151
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Zheng Y, Ding Y, Sun X, Xie S, Wang D, Liu X, Su L, Wei W, Pan L, Zhou DX. Histone deacetylase HDA9 negatively regulates salt and drought stress responsiveness in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1703-13. [PMID: 26733691 DOI: 10.1093/jxb/erv562] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Histone modification is an important epigenetic regulation in higher plants adapting to environment changes including salt and drought stresses. In this report, we show that the Arabidopsis RPD3-type histone deacetylase HDA9 is involved in modulating plant responses to salt and drought stresses in Arabidopsis. Loss-of-function mutants of the gene displayed phenotypes (such as seedling root growth and seed germination) insensitive to NaCl and polyethylene glycol (PEG) treatments. HDA9 mutation led to up-regulation of many genes, among which those involved in response to water deprivation stress (GO: 0009414) were enriched. These genes were much more induced in the mutants than wild-type plants when treated with PEG and NaCl. In addition, we found that in the mutants, salt and drought stresses led to much higher levels of histone H3K9 acetylation at promoters of 14 genes randomly selected from those that respond to water-deprivation stress than in wild-type plants. Our study suggested that HDA9 might be a novel chromatin protein that negatively regulates plant sensitivity to salt and drought stresses by regulating histone acetylation levels of a large number of stress-responsive genes in Arabidopsis.
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Affiliation(s)
- Yu Zheng
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Yue Ding
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Xuan Sun
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Sisi Xie
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Dan Wang
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Lufang Su
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Wei Wei
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Lei Pan
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Dao-Xiu Zhou
- Institute of Plant Sciences Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
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152
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Li KQ, Xu XY, Huang XS. Identification of Differentially Expressed Genes Related to Dehydration Resistance in a Highly Drought-Tolerant Pear, Pyrus betulaefolia, as through RNA-Seq. PLoS One 2016; 11:e0149352. [PMID: 26900681 PMCID: PMC4762547 DOI: 10.1371/journal.pone.0149352] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/29/2016] [Indexed: 12/03/2022] Open
Abstract
Drought is a major abiotic stress that affects plant growth, development and productivity. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms of drought tolerance in this plant are still unclear. To better understand the molecular basis regarding drought stress response, RNA-seq was performed on samples collected before and after dehydration in Pyrus betulaefolia. In total, 19,532 differentially expressed genes (DEGs) were identified. These genes were annotated into 144 Gene Ontology (GO) terms and 18 clusters of orthologous groups (COG) involved in 129 Kyoto Encyclopedia of Genes and Genomes (KEGG) defined pathways. These DEGs comprised 49 (26 up-regulated, 23 down-regulated), 248 (166 up-regulated, 82 down-regulated), 3483 (1295 up-regulated, 2188 down-regulated), 1455 (1065 up-regulated, 390 down-regulated) genes from the 1 h, 3 h and 6 h dehydration-treated samples and a 24 h recovery samples, respectively. RNA-seq was validated by analyzing the expresson patterns of randomly selected 16 DEGs by quantitative real-time PCR. Photosynthesis, signal transduction, innate immune response, protein phosphorylation, response to water, response to biotic stimulus, and plant hormone signal transduction were the most significantly enriched GO categories amongst the DEGs. A total of 637 transcription factors were shown to be dehydration responsive. In addition, a number of genes involved in the metabolism and signaling of hormones were significantly affected by the dehydration stress. This dataset provides valuable information regarding the Pyrus betulaefolia transcriptome changes in response to dehydration and may promote identification and functional analysis of potential genes that could be used for improving drought tolerance via genetic engineering of non-model, but economically-important, perennial species.
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Affiliation(s)
- Kong-Qing Li
- College of Rural Development, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao-Yong Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Xiao-San Huang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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153
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Shaw AK, Bhardwaj PK, Ghosh S, Roy S, Saha S, Sherpa AR, Saha SK, Hossain Z. β-aminobutyric acid mediated drought stress alleviation in maize (Zea mays L.). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:2437-53. [PMID: 26416125 DOI: 10.1007/s11356-015-5445-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/16/2015] [Indexed: 05/23/2023]
Abstract
The present study highlights the role of β-aminobutyric acid (BABA) in alleviating drought stress effects in maize (Zea mays L.). Chemical priming was imposed by pretreating 1-week-old plants with 600 μM BABA prior to applying drought stress. Specific activities of key antioxidant enzymes and metabolites (ascorbate and glutathione) levels of ascorbate-glutathione cycle were studied to unravel the priming-induced modulation of plant defense system. Furthermore, changes in endogenous ABA and JA concentrations as well as mRNA expressions of key genes involved in their respective biosynthesis pathways were monitored in BABA-primed (BABA+) and non-primed (BABA-) leaves of drought-challenged plants to better understand the mechanistic insights into the BABA-induced hormonal regulation of plant response to water-deficit stress. Accelerated stomatal closure, high relative water content, and less membrane damage were observed in BABA-primed leaves under water-deficit condition. Elevated APX and SOD activity in non-primed leaves found to be insufficient to scavenge all H2O2 and O2 (·-) resulting in oxidative burst as evident after histochemical staining with NBT and DAB. A higher proline accumulation in non-primed leaves also does not give much protection against drought stress. Increased GR activity supported with the enhanced mRNA and protein expressions might help the BABA-primed plants to maintain a high GSH pool essential for sustaining balanced redox status to counter drought-induced oxidative stress damages. Hormonal analysis suggests that in maize, BABA-potentiated drought tolerance is primarily mediated through JA-dependent pathway by the activation of antioxidant defense systems while ABA biosynthesis pathway also plays an important role in fine-tuning of drought stress response.
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Affiliation(s)
- Arun K Shaw
- Plant Stress Biology Laboratory, Department of Botany, West Bengal State University, Kolkata, 700126, West Bengal, India
| | - Pardeep K Bhardwaj
- Plant Bioresources Division, Regional Centre of Institute of Bioresources and Sustainable Development, Gangtok, 737102, Sikkim, India
| | - Supriya Ghosh
- Plant Stress Biology Laboratory, Department of Botany, West Bengal State University, Kolkata, 700126, West Bengal, India
| | - Sankhajit Roy
- Department of Agricultural Chemicals, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, West Bengal, India
| | - Suman Saha
- Department of Agricultural Chemicals, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, West Bengal, India
| | - Ang R Sherpa
- Plant Stress Biology Laboratory, Department of Botany, West Bengal State University, Kolkata, 700126, West Bengal, India
| | - Samir K Saha
- Department of Zoology, West Bengal State University, Kolkata, 700126, West Bengal, India
| | - Zahed Hossain
- Department of Botany, University of Kalyani, Nadia, 741235, West Bengal, India.
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154
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Wang S, Zhang H, Zheng Y, Li Z, Xiang F, Ding Y, Xiang J. Environmental factors and phytohormones enhancing expression of α-momorcharin gene in Momordica charantia. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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155
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Suzuki N, Bassil E, Hamilton JS, Inupakutika MA, Zandalinas SI, Tripathy D, Luo Y, Dion E, Fukui G, Kumazaki A, Nakano R, Rivero RM, Verbeck GF, Azad RK, Blumwald E, Mittler R. ABA Is Required for Plant Acclimation to a Combination of Salt and Heat Stress. PLoS One 2016; 11:e0147625. [PMID: 26824246 PMCID: PMC4733103 DOI: 10.1371/journal.pone.0147625] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/06/2016] [Indexed: 11/30/2022] Open
Abstract
Abiotic stresses such as drought, heat or salinity are a major cause of yield loss worldwide. Recent studies revealed that the acclimation of plants to a combination of different environmental stresses is unique and cannot be directly deduced from studying the response of plants to each of the different stresses applied individually. Here we report on the response of Arabidopsis thaliana to a combination of salt and heat stress using transcriptome analysis, physiological measurements and mutants deficient in abscisic acid, salicylic acid, jasmonic acid or ethylene signaling. Arabidopsis plants were found to be more susceptible to a combination of salt and heat stress compared to each of the different stresses applied individually. The stress combination resulted in a higher ratio of Na+/K+ in leaves and caused the enhanced expression of 699 transcripts unique to the stress combination. Interestingly, many of the transcripts that specifically accumulated in plants in response to the salt and heat stress combination were associated with the plant hormone abscisic acid. In accordance with this finding, mutants deficient in abscisic acid metabolism and signaling were found to be more susceptible to a combination of salt and heat stress than wild type plants. Our study highlights the important role abscisic acid plays in the acclimation of plants to a combination of two different abiotic stresses.
