regulated cyPPDK mRNA and protein levels. The temperature effects on the developmental regulation of PPDK activity were confirmed at transcription, translation and post-translational levels. PPDK activities were insensitive to variation in PPDK levels, suggesting the rapid phosphorylation mechanism of this protein. The two varieties showed similar responses to the high temperature treatment in both PPDK activities and chalkiness. We concluded that high temperature-induced chalkiness was associated with the reduction of PPDK activity.
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Affiliation(s)
- Zhen-mei Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hai-xia Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiong-feng Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying He
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Han-lai Zeng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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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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Jäger K, Fábián A, Eitel G, Szabó L, Deák C, Barnabás B, Papp I. A morpho-physiological approach differentiates bread wheat cultivars of contrasting tolerance under cyclic water stress. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1256-66. [PMID: 25014261 DOI: 10.1016/j.jplph.2014.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/15/2014] [Accepted: 04/15/2014] [Indexed: 05/21/2023]
Abstract
Leaf micromorphological traits and some physiological parameters with potential relevance to drought tolerance mechanisms were investigated in four selected winter wheat varieties. Plants were subjected to two cycles of drought treatment at anthesis. Yield components confirmed contrasting drought-sensitive and -tolerant behavior of the genotypes. Drought tolerance was associated with small flag leaf surfaces and less frequent occurrence of stomata. Substantial variation of leaf cuticular thickness was found among the cultivars. Thin cuticle coincided with drought sensitivity and correlated with a high rate of dark-adapted water loss from leaves. Unlike in Arabidopsis, thickening of the cuticular matrix in response to water deprivation did not occur. Water stress induced epicuticular wax crystal depositions preferentially on the abaxial leaf surfaces. According to microscopy and electrolyte leakage measurements from leaf tissues, membrane integrity was lost earlier or to a higher extent in sensitive than in tolerant genotypes. Cellular damage and a decline of relative water content of leaves in sensitive cultivars became distinctive during the second cycle of water deprivation. Our results indicate strong variation of traits with potential contribution to the complex phenotype of drought tolerance in wheat genotypes. The maintained membrane integrity and relative water content values during repeated water limited periods were found to correlate with drought tolerance in the selection of cultivars investigated.
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Affiliation(s)
- Katalin Jäger
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, 2462 Martonvásár, Hungary
| | - Attila Fábián
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, 2462 Martonvásár, Hungary
| | - Gabriella Eitel
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, 2462 Martonvásár, Hungary
| | - László Szabó
- Department of Functional and Structural Materials, Institute of Materials and Environmental Chemistry, Chemical Research Center, Hungarian Academy of Sciences, Pusztaszeri út 59-67, 1025 Budapest, Hungary
| | - Csilla Deák
- Department of Plant Physiology and Plant Biochemistry, Faculty of Horticultural Science, Corvinus University of Budapest, Villányi út 29-43, 1118 Budapest, Hungary
| | - Beáta Barnabás
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, 2462 Martonvásár, Hungary
| | - István Papp
- Department of Plant Physiology and Plant Biochemistry, Faculty of Horticultural Science, Corvinus University of Budapest, Villányi út 29-43, 1118 Budapest, Hungary.
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Drought tolerance in modern and wild wheat. ScientificWorldJournal 2013; 2013:548246. [PMID: 23766697 PMCID: PMC3671283 DOI: 10.1155/2013/548246] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/03/2013] [Indexed: 11/18/2022] Open
Abstract
The genus Triticum includes bread (Triticum aestivum) and durum wheat (Triticum durum) and constitutes a major source for human food consumption. Drought is currently the leading threat on world's food supply, limiting crop yield, and is complicated since drought tolerance is a quantitative trait with a complex phenotype affected by the plant's developmental stage. Drought tolerance is crucial to stabilize and increase food production since domestication has limited the genetic diversity of crops including wild wheat, leading to cultivated species, adapted to artificial environments, and lost tolerance to drought stress. Improvement for drought tolerance can be achieved by the introduction of drought-grelated genes and QTLs to modern wheat cultivars. Therefore, identification of candidate molecules or loci involved in drought tolerance is necessary, which is undertaken by "omics" studies and QTL mapping. In this sense, wild counterparts of modern varieties, specifically wild emmer wheat (T. dicoccoides), which are highly tolerant to drought, hold a great potential. Prior to their introgression to modern wheat cultivars, drought related candidate genes are first characterized at the molecular level, and their function is confirmed via transgenic studies. After integration of the tolerance loci, specific environment targeted field trials are performed coupled with extensive analysis of morphological and physiological characteristics of developed cultivars, to assess their performance under drought conditions and their possible contributions to yield in certain regions. This paper focuses on recent advances on drought related gene/QTL identification, studies on drought related molecular pathways, and current efforts on improvement of wheat cultivars for drought tolerance.