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Affiliation(s)
- Nobuhiro Suzuki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7–1 Kioi-cho, Chiyoda-ku, 102–8554, Tokyo, Japan
- * E-mail: (NS); (RM)
| | - Elias Bassil
- Department of Plant Sciences, Mail Stop 5, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, United States of America
| | - Jason S. Hamilton
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Madhuri A. Inupakutika
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Sara Izquierdo Zandalinas
- Departamento de Ciencias Agrarias y del Medio Natural, Universitat Jaume I, Campus Riu Sec, E- 12071, Castello de la Plana, Spain
| | - Deesha Tripathy
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Yuting Luo
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Erin Dion
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Ginga Fukui
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7–1 Kioi-cho, Chiyoda-ku, 102–8554, Tokyo, Japan
| | - Ayana Kumazaki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7–1 Kioi-cho, Chiyoda-ku, 102–8554, Tokyo, Japan
| | - Ruka Nakano
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7–1 Kioi-cho, Chiyoda-ku, 102–8554, Tokyo, Japan
| | - Rosa M. Rivero
- Centro de Edafología y Biología Aplicada del Segura, Campus Universitario de Espinardo, Espinardo, Murcia, 30100, Spain
| | - Guido F. Verbeck
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
| | - Rajeev K. Azad
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
- Department of Mathematics, University of North Texas, Denton, TX, 76203, United States of America
| | - Eduardo Blumwald
- Department of Plant Sciences, Mail Stop 5, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, United States of America
| | - Ron Mittler
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203–5017, United States of America
- * E-mail: (NS); (RM)
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156
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Rasheed S, Bashir K, Matsui A, Tanaka M, Seki M. Transcriptomic Analysis of Soil-Grown Arabidopsis thaliana Roots and Shoots in Response to a Drought Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:180. [PMID: 26941754 PMCID: PMC4763085 DOI: 10.3389/fpls.2016.00180] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/02/2016] [Indexed: 05/04/2023]
Abstract
Drought stress has a negative impact on crop yield. Thus, understanding the molecular mechanisms responsible for plant drought stress tolerance is essential for improving this beneficial trait in crops. In the current study, a transcriptional analysis was conducted of gene regulatory networks in roots of soil-grown Arabidopsis plants in response to a drought stress treatment. A microarray analysis of drought-stressed roots and shoots was performed at 0, 1, 3, 5, 7, and 9 days. Results indicated that the expression of many drought stress-responsive genes and abscisic acid biosynthesis-related genes was differentially regulated in roots and shoots from days 3 to 9. The expression of cellular and metabolic process-related genes was up-regulated at an earlier time-point in roots than in shoots. In this regard, the expression of genes involved in oxidative signaling, chromatin structure, and cell wall modification also increased significantly in roots compared to shoots. Moreover, the increased expression of genes involved in the transport of amino acids and other solutes; including malate, iron, and sulfur, was observed in roots during the early time points following the initiation of the drought stress. These data suggest that plants may utilize these signaling channels and metabolic adjustments as adaptive responses in the early stages of a drought stress. Collectively, the results of the present study increases our understanding of the differences pertaining to the molecular mechanisms occurring in roots vs. shoots in response to a drought stress. Furthermore, these findings also aid in the selection of novel genes and promoters that can be used to potentially produce crop plants with increased drought tolerance.
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Affiliation(s)
- Sultana Rasheed
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
- CREST, Japan Science and Technology AgencySaitama, Japan
- *Correspondence: Motoaki Seki
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157
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Shavrukov Y, Baho M, Lopato S, Langridge P. The TaDREB3 transgene transferred by conventional crossings to different genetic backgrounds of bread wheat improves drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:313-22. [PMID: 25940960 DOI: 10.1111/pbi.12385] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 05/03/2023]
Abstract
Drought tolerance of the wheat cultivar Bobwhite was previously enhanced by transformation with a construct containing the wheat DREB3 gene driven by the stress-inducible maize Rab17 promoter. Progeny of a single T2 transgenic line were used as pollinators in crosses with four elite bread wheat cultivars from Western Australia: Bonnie Rock, IGW-2971, Magenta and Wyalkatchem, with the aim of evaluating transgene performance in different genetic backgrounds. The selected pollinator line, BW8-9-10-3, contained multiple transgene copies, had significantly improved drought tolerance compared with wild-type plants and showed no growth and development penalties or abnormalities. A single hybrid plant was selected from each cross-combination for three rounds of backcrossing with the corresponding maternal wheat cultivar. The transgene was detected in all four F1 BC3 combinations, but stress-inducible transgene expression was found in only three of the four combinations. Under well-watered conditions, the phenotypes and grain yield components of the F2 BC3 transgene-expressing lines were similar to those of corresponding recurrent parents and null-segregants. Under severe drought conditions, the backcross lines demonstrated 12-18% higher survival rates than the corresponding control plants. Two from four F3 BC3 transgenic lines showed significantly higher yield (18.9% and 21.5%) than control plants under limited water conditions. There was no induction of transgene expression under cold stress, and therefore, no improvement of frost tolerance observed in the progenies of drought-tolerant F3 BC3 lines.
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Affiliation(s)
- Yuri Shavrukov
- Australian Centre for Plant Functional Genomics, University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Manahil Baho
- Australian Centre for Plant Functional Genomics, University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Sergiy Lopato
- Australian Centre for Plant Functional Genomics, University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Peter Langridge
- Australian Centre for Plant Functional Genomics, University of Adelaide, Urrbrae, SA, 5064, Australia
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158
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Llanes A, Andrade A, Alemano S, Luna V. Alterations of Endogenous Hormonal Levels in Plants under Drought and Salinity. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/ajps.2016.79129] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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159
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Saha G, Park JI, Kayum MA, Nou IS. A Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of TIFY Family Genes in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2016; 7:936. [PMID: 27446164 PMCID: PMC4923152 DOI: 10.3389/fpls.2016.00936] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/13/2016] [Indexed: 05/13/2023]
Abstract
The TIFY family is a plant-specific group of proteins with a diversity of functions and includes four subfamilies, viz. ZML, TIFY, PPD, and JASMONATE ZIM-domain (JAZ) proteins. TIFY family members, particularly JAZ subfamily proteins, play roles in biological processes such as development and stress and hormone responses in Arabidopsis, rice, chickpea, and grape. However, there is no information about this family in any Brassica crop. This study identifies 36 TIFY genes in Brassica rapa, an economically important crop species in the Brassicaceae. An extensive in silico analysis of phylogenetic grouping, protein motif organization and intron-exon distribution confirmed that there are four subfamilies of BrTIFY proteins. Out of 36 BrTIFY genes, we identified 21 in the JAZ subfamily, seven in the TIFY subfamily, six in ZML and two in PPD. Extensive expression profiling of 21 BrTIFY JAZs in various tissues, especially in floral organs and at different flower growth stages revealed constitutive expression patterns, which suggest that BrTIFY JAZ genes are important during growth and development of B. rapa flowers. A protein interaction network analysis also pointed to association of these proteins with fertility and defense processes of B. rapa. Using a low temperature-treated whole-genome microarray data set, most of the JAZ genes were found to have variable transcript abundance between the contrasting inbred lines Chiifu and Kenshin of B. rapa. Subsequently, the expression of all 21 BrTIFY JAZs in response to cold stress was characterized in the same two lines via qPCR, demonstrating that nine genes were up-regulated. Importantly, the BrTIFY JAZs showed strong and differential expression upon JA treatment, pointing to their probable involvement in JA-mediated growth regulatory functions, especially during flower development and stress responses. Additionally, BrTIFY JAZs were induced in response to salt, drought, Fusarium, ABA, and SA treatments, and six genes (BrTIFY3a, 3b, 6a, 9a, 9b, and 9c) were identified to have co-responsive expression patterns. The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of TIFY genes in stress resistance and different developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate TIFY genes for genetic engineering of B. rapa.
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160
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Gruszka D, Janeczko A, Dziurka M, Pociecha E, Oklestkova J, Szarejko I. Barley Brassinosteroid Mutants Provide an Insight into Phytohormonal Homeostasis in Plant Reaction to Drought Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:1824. [PMID: 27994612 PMCID: PMC5133261 DOI: 10.3389/fpls.2016.01824] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/18/2016] [Indexed: 05/02/2023]
Abstract
Brassinosteroids (BRs) are a class of steroid phytohormones, which regulate various processes of morphogenesis and physiology-from seed development to regulation of flowering and senescence. An accumulating body of evidence indicates that BRs take part in regulation of physiological reactions to various stress conditions, including drought. Many of the physiological functions of BRs are regulated by a complicated, and not fully elucidated network of interactions with metabolic pathways of other phytohormones. Therefore, the aim of this study was to characterize phytohormonal homeostasis in barley (Hordeum vulgare) in reaction to drought and validate role of BRs in regulation of this process. Material of this study included the barley cultivar "Bowman" and five Near-Isogenic Lines (NILs) representing characterized semi-dwarf mutants of several genes encoding enzymes participating in BR biosynthesis and signaling. Analysis of endogenous BRs concentrations in these NILs confirmed that their phenotypes result from abnormalities in BR metabolism. In general, concentrations of 18 compounds, representing various classes of phytohormones, including brassinosteroids, auxins, cytokinins, gibberellins, abscisic acid, salicylic acid and jasmonic acid were analyzed under control and drought conditions in the "Bowman" cultivar and the BR-deficient NILs. Drought induced a significant increase in accumulation of the biologically active form of BRs-castasterone in all analyzed genotypes. Another biologically active form of BRs-24-epi-brassinolide-was identified in one, BR-insensitive NIL under normal condition, but its accumulation was drought-induced in all analyzed genotypes. Analysis of concentration profiles of several compounds representing gibberellins allowed an insight into the BR-dependent regulation of gibberellin biosynthesis. The concentration of the gibberellic acid GA7 was significantly lower in all NILs when compared with the "Bowman" cultivar, indicating that GA7 biosynthesis represents an enzymatic step at which the stimulating effect of BRs on gibberellin biosynthesis occurs. Moreover, the accumulation of GA7 is significantly induced by drought in all the genotypes. Biosynthesis of jasmonic acid is also a BR-dependent process, as all the NILs accumulated much lower concentrations of this hormone when compared with the "Bowman" cultivar under normal condition, however the accumulation of jasmonic acid, abscisic acid and salicylic acid were significantly stimulated by drought.
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Affiliation(s)
- Damian Gruszka
- Department of Genetics, Faculty of Biology and Environment Protection, University of SilesiaKatowice, Poland
- *Correspondence: Damian Gruszka
| | - Anna Janeczko
- Franciszek Gorski Institute of Plant Physiology, Polish Academy of SciencesKrakow, Poland
| | - Michal Dziurka
- Franciszek Gorski Institute of Plant Physiology, Polish Academy of SciencesKrakow, Poland
| | - Ewa Pociecha
- Department of Plant Physiology, University of Agriculture in KrakowKrakow, Poland
| | - Jana Oklestkova
- Laboratory of Growth Regulators, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Czech Academy of Sciences, Palacký UniversityOlomouc, Czechia
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environment Protection, University of SilesiaKatowice, Poland
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161
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Bac-Molenaar JA, Granier C, Keurentjes JJB, Vreugdenhil D. Genome-wide association mapping of time-dependent growth responses to moderate drought stress in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:88-102. [PMID: 26138664 DOI: 10.1111/pce.12595] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 05/25/2023]
Abstract
Large areas of arable land are often confronted with irregular rainfall resulting in limited water availability for part(s) of the growing seasons, which demands research for drought tolerance of plants. Natural variation was observed for biomass accumulation upon controlled moderate drought stress in 324 natural accessions of Arabidopsis. Improved performance under drought stress was correlated with early flowering and lack of vernalization requirement, indicating overlap in the regulatory networks of flowering time and drought response or correlated responses of these traits to natural selection. In addition, plant size was negatively correlated with relative water content (RWC) independent of the absolute water content (WC), indicating a prominent role for soluble compounds. Growth in control and drought conditions was determined over time and was modelled by an exponential function. Genome-wide association (GWA) mapping of temporal plant size data and of model parameters resulted in the detection of six time-dependent quantitative trait loci (QTLs) strongly associated with drought. Most QTLs would not have been identified if plant size was determined at a single time point. Analysis of earlier reported gene expression changes upon drought enabled us to identify for each QTL the most likely candidates.
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Affiliation(s)
| | - Christine Granier
- Laboratoire d'Ecop0068ysiologie des Plantes sous Stress Environnementaux, UMR 759, Institut National de la Recherche Agronomique/Ecole Nationale Supérieure d'Agronomie, Place Viala, F-34060, Montpellier, Cedex 1, France
| | | | - Dick Vreugdenhil
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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162
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Tabib A, Vishwanathan S, Seleznev A, McKeown PC, Downing T, Dent C, Sanchez-Bermejo E, Colling L, Spillane C, Balasubramanian S. A Polynucleotide Repeat Expansion Causing Temperature-Sensitivity Persists in Wild Irish Accessions of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1311. [PMID: 27630650 PMCID: PMC5006647 DOI: 10.3389/fpls.2016.01311] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/16/2016] [Indexed: 05/15/2023]
Abstract
Triplet repeat expansions underlie several human genetic diseases such as Huntington's disease and Friedreich's ataxia. Although such mutations are primarily known from humans, a triplet expansion associated genetic defect has also been reported at the IIL1 locus in the Bur-0 accession of the model plant Arabidopsis thaliana. The IIL1 triplet expansion is an example of cryptic genetic variation as its phenotypic effects are seen only under genetic or environmental perturbation, with high temperatures resulting in a growth defect. Here we demonstrate that the IIL1 triplet expansion associated growth defect is not a general stress response and is specific to particular environmental perturbations. We also confirm and map genetic modifiers that suppress the effect of IIL1 triplet repeat expansion. By collecting and analyzing accessions from the island of Ireland, we recover the repeat expansion in wild populations suggesting that the repeat expansion has persisted at least 60 years in Ireland. Through genome-wide genotyping, we show that the repeat expansion is present in diverse Irish populations. Our findings indicate that even deleterious alleles can persist in populations if their effect is conditional. Our study demonstrates that analysis of groups of wild populations is a powerful tool for understanding the dynamics of cryptic genetic variation.
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Affiliation(s)
- Amanda Tabib
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | | | - Andrei Seleznev
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Peter C. McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
| | - Tim Downing
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
- School of Biotechnology, Dublin City UniversityDublin, Ireland
| | - Craig Dent
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | | | - Luana Colling
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
| | - Sureshkumar Balasubramanian
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
- *Correspondence: Sureshkumar Balasubramanian
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163
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Leida C, Dal Rì A, Dalla Costa L, Gómez MD, Pompili V, Sonego P, Engelen K, Masuero D, Ríos G, Moser C. Insights into the Role of the Berry-Specific Ethylene Responsive Factor VviERF045. FRONTIERS IN PLANT SCIENCE 2016; 7:1793. [PMID: 28018369 PMCID: PMC5146979 DOI: 10.3389/fpls.2016.01793] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 11/15/2016] [Indexed: 05/03/2023]
Abstract
During grape ripening, numerous transcriptional and metabolic changes are required in order to obtain colored, sweet, and flavored berries. There is evidence that ethylene, together with other signals, plays an important role in triggering the onset of ripening. Here, we report the functional characterization of a berry-specific Ethylene Responsive Factor (ERF), VviERF045, which is induced just before véraison and peaks at ripening. Phylogenetic analysis revealed it is close to the SHINE clade of ERFs, factors involved in the regulation of wax biosynthesis and cuticle morphology. Transgenic grapevines lines overexpressing VviERF045 were obtained, in vitro propagated, phenotypically characterized, and analyzed for the content of specific classes of metabolites. The effect of VviERF045 was correlated with the level of transgene expression, with high-expressing lines showing stunted growth, discolored and smaller leaves, and a lower level of chlorophylls and carotenoids. One line with intermediate expression, L15, was characterized at the transcriptomic level and showed 573 differentially expressed genes compared to wild type plants. Microscopy and gene expression analyses point toward a major role of VviERF045 in epidermis patterning by acting on waxes and cuticle. They also indicate that VviERF045 affects phenolic secondary metabolism and induces a reaction resembling a plant immune response with modulation of receptor like-kinases and pathogen related genes. These results suggest also a possible role of this transcription factor in berry ripening, likely related to changes in epidermis and cuticle of the berry, cell expansion, a decrease in photosynthetic capacity, and the activation of several defense related genes as well as from the phenylpropanoid metabolism. All these processes occur in the berry during ripening.