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Vincent J, Dai Z, Ravel C, Choulet F, Mouzeyar S, Bouzidi MF, Agier M, Martre P. dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat014. [PMID: 23660284 PMCID: PMC3649639 DOI: 10.1093/database/bat014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The functional annotation of genes based on sequence homology with genes from model species genomes is time-consuming because it is necessary to mine several unrelated databases. The aim of the present work was to develop a functional annotation database for common wheat Triticum aestivum (L.). The database, named dbWFA, is based on the reference NCBI UniGene set, an expressed gene catalogue built by expressed sequence tag clustering, and on full-length coding sequences retrieved from the TriFLDB database. Information from good-quality heterogeneous sources, including annotations for model plant species Arabidopsis thaliana (L.) Heynh. and Oryza sativa L., was gathered and linked to T. aestivum sequences through BLAST-based homology searches. Even though the complexity of the transcriptome cannot yet be fully appreciated, we developed a tool to easily and promptly obtain information from multiple functional annotation systems (Gene Ontology, MapMan bin codes, MIPS Functional Categories, PlantCyc pathway reactions and TAIR gene families). The use of dbWFA is illustrated here with several query examples. We were able to assign a putative function to 45% of the UniGenes and 81% of the full-length coding sequences from TriFLDB. Moreover, comparison of the annotation of the whole T. aestivum UniGene set along with curated annotations of the two model species assessed the accuracy of the annotation provided by dbWFA. To further illustrate the use of dbWFA, genes specifically expressed during the early cell division or late storage polymer accumulation phases of T. aestivum grain development were identified using a clustering analysis and then annotated using dbWFA. The annotation of these two sets of genes was consistent with previous analyses of T. aestivum grain transcriptomes and proteomes. Database URL:urgi.versailles.inra.fr/dbWFA/
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Affiliation(s)
- Jonathan Vincent
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, Clermont-Ferrand, F-63 039 Cedex 2, France
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Domoki M, Szűcs A, Jäger K, Bottka S, Barnabás B, Fehér A. Identification of genes preferentially expressed in wheat egg cells and zygotes. PLANT CELL REPORTS 2013; 32:339-48. [PMID: 23160639 DOI: 10.1007/s00299-012-1367-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/28/2012] [Accepted: 10/31/2012] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE : Wheat genes differentially expressed in the egg cell before and after fertilization were identified. The data support zygotic gene activation before the first cell division in wheat. To have an insight into fertilization-induced gene expression, cDNA libraries have been prepared from isolated wheat egg cells and one-celled zygotes. Two-hundred and twenty-six egg cell and 253 zygote-expressed EST sequences were determined. Most of the represented transcripts were detected in the wheat egg cell or zygote transcriptome at the first time. Expression analysis of fourteen of the identified genes and three controls was carried out by real-time quantitative PCR. The preferential expression of all investigated genes in the female gametophyte-derived samples (egg cells, zygotes, two-celled proembryos, and basal ovule parts with synergids) in comparison to the anthers, and the leaves were verified. Three genes with putative signaling/regulatory functions were expressed at a low level in the egg cell but exhibited increased (2-to-33-fold) relative expression in the zygote and the proembryo. Genes with high EST abundance in cDNA libraries exhibited strong expression in the egg cell and the zygote, while the ones coding for unknown or hypothetical proteins exhibited differential expression patterns with preferential transcript accumulation in egg cells and/or zygotes. The obtained data support the activation of the zygotic genome before the first cell division in wheat.