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Affiliation(s)
- Carmen Leida
- Genomics and Biology of Fruit Crops Department, Research and Innovation Center, Fondazione Edmund MachSan Michele all’Adige, Italy
- *Correspondence: Carmen Leida,
| | - Antonio Dal Rì
- Genomics and Biology of Fruit Crops Department, Research and Innovation Center, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Lorenza Dalla Costa
- Genomics and Biology of Fruit Crops Department, Research and Innovation Center, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Maria D. Gómez
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Valerio Pompili
- Genomics and Biology of Fruit Crops Department, Research and Innovation Center, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Paolo Sonego
- Computational Biology Department, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Kristof Engelen
- Computational Biology Department, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Domenico Masuero
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund MachTrento, Italy
| | - Gabino Ríos
- Fruit Tree Breeding Department, Instituto Valenciano de Investigaciones AgrariasMoncada, Spain
| | - Claudio Moser
- Genomics and Biology of Fruit Crops Department, Research and Innovation Center, Fondazione Edmund MachSan Michele all’Adige, Italy
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164
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Riemann M, Dhakarey R, Hazman M, Miro B, Kohli A, Nick P. Exploring Jasmonates in the Hormonal Network of Drought and Salinity Responses. FRONTIERS IN PLANT SCIENCE 2015; 6:1077. [PMID: 26648959 PMCID: PMC4665137 DOI: 10.3389/fpls.2015.01077] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 11/17/2015] [Indexed: 05/18/2023]
Abstract
Present and future food security is a critical issue compounded by the consequences of climate change on agriculture. Stress perception and signal transduction in plants causes changes in gene or protein expression which lead to metabolic and physiological responses. Phytohormones play a central role in the integration of different upstream signals into different adaptive outputs such as changes in the activity of ion-channels, protein modifications, protein degradation, and gene expression. Phytohormone biosynthesis and signaling, and recently also phytohormone crosstalk have been investigated intensively, but the function of jasmonates under abiotic stress is still only partially understood. Although most aspects of jasmonate biosynthesis, crosstalk and signal transduction appear to be similar for biotic and abiotic stress, novel aspects have emerged that seem to be unique for the abiotic stress response. Here, we review the knowledge on the role of jasmonates under drought and salinity. The crosstalk of jasmonate biosynthesis and signal transduction pathways with those of abscisic acid (ABA) is particularly taken into account due to the well-established, central role of ABA under abiotic stress. Likewise, the accumulating evidence of crosstalk of jasmonate signaling with other phytohormones is considered as important element of an integrated phytohormonal response. Finally, protein post-translational modification, which can also occur without de novo transcription, is treated with respect to its implications for phytohormone biosynthesis, signaling and crosstalk. To breed climate-resilient crop varieties, integrated understanding of the molecular processes is required to modulate and tailor particular nodes of the network to positively affect stress tolerance.
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Affiliation(s)
- Michael Riemann
- Molecular Cell Biology, Institute of Botany, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Rohit Dhakarey
- Molecular Cell Biology, Institute of Botany, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Mohamed Hazman
- Molecular Cell Biology, Institute of Botany, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Berta Miro
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute, Makati, Philippines
| | - Ajay Kohli
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute, Makati, Philippines
| | - Peter Nick
- Molecular Cell Biology, Institute of Botany, Karlsruhe Institute of Technology, Karlsruhe, Germany
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165
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Cohen AC, Bottini R, Piccoli P. Role of Abscisic Acid Producing PGPR in Sustainable Agriculture. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-24654-3_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
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166
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Suzuki N, Devireddy AR, Inupakutika MA, Baxter A, Miller G, Song L, Shulaev E, Azad RK, Shulaev V, Mittler R. Ultra-fast alterations in mRNA levels uncover multiple players in light stress acclimation in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:760-72. [PMID: 26408339 PMCID: PMC5019327 DOI: 10.1111/tpj.13039] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/12/2015] [Accepted: 09/15/2015] [Indexed: 05/19/2023]
Abstract
The acclimation of plants to changes in light intensity requires rapid responses at several different levels. These include biochemical and biophysical responses as well as alterations in the steady-state level of different transcripts and proteins. Recent studies utilizing promoter::reporter constructs suggested that transcriptional responses to changes in light intensity could occur within seconds, rates for which changes in mRNA expression are not routinely measured or functionally studied. To identify and characterize rapid changes in the steady-state level of different transcripts in response to light stress we performed RNA sequencing analysis of Arabidopsis thaliana plants subjected to light stress. Here we report that mRNA accumulation of 731 transcripts occurs as early as 20-60 sec following light stress application, and that at least five of these early response transcripts play an important biological role in the acclimation of plants to light stress. More than 20% of transcripts accumulating in plants within 20-60 sec of initiation of light stress are H2 O2 - and ABA-response transcripts, and the accumulation of several of these transcripts is inhibited by transcriptional inhibitors. In accordance with the association of rapid response transcripts with H2 O2 and ABA signaling, a mutant impaired in ABA sensing (abi-1) was found to be more tolerant to light stress, and the response of several of the rapid response transcripts was altered in mutants impaired in reactive oxygen metabolism. Our findings reveal that transcriptome reprogramming in plants could occur within seconds of initiation of abiotic stress and that this response could invoke known as well as unknown proteins and pathways.
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Affiliation(s)
- Nobuhiro Suzuki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554, Tokyo, Japan
| | - Amith R Devireddy
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Madhuri A Inupakutika
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Aaron Baxter
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Life Sciences Building (204) Room 211, Ramat-Gan, 5290002, Israel
| | - Luhua Song
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Elena Shulaev
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Rajeev K Azad
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
- Department of Mathematics, University of North Texas, Denton, TX, 76203, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Ron Mittler
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
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167
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Boudichevskaia A, Heckwolf M, Kaldenhoff R. T-DNA insertion in aquaporin gene AtPIP1;2 generates transcription profiles reminiscent of a low CO2 response. PLANT, CELL & ENVIRONMENT 2015; 38:2286-2298. [PMID: 25850563 DOI: 10.1111/pce.12547] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/22/2015] [Indexed: 06/04/2023]
Abstract
Results from CO2 diffusion studies and characterization of Arabidopsis thaliana aquaporin AtPIP1;2 T-DNA insertion lines support the idea that specific aquaporins facilitate the diffusion of CO2 through biological membranes. However, their function as CO2 diffusion facilitators in plant physiology is still a matter of debate. Assuming that a lack of AtPIP1;2 causes a characteristic transcriptional response, we compared data from a AtPIP1;2 T-DNA insertion line obtained by Illumina sequencing, Affymetrix chip analysis and quantitative RT-PCR to the transcriptome of plants grown under drought stress or under low CO2 conditions. The plant reaction to the deficit of AtPIP1;2 was unlike drought stress responses but comparable with that of low CO2 conditions. In addition, we observed a phenotype characteristic to plants grown under low CO2 . The findings support the hypothesis that the AtPIP1;2 function in plant physiology is not to facilitate water but CO2 diffusion.
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Affiliation(s)
| | - Marlies Heckwolf
- Applied Plant Science, Darmstadt University of Technology, Darmstadt, D-64287, Germany
- Department of Energy Great Lakes Bioenergy Research Center, Department of Agronomy, University of Wisconsin, Madison, WI, 53703, USA
| | - Ralf Kaldenhoff
- Applied Plant Science, Darmstadt University of Technology, Darmstadt, D-64287, Germany
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168
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Pang T, Guo L, Shim D, Cannon N, Tang S, Chen J, Xia X, Yin W, Carlson JE. Characterization of the Transcriptome of the Xerophyte Ammopiptanthus mongolicus Leaves under Drought Stress by 454 Pyrosequencing. PLoS One 2015; 10:e0136495. [PMID: 26313687 PMCID: PMC4552034 DOI: 10.1371/journal.pone.0136495] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/04/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ammopiptanthus mongolicus (Maxim. Ex Kom.) Cheng f., an endangered ancient legume species, endemic to the Gobi desert in north-western China. As the only evergreen broadleaf shrub in this area, A. mongolicus plays an important role in the region's ecological-environmental stability. Despite the strong potential of A. mongolicus in providing new insights on drought tolerance, sequence information on the species in public databases remains scarce. To both learn about the role of gene expression in drought stress tolerance in A. mongolicus and to expand genomic resources for the species, transcriptome sequencing of stress-treated A. mongolicus plants was performed. RESULTS Using 454 pyrosequencing technology, 8,480 and 7,474 contigs were generated after de novo assembly of RNA sequences from leaves of untreated and drought-treated plants, respectively. After clustering using TGICL and CAP3 programs, a combined assembly of all reads produced a total of 11,357 putative unique transcripts (PUTs). Functional annotation and classification of the transcripts were conducted by aligning the 11,357 PUTs against the public protein databases and nucleotide database (Nt). Between control and drought-treated plants, 1,620 differentially expressed genes (DEGs) were identified, of which 1,106 were up-regulated and 514 were down-regulated. The differential expression of twenty candidate genes in metabolic pathways and transcription factors families related to stress-response were confirmed by quantitative real-time PCR. Representatives of several large gene families, such as WRKY and P5CS, were identified and verified in A. mongolicus for the first time. CONCLUSIONS The additional transcriptome resources, gene expression profiles, functional annotations, and candidate genes provide a more comprehensive understanding of the stress response pathways in xeric-adapted plant species such as A. mongolicus.
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Affiliation(s)
- Tao Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Lili Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
- College of Agricultural, Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Donghwan Shim
- The Schatz Center for Tree Molecular Genetics, Department Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Forest Genetic Resources, Korea Forest Research Institute, Suwon 441–350, Korea
| | - Nathaniel Cannon
- The Schatz Center for Tree Molecular Genetics, Department Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sha Tang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Jinhuan Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Weilun Yin
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - John E. Carlson
- The Schatz Center for Tree Molecular Genetics, Department Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States of America
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169
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Comparative Analysis of the Brassica napus Root and Leaf Transcript Profiling in Response to Drought Stress. Int J Mol Sci 2015; 16:18752-77. [PMID: 26270661 PMCID: PMC4581270 DOI: 10.3390/ijms160818752] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 02/03/2023] Open
Abstract
Drought stress is one of the major abiotic factors affecting Brassica napus (B. napus) productivity. In order to identify genes of potential importance to drought stress and obtain a deeper understanding of the molecular mechanisms regarding the responses of B. napus to dehydration stress, we performed large-scale transcriptome sequencing of B. napus plants under dehydration stress using the Illumina sequencing technology. In this work, a relatively drought tolerant B. napus line, Q2, identified in our previous study, was used. Four cDNA libraries constructed from mRNAs of control and dehydration-treated root and leaf were sequenced by Illumina technology. A total of 6018 and 5377 differentially expressed genes (DEGs) were identified in root and leaf. In addition, 1745 genes exhibited a coordinated expression profile between the two tissues under drought stress, 1289 (approximately 74%) of which showed an inverse relationship, demonstrating different regulation patterns between the root and leaf. The gene ontology (GO) enrichment test indicated that up-regulated genes in root were mostly involved in “stimulus” “stress” biological process, and activated genes in leaf mainly functioned in “cell” “cell part” components. Furthermore, a comparative network related to plant hormone signal transduction and AREB/ABF, AP2/EREBP, NAC, WRKY and MYC/MYB transcription factors (TFs) provided a view of different stress tolerance mechanisms between root and leaf. Some of the DEGs identified may be candidates for future research aimed at detecting drought-responsive genes and will be useful for understanding the molecular mechanisms of drought tolerance in root and leaf of B. napus.
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170
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Costa MCD, Righetti K, Nijveen H, Yazdanpanah F, Ligterink W, Buitink J, Hilhorst HWM. A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds. PLANTA 2015; 242:435-49. [PMID: 25809152 PMCID: PMC4498281 DOI: 10.1007/s00425-015-2283-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/16/2015] [Indexed: 05/19/2023]
Abstract
During re-establishment of desiccation tolerance (DT), early events promote initial protection and growth arrest, while late events promote stress adaptation and contribute to survival in the dry state. Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose desiccation tolerance (DT) while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with abscisic acid (ABA). To gain temporal resolution and identify relevant genes in this process, data from a time series of microarrays were used to build a gene co-expression network. The network has two regions, namely early response (ER) and late response (LR). Genes in the ER region are related to biological processes, such as dormancy, acquisition of DT and drought, amplification of signals, growth arrest and induction of protection mechanisms (such as LEA proteins). Genes in the LR region lead to inhibition of photosynthesis and primary metabolism, promote adaptation to stress conditions and contribute to seed longevity. Phenotyping of 12 hubs in relation to re-establishment of DT with T-DNA insertion lines indicated a significant increase in the ability to re-establish DT compared with the wild-type in the lines cbsx4, at3g53040 and at4g25580, suggesting the operation of redundant and compensatory mechanisms. Moreover, we show that re-establishment of DT by polyethylene glycol and ABA occurs through partially overlapping mechanisms. Our data confirm that co-expression network analysis is a valid approach to examine data from time series of transcriptome analysis, as it provides promising insights into biologically relevant relations that help to generate new information about the roles of certain genes for DT.
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Affiliation(s)
- Maria Cecília D Costa
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands,
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171
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Lim CW, Baek W, Jung J, Kim JH, Lee SC. Function of ABA in Stomatal Defense against Biotic and Drought Stresses. Int J Mol Sci 2015; 16:15251-70. [PMID: 26154766 PMCID: PMC4519898 DOI: 10.3390/ijms160715251] [Citation(s) in RCA: 260] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 12/21/2022] Open
Abstract
The plant hormone abscisic acid (ABA) regulates many key processes involved in plant development and adaptation to biotic and abiotic stresses. Under stress conditions, plants synthesize ABA in various organs and initiate defense mechanisms, such as the regulation of stomatal aperture and expression of defense-related genes conferring resistance to environmental stresses. The regulation of stomatal opening and closure is important to pathogen defense and control of transpirational water loss. Recent studies using a combination of approaches, including genetics, physiology, and molecular biology, have contributed considerably to our understanding of ABA signal transduction. A number of proteins associated with ABA signaling and responses—especially ABA receptors—have been identified. ABA signal transduction initiates signal perception by ABA receptors and transfer via downstream proteins, including protein kinases and phosphatases. In the present review, we focus on the function of ABA in stomatal defense against biotic and abiotic stresses, through analysis of each ABA signal component and the relationships of these components in the complex network of interactions. In particular, two ABA signal pathway models in response to biotic and abiotic stress were proposed, from stress signaling to stomatal closure, involving the pyrabactin resistance (PYR)/PYR-like (PYL) or regulatory component of ABA receptor (RCAR) family proteins, 2C-type protein phosphatases, and SnRK2-type protein kinases.
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Affiliation(s)
- Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul 156-756, Korea.
| | - Woonhee Baek
- Department of Life Science (BK21 program), Chung-Ang University, Seoul 156-756, Korea.
| | - Jangho Jung
- Department of Life Science (BK21 program), Chung-Ang University, Seoul 156-756, Korea.
| | - Jung-Hyun Kim
- Department of Home Economics Education, Chung-Ang University, Seoul 156-756, Korea.
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Seoul 156-756, Korea.
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172
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Lim CW, Baek W, Jung J, Kim JH, Lee SC. Function of ABA in Stomatal Defense against Biotic and Drought Stresses. Int J Mol Sci 2015; 16:15251-15270. [PMID: 26154766 DOI: 10.3390/ijms16071525111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 05/20/2023] Open
Abstract
The plant hormone abscisic acid (ABA) regulates many key processes involved in plant development and adaptation to biotic and abiotic stresses. Under stress conditions, plants synthesize ABA in various organs and initiate defense mechanisms, such as the regulation of stomatal aperture and expression of defense-related genes conferring resistance to environmental stresses. The regulation of stomatal opening and closure is important to pathogen defense and control of transpirational water loss. Recent studies using a combination of approaches, including genetics, physiology, and molecular biology, have contributed considerably to our understanding of ABA signal transduction. A number of proteins associated with ABA signaling and responses--especially ABA receptors--have been identified. ABA signal transduction initiates signal perception by ABA receptors and transfer via downstream proteins, including protein kinases and phosphatases. In the present review, we focus on the function of ABA in stomatal defense against biotic and abiotic stresses, through analysis of each ABA signal component and the relationships of these components in the complex network of interactions. In particular, two ABA signal pathway models in response to biotic and abiotic stress were proposed, from stress signaling to stomatal closure, involving the pyrabactin resistance (PYR)/PYR-like (PYL) or regulatory component of ABA receptor (RCAR) family proteins, 2C-type protein phosphatases, and SnRK2-type protein kinases.
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Affiliation(s)
- Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul 156-756, Korea.
| | - Woonhee Baek
- Department of Life Science (BK21 program), Chung-Ang University, Seoul 156-756, Korea.
| | - Jangho Jung
- Department of Life Science (BK21 program), Chung-Ang University, Seoul 156-756, Korea.
| | - Jung-Hyun Kim
- Department of Home Economics Education, Chung-Ang University, Seoul 156-756, Korea.
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Seoul 156-756, Korea.