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Affiliation(s)
- Mónika Domoki
- Biological Research Centre, Institute of Plant Biology, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary
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Mittal D, Madhyastha DA, Grover A. Gene expression analysis in response to low and high temperature and oxidative stresses in rice: combination of stresses evokes different transcriptional changes as against stresses applied individually. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 197:102-13. [PMID: 23116677 DOI: 10.1016/j.plantsci.2012.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 09/16/2012] [Accepted: 09/18/2012] [Indexed: 05/04/2023]
Abstract
Transcript expression profiles of rice seedlings were analyzed in response to (a) prior exposure with oxidative stress followed by heat or cold stress and (b) simultaneous exposure to oxidative stress along with heat stress or cold stress. The numbers of genes differentially regulated during stress combination of cold and oxidative stress as well as heat and oxidative stress treatments were higher when compared with the number of genes differentially regulated in response to individual stress conditions. A large number of transcript changes were noted unique to the stress combination mode as compared with when individual stresses were applied. Specific differences in the transcript expression profiles of OsHsf and OsClp gene family members were noted during combination of stresses as against individual stresses. For instance, OsHsf26 induction was specific to stress combinations, while OsHsfA2a, OsHsfA2f, and OsHsfA3 transcript levels were additively affected during combination of stresses. Unique promoter models and transcription factor binding sites (i.e. P$KNOX3_01, P$OSBZ8_Q6) were noted in the promoters of differentially regulated genes during combination of stresses. It is proposed that stress combinations represent a novel state of abiotic stresses for rice seedlings that might involve a different type of molecular response.
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Affiliation(s)
- Dheeraj Mittal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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He JF, Goyal R, Laroche A, Zhao ML, Lu ZX. Water stress during grain development affects starch synthesis, composition and physicochemical properties in triticale. J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2012.07.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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New insights into the effects of high temperature, drought and post-anthesis fertilizer on wheat grain development. J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2011.12.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Capron D, Mouzeyar S, Boulaflous A, Girousse C, Rustenholz C, Laugier C, Paux E, Bouzidi MF. Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development. BMC PLANT BIOLOGY 2012; 12:35. [PMID: 22416807 PMCID: PMC3405487 DOI: 10.1186/1471-2229-12-35] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 03/14/2012] [Indexed: 05/23/2023]
Abstract
BACKGROUND Wheat grains are an important source of food, stock feed and raw materials for industry, but current production levels cannot meet world needs. Elucidation of the molecular mechanisms underlying wheat grain development will contribute valuable information to improving wheat cultivation. One of the most important mechanisms implicated in plant developmental processes is the ubiquitin-proteasome system (UPS). Among the different roles of the UPS, it is clear that it is essential to hormone signaling. In particular, E3 ubiquitin ligases of the UPS have been shown to play critical roles in hormone perception and signal transduction. RESULTS A NimbleGen microarray containing 39,179 UniGenes was used to study the kinetics of gene expression during wheat grain development from the early stages of cell division to the mid-grain filling stage. By comparing 11 consecutive time-points, 9284 differentially expressed genes were identified and annotated during this study. A comparison of the temporal profiles of these genes revealed dynamic transcript accumulation profiles with major reprogramming events that occurred during the time intervals of 80-120 and 220-240°Cdays. The list of the genes expressed differentially during these transitions were identified and annotated. Emphasis was placed on E3 ligase and hormone-related genes. In total, 173 E3 ligase coding genes and 126 hormone-related genes were differentially expressed during the cell division and grain filling stages, with each family displaying a different expression profile. CONCLUSIONS The differential expression of genes involved in the UPS and plant hormone pathways suggests that phytohormones and UPS crosstalk might play a critical role in the wheat grain developmental process. Some E3 ligase and hormone-related genes seem to be up- or down-regulated during the early and late stages of the grain development.
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Affiliation(s)
- Delphine Capron
- Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France
| | - Said Mouzeyar
- Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France
| | - Aurélia Boulaflous
- Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France
| | - Christine Girousse
- INRA, UMR 1095 GDEC, 234 avenue du Brézet, F-63100 Clermont-Ferrand, France
| | - Camille Rustenholz
- INRA, UMR 1095 GDEC, 234 avenue du Brézet, F-63100 Clermont-Ferrand, France
| | - Christel Laugier
- INRA, UMR 1095 GDEC, 234 avenue du Brézet, F-63100 Clermont-Ferrand, France
| | - Etienne Paux
- INRA, UMR 1095 GDEC, 234 avenue du Brézet, F-63100 Clermont-Ferrand, France
| | - Mohamed Fouad Bouzidi
- Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France
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