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173
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Boudichevskaia A, Heckwolf M, Althaus L, Kaldenhoff R. Transcriptome analysis of the aquaporin AtPIP1;2 deficient line in Arabidopsis thaliana. GENOMICS DATA 2015; 4:162-4. [PMID: 26484207 PMCID: PMC4535893 DOI: 10.1016/j.gdata.2015.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/21/2015] [Indexed: 11/28/2022]
Abstract
Atmospheric CO2 impacts all aspects of plant development. It has changed in the past and is predicted to change further on. Studies on the response of crop plants to low and elevated CO2 concerning growth, productivity and physiological processes are intense. In contrast, the molecular mechanisms of cellular CO2 exchange are still under discussion. At the same time it becomes more and more accepted that carbon dioxide is transported across cellular biomembranes by CO2 conducting aquaporins. Our recent study (Boudichevskaia et al., 2015) demonstrates that the lack of a single gene product – aquaporin AtPIP1;2 – resulted in massive transcriptional reprogramming in Arabidopsis as a consequence of reduced tissue CO2 diffusion rates. Therefore, the transcriptome data of the aquaporin AtPIP1;2 deficient line can be used in the comparative expression analyses for better understanding the role of aquaporins with regard to CO2 and water transport in plants. Here we describe a gene expression dataset generated for three biological replicates per genotype on Affymetrix platform. We provide detailed methods and analysis on microarray data which has been deposited in Gene Expression Omnibus (GEO): GSE62167. Additionally, we provide the R code for data preprocessing and quality control.
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Affiliation(s)
- Anastassia Boudichevskaia
- Darmstadt University of Technology, Applied Plant Science, Schnittspahnstr. 10, D-64287 Darmstadt, Germany
| | - Marlies Heckwolf
- Darmstadt University of Technology, Applied Plant Science, Schnittspahnstr. 10, D-64287 Darmstadt, Germany ; Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53703, USA ; Department of Agronomy, University of Wisconsin, Madison, WI 53703, USA
| | - Lea Althaus
- Darmstadt University of Technology, Applied Plant Science, Schnittspahnstr. 10, D-64287 Darmstadt, Germany
| | - Ralf Kaldenhoff
- Darmstadt University of Technology, Applied Plant Science, Schnittspahnstr. 10, D-64287 Darmstadt, Germany
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174
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Kumari A, Kumar J, Kumar A, Chaudhury A, Singh SP. Grafting triggers differential responses between scion and rootstock. PLoS One 2015; 10:e0124438. [PMID: 25874958 PMCID: PMC4395316 DOI: 10.1371/journal.pone.0124438] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 03/13/2015] [Indexed: 02/06/2023] Open
Abstract
Grafting is a well-established practice to facilitate asexual propagation in horticultural and agricultural crops. It has become a method for studying molecular aspects of root-to-shoot and/or shoot-to-root signaling events. The objective of this study was to investigate differences in gene expression between the organs of the scion and rootstock of a homograft (Arabidopsis thaliana). MapMan and Gene Ontology enrichment analysis revealed differentially expressed genes from numerous functional categories related to stress responses in the developing flower buds and leaves of scion and rootstock. Meta-analysis suggested induction of drought-type responses in flower buds and leaves of the scion. The flower buds of scion showed over-representation of the transcription factor genes, such as Homeobox, NAC, MYB, bHLH, B3, C3HC4, PLATZ etc. The scion leaves exhibited higher accumulation of the regulatory genes for flower development, such as SEPALLATA 1-4, Jumonji C and AHL16. Differential transcription of genes related to ethylene, gibberellic acid and other stimuli was observed between scion and rootstock. The study is useful in understanding the molecular basis of grafting and acclimation of scion on rootstock.
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Affiliation(s)
- Anita Kumari
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
- Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Anil Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ashok Chaudhury
- Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India
| | - Sudhir P. Singh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
- * E-mail:
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175
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Clauw P, Coppens F, De Beuf K, Dhondt S, Van Daele T, Maleux K, Storme V, Clement L, Gonzalez N, Inzé D. Leaf responses to mild drought stress in natural variants of Arabidopsis. PLANT PHYSIOLOGY 2015; 167:800-16. [PMID: 25604532 PMCID: PMC4348775 DOI: 10.1104/pp.114.254284] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/16/2015] [Indexed: 05/18/2023]
Abstract
Although the response of plants exposed to severe drought stress has been studied extensively, little is known about how plants adapt their growth under mild drought stress conditions. Here, we analyzed the leaf and rosette growth response of six Arabidopsis (Arabidopsis thaliana) accessions originating from different geographic regions when exposed to mild drought stress. The automated phenotyping platform WIWAM was used to impose stress early during leaf development, when the third leaf emerges from the shoot apical meristem. Analysis of growth-related phenotypes showed differences in leaf development between the accessions. In all six accessions, mild drought stress reduced both leaf pavement cell area and number without affecting the stomatal index. Genome-wide transcriptome analysis (using RNA sequencing) of early developing leaf tissue identified 354 genes differentially expressed under mild drought stress in the six accessions. Our results indicate the existence of a robust response over different genetic backgrounds to mild drought stress in developing leaves. The processes involved in the overall mild drought stress response comprised abscisic acid signaling, proline metabolism, and cell wall adjustments. In addition to these known severe drought-related responses, 87 genes were found to be specific for the response of young developing leaves to mild drought stress.
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Affiliation(s)
- Pieter Clauw
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
| | - Kristof De Beuf
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
| | - Stijn Dhondt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
| | - Twiggy Van Daele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
| | - Katrien Maleux
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
| | - Veronique Storme
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
| | - Lieven Clement
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.C., F.C., S.D., T.V.D., K.M., V.S., N.G., D.I.); andDepartment of Applied Mathematics Computer Science and Statistics (K.D.B., L.C.) and Stat-Gent CRESCENDO, Department of Applied Mathematics and Computer Science (K.D.B.), Ghent University, 9000 Ghent, Belgium
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176
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Meng J, Zhang J, Luan Y. Gene Selection Integrated with Biological Knowledge for Plant Stress Response Using Neighborhood System and Rough Set Theory. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:433-444. [PMID: 26357229 DOI: 10.1109/tcbb.2014.2361329] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Mining knowledge from gene expression data is a hot research topic and direction of bioinformatics. Gene selection and sample classification are significant research trends, due to the large amount of genes and small size of samples in gene expression data. Rough set theory has been successfully applied to gene selection, as it can select attributes without redundancy. To improve the interpretability of the selected genes, some researchers introduced biological knowledge. In this paper, we first employ neighborhood system to deal directly with the new information table formed by integrating gene expression data with biological knowledge, which can simultaneously present the information in multiple perspectives and do not weaken the information of individual gene for selection and classification. Then, we give a novel framework for gene selection and propose a significant gene selection method based on this framework by employing reduction algorithm in rough set theory. The proposed method is applied to the analysis of plant stress response. Experimental results on three data sets show that the proposed method is effective, as it can select significant gene subsets without redundancy and achieve high classification accuracy. Biological analysis for the results shows that the interpretability is well.
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177
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Min JH, Chung JS, Lee KH, Kim CS. The CONSTANS-like 4 transcription factor, AtCOL4, positively regulates abiotic stress tolerance through an abscisic acid-dependent manner in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:313-24. [PMID: 25073793 DOI: 10.1111/jipb.12246] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 07/28/2014] [Indexed: 05/23/2023]
Abstract
The precise roles of the B-box zinc finger family of transcription factors in plant stress are poorly understood. Functional analysis was performed on AtCOL4, an Arabidopsis thaliana L. CONSTANS-like 4 protein that is a putative novel transcription factor, and which contains a predicted transcriptional activation domain. Analyses of an AtCOL4 promoter-β-glucuronidase (GUS) construct revealed substantial GUS activity in whole seedlings. The expression of AtCOL4 was strongly induced by abscisic acid (ABA), salt, and osmotic stress. Mutation in atcol4 resulted in increased sensitivity to ABA and salt stress during seed germination and the cotyledon greening process. In contrast, AtCOL4-overexpressing plants were less sensitive to ABA and salt stress compared to the wild type. Interestingly, in the presence of ABA or salt stress, the transcript levels of other ABA biosynthesis and stress-related genes were enhanced induction in AtCOL4-overexpressing and WT plants, rather than in the atcol4 mutant. Thus, AtCOL4 is involved in ABA and salt stress response through the ABA-dependent signaling pathway. Taken together, these findings provide compelling evidence that AtCOL4 is an important regulator for plant tolerance to abiotic stress.
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Affiliation(s)
- Ji-Hee Min
- Department of Plant Biotechnology, Chonnam National University, Gwangju 500-757, South Korea
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178
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Guerra D, Crosatti C, Khoshro HH, Mastrangelo AM, Mica E, Mazzucotelli E. Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider's web of mechanisms. FRONTIERS IN PLANT SCIENCE 2015; 6:57. [PMID: 25717333 PMCID: PMC4324062 DOI: 10.3389/fpls.2015.00057] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/22/2015] [Indexed: 05/14/2023]
Abstract
Drought and heat tolerance are complex quantitative traits. Moreover, the adaptive significance of some stress-related traits is more related to plant survival than to agronomic performance. A web of regulatory mechanisms fine-tunes the expression of stress-related traits and integrates both environmental and developmental signals. Both post-transcriptional and post-translational modifications contribute substantially to this network with a pivotal regulatory function of the transcriptional changes related to cellular and plant stress response. Alternative splicing and RNA-mediated silencing control the amount of specific transcripts, while ubiquitin and SUMO modify activity, sub-cellular localization and half-life of proteins. Interactions across these modification mechanisms ensure temporally and spatially appropriate patterns of downstream-gene expression. For key molecular components of these regulatory mechanisms, natural genetic diversity exists among genotypes with different behavior in terms of stress tolerance, with effects upon the expression of adaptive morphological and/or physiological target traits.
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Affiliation(s)
- Davide Guerra
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Cristina Crosatti
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Hamid H. Khoshro
- Department of Agronomy and Plant Breeding, Ilam University, Ilam, Iran
| | - Anna M. Mastrangelo
- Cereal Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Foggia, Italy
| | - Erica Mica
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Elisabetta Mazzucotelli
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
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179
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Li X, Yin X, Wang H, Li J, Guo C, Gao H, Zheng Y, Fan C, Wang X. Genome-wide identification and analysis of the apple (Malus × domestica Borkh.) TIFY gene family. TREE GENETICS & GENOMES 2015. [PMID: 0 DOI: 10.1007/s11295-014-0808-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
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180
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Li H, Yao W, Fu Y, Li S, Guo Q. De novo assembly and discovery of genes that are involved in drought tolerance in Tibetan Sophora moorcroftiana. PLoS One 2015; 10:e111054. [PMID: 25559297 PMCID: PMC4283959 DOI: 10.1371/journal.pone.0111054] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/22/2014] [Indexed: 11/18/2022] Open
Abstract
Sophora moorcroftiana, a Leguminosae shrub species that is restricted to the arid and semi-arid regions of the Qinghai-Tibet Plateau, is an ecologically important foundation species and exhibits substantial drought tolerance in the Plateau. There are no functional genomics resources in public databases for understanding the molecular mechanism underlying the drought tolerance of S. moorcroftiana. Therefore, we performed a large-scale transcriptome sequencing of this species under drought stress using the Illumina sequencing technology. A total of 62,348,602 clean reads were obtained. The assembly of the clean reads resulted in 146,943 transcripts, including 66,026 unigenes. In the assembled sequences, 1534 transcription factors were identified and classified into 23 different common families, and 9040 SSR loci, from di- to hexa-nucleotides, whose repeat number is greater than five, were presented. In addition, we performed a gene expression profiling analysis upon dehydration treatment. The results indicated significant differences in the gene expression profiles among the control, mild stress and severe stress. In total, 4687, 5648 and 5735 genes were identified from the comparison of mild versus control, severe versus control and severe versus mild stress, respectively. Based on the differentially expressed genes, a Gene Ontology annotation analysis indicated many dehydration-relevant categories, including 'response to water 'stimulus' and 'response to water deprivation'. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways, such as 'metabolic pathways' and 'plant hormone signal transduction'. In addition, the expression patterns of 25 putative genes that are involved in drought tolerance resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The globally sequenced genes covered a considerable proportion of the S. moorcroftiana transcriptome, and the expression results may be useful to further extend the knowledge on the drought tolerance of this plant species that survives under Plateau conditions.
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Affiliation(s)
- Huie Li
- Agricultural and Animal Husbandry College, Tibet University, Nyingchi, Tibet, China
| | - Weijie Yao
- Agricultural and Animal Husbandry College, Tibet University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet University), Ministry of Education, Nyingchi, Tibet, China
- National Key Station for Field Scientific Observation & Experiment, Nyingchi, Tibet, China
| | - Yaru Fu
- Agricultural and Animal Husbandry College, Tibet University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet University), Ministry of Education, Nyingchi, Tibet, China
- National Key Station for Field Scientific Observation & Experiment, Nyingchi, Tibet, China
| | - Shaoke Li
- Agricultural and Animal Husbandry College, Tibet University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet University), Ministry of Education, Nyingchi, Tibet, China
- National Key Station for Field Scientific Observation & Experiment, Nyingchi, Tibet, China
| | - Qiqiang Guo
- Agricultural and Animal Husbandry College, Tibet University, Nyingchi, Tibet, China
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet University), Ministry of Education, Nyingchi, Tibet, China
- National Key Station for Field Scientific Observation & Experiment, Nyingchi, Tibet, China
- * E-mail:
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181
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Belkadhi A, De Haro A, Obregon S, Chaïbi W, Djebali W. Positive effects of salicylic acid pretreatment on the composition of flax plastidial membrane lipids under cadmium stress. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:1457-1467. [PMID: 25163565 DOI: 10.1007/s11356-014-3475-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/18/2014] [Indexed: 05/28/2023]
Abstract
Interest in use of flax (Linum usitatissimum L.) as cadmium (Cd)-accumulating plant for phytoextraction of contaminated soils opened up a new and promising avenue toward improving tolerance of its varieties and cultivars to Cd stress. The aim of this study is to get insights into the mechanisms of Cd detoxification in cell membranes, by exploring the effects of salicylic acid (SA)-induced priming on fatty acids and lipid composition of flax plantlets, grown for 10 days with 50 and 100 μM Cd. At leaf level, levels of monogalactosyldiacylglycerol (MGDG), phosphatidylcholine (PC), phosphatidylglycerol (PG), and neutral lipids (NL) have shifted significantly in flax plantlets exposed to toxic CdCl2 concentrations, as compared to that of the control. At 100 μM Cd, the linoleic acid (C18:2) decreases mainly in digalactosyldiacylglycerol (DGDG) and all phospholipid species, while linolenic acid (C18:3) declines mostly in MGDG and NL. Conversely, at the highest concentration of the metal, SA significantly enhances the levels of MGDG, PG and phosphatidic acid (PA), and polyunsaturated fatty acids mainly C18:2 and C18:3. Furthermore, SA pretreatment seems to reduce the Cd-induced alterations in both plastidial and extraplastidial lipid classes, but preferentially preserves the plastidial lipids by acquiring higher levels of polyunsaturated fatty acids. These results suggest that flax plantlets pretreated with SA exhibits more stability of their membranes under Cd-stress conditions.
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Affiliation(s)
- Aïcha Belkadhi
- Département de Biologie, Unité de Recherche de Physiologie et Biochimie de la tolérance des plantes aux contraintes abiotiques, Faculté des Sciences de Tunis, Campus Universitaire, 1060, Tunis, Tunisia,
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182
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Zhang J, Mason AS, Wu J, Liu S, Zhang X, Luo T, Redden R, Batley J, Hu L, Yan G. Identification of Putative Candidate Genes for Water Stress Tolerance in Canola (Brassica napus). FRONTIERS IN PLANT SCIENCE 2015; 6:1058. [PMID: 26640475 PMCID: PMC4661274 DOI: 10.3389/fpls.2015.01058] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/13/2015] [Indexed: 05/20/2023]
Abstract
Drought stress can directly inhibit seedling establishment in canola (Brassica napus), resulting in lower plant densities and reduced yields. To dissect this complex trait, 140 B. napus accessions were phenotyped under normal (0.0 MPa, S0) and water-stressed conditions simulated by polyethylene glycol (PEG) 6000 (-0.5 MPa, S5) in a hydroponic system. Phenotypic variation and heritability indicated that the root to shoot length ratio was a reliable indicator for water stress tolerance. Thereafter, 66 accessions (16 water stress tolerant, 34 moderate and 16 sensitive lines) were genotyped using 25,495 Brassica single nucleotide polymorphisms (SNPs). Genome-wide association studies (GWAS) identified 16 loci significantly associated with water stress response. Two B. napus accessions were used for RNA sequencing, with differentially-expressed genes under normal and water-stressed conditions examined. By combining differentially-expressed genes detected by RNA sequencing with significantly associated loci from GWAS, 79 candidate genes were identified, of which eight were putatively associated with drought tolerance based on gene ontology of Arabidopsis. Functional validation of these genes may confirm key drought-related genes for selection and breeding in B. napus. Our results provide insight into the genetic basis of water stress tolerance in canola.
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Affiliation(s)
- Jing Zhang
- Ministry of Agriculture (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 UniversityWuhan, China
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Annaliese S. Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of QueenslandBrisbane, QLD, Australia
| | - Jian Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Sheng Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xuechen Zhang
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Tao Luo
- Ministry of Agriculture (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 UniversityWuhan, China
| | - Robert Redden
- Australian Grains Genebank, Department of Economic Development Jobs Transport and ResourcesHorsham, VIC, Australia
| | - Jacqueline Batley
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of QueenslandBrisbane, QLD, Australia
| | - Liyong Hu
- Ministry of Agriculture (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 UniversityWuhan, China
- *Correspondence: Liyong Hu
| | - Guijun Yan
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
- Guijun Yan
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183
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Gene selection using rough set based on neighborhood for the analysis of plant stress response. Appl Soft Comput 2014. [DOI: 10.1016/j.asoc.2014.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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184
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Belamkar V, Weeks NT, Bharti AK, Farmer AD, Graham MA, Cannon SB. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. BMC Genomics 2014; 15:950. [PMID: 25362847 PMCID: PMC4226900 DOI: 10.1186/1471-2164-15-950] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/16/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement. RESULTS In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~13 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses. CONCLUSIONS We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.
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Affiliation(s)
- Vikas Belamkar
- />Interdepartmental Genetics, Iowa State University, Ames, IA 50011 USA
- />Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Nathan T Weeks
- />United States Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011 USA
| | - Arvind K Bharti
- />National Center for Genome Resources, Santa Fe, NM 87505 USA
| | - Andrew D Farmer
- />National Center for Genome Resources, Santa Fe, NM 87505 USA
| | - Michelle A Graham
- />Department of Agronomy, Iowa State University, Ames, IA 50011 USA
- />United States Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011 USA
| | - Steven B Cannon
- />Department of Agronomy, Iowa State University, Ames, IA 50011 USA
- />United States Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011 USA
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185
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Liu JX, Liu J, Gao YL, Mi JX, Ma CX, Wang D. A class-information-based penalized matrix decomposition for identifying plants core genes responding to abiotic stresses. PLoS One 2014; 9:e106097. [PMID: 25180509 PMCID: PMC4152128 DOI: 10.1371/journal.pone.0106097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/29/2014] [Indexed: 12/03/2022] Open
Abstract
In terms of making genes expression data more interpretable and comprehensible, there exists a significant superiority on sparse methods. Many sparse methods, such as penalized matrix decomposition (PMD) and sparse principal component analysis (SPCA), have been applied to extract plants core genes. Supervised algorithms, especially the support vector machine-recursive feature elimination (SVM-RFE) method, always have good performance in gene selection. In this paper, we draw into class information via the total scatter matrix and put forward a class-information-based penalized matrix decomposition (CIPMD) method to improve the gene identification performance of PMD-based method. Firstly, the total scatter matrix is obtained based on different samples of the gene expression data. Secondly, a new data matrix is constructed by decomposing the total scatter matrix. Thirdly, the new data matrix is decomposed by PMD to obtain the sparse eigensamples. Finally, the core genes are identified according to the nonzero entries in eigensamples. The results on simulation data show that CIPMD method can reach higher identification accuracies than the conventional gene identification methods. Moreover, the results on real gene expression data demonstrate that CIPMD method can identify more core genes closely related to the abiotic stresses than the other methods.
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Affiliation(s)
- Jin-Xing Liu
- School of Information Science and Engineering, Qufu Normal University, Rizhao, Shandong, China
- Bio-Computing Research Center, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, Guangdong, China
- * E-mail:
| | - Jian Liu
- School of Communication, Qufu Normal University, Rizhao, Shandong, China
| | - Ying-Lian Gao
- Library of Qufu Normal University, Qufu Normal University, Rizhao, Shandong, China
| | - Jian-Xun Mi
- College of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, China
- Chongqing Key Laboratory of Computational Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Chun-Xia Ma
- School of Information Science and Engineering, Qufu Normal University, Rizhao, Shandong, China
| | - Dong Wang
- School of Information Science and Engineering, Qufu Normal University, Rizhao, Shandong, China
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186
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Hatzig S, Zaharia LI, Abrams S, Hohmann M, Legoahec L, Bouchereau A, Nesi N, Snowdon RJ. Early osmotic adjustment responses in drought-resistant and drought-sensitive oilseed rape. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:797-809. [PMID: 24667002 DOI: 10.1111/jipb.12199] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 03/24/2014] [Indexed: 05/09/2023]
Abstract
The impact of osmotic stress on growth, physiology, and metabolism of winter oilseed rape (Brassica napus L.) was investigated by detailed analysis of biomass traits, hormone metabolites and osmolytes in two genetically unrelated drought-tolerant genotypes and two unrelated drought-sensitive genotypes. Seedlings were grown in vitro under controlled conditions and osmotic stress was simulated by applying a gradual treatment with polyethylene glycol (PEG 6000), followed by hypo-osmotic treatment of variants used for metabolite determination. The results provide a basis for the identification of reliable selection criteria for drought resistance in oilseed rape. The in vitro cultivation system established during this study enabled effective discrimination of early osmotic stress responses between drought-resistant and -susceptible oilseed rape genotypes that also show large differences in relative seed yield under drought conditions in the field. Clear physiological and metabolic differences were observed between the drought-resistant and drought-sensitive genotypes, suggesting that osmotic adjustment is a key component of drought response in oilseed rape. Unexpectedly, however, the drought-resistant genotypes did not show typical hormonal adjustment and osmolyte accumulation, suggesting that they possess alternative physiological mechanisms enabling avoidance of stress symptoms.
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Affiliation(s)
- Sarah Hatzig
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
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187
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Dash PK, Cao Y, Jailani AK, Gupta P, Venglat P, Xiang D, Rai R, Sharma R, Thirunavukkarasu N, Abdin MZ, Yadava DK, Singh NK, Singh J, Selvaraj G, Deyholos M, Kumar PA, Datla R. Genome-wide analysis of drought induced gene expression changes in flax (Linum usitatissimum). GM CROPS & FOOD 2014; 5:106-19. [PMID: 25072186 DOI: 10.4161/gmcr.29742] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A robust phenotypic plasticity to ward off adverse environmental conditions determines performance and productivity in crop plants. Flax (linseed), is an important cash crop produced for natural textile fiber (linen) or oilseed with many health promoting products. This crop is prone to drought stress and yield losses in many parts of the world. Despite recent advances in drought research in a number of important crops, related progress in flax is very limited. Since, response of this plant to drought stress has not been addressed at the molecular level; we conducted microarray analysis to capture transcriptome associated with induced drought in flax. This study identified 183 differentially expressed genes (DEGs) associated with diverse cellular, biophysical and metabolic programs in flax. The analysis also revealed especially the altered regulation of cellular and metabolic pathways governing photosynthesis. Additionally, comparative transcriptome analysis identified a plethora of genes that displayed differential regulation both spatially and temporally. These results revealed co-regulated expression of 26 genes in both shoot and root tissues with implications for drought stress response. Furthermore, the data also showed that more genes are upregulated in roots compared to shoots, suggesting that roots may play important and additional roles in response to drought in flax. With prolonged drought treatment, the number of DEGs increased in both tissue types. Differential expression of selected genes was confirmed by qRT-PCR, thus supporting the suggested functional association of these intrinsic genes in maintaining growth and homeostasis in response to imminent drought stress in flax. Together the present study has developed foundational and new transcriptome data sets for drought stress in flax.
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Affiliation(s)
- Prasanta K Dash
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | - Yongguo Cao
- National Research Council of Canada; Saskatoon, SK Canada
| | - Abdul K Jailani
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | - Payal Gupta
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | | | - Daoquan Xiang
- National Research Council of Canada; Saskatoon, SK Canada
| | - Rhitu Rai
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | - Rinku Sharma
- Indian Agricultural Research Institute; PUSA Campus; New Delhi, India
| | | | - Malik Z Abdin
- Faculty of Science; Hamdard University; Hamdard Nagar, New Delhi, India
| | - Devendra K Yadava
- Indian Agricultural Research Institute; PUSA Campus; New Delhi, India
| | - Nagendra K Singh
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | - Jas Singh
- Eastern Cereal and Oilseed Research Centre; Agriculture and Agri-Food Canada; Ottawa, ON Canada
| | | | - Mike Deyholos
- Department of Biological Sciences; University of Alberta; Edmonton, AB Canada
| | | | - Raju Datla
- National Research Council of Canada; Saskatoon, SK Canada
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188
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Meyer E, Aspinwall MJ, Lowry DB, Palacio-Mejía JD, Logan TL, Fay PA, Juenger TE. Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.). BMC Genomics 2014; 15:527. [PMID: 24964784 PMCID: PMC4122788 DOI: 10.1186/1471-2164-15-527] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 06/05/2014] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light: dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. RESULTS Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. CONCLUSIONS Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses.
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Affiliation(s)
- Eli Meyer
- />Department of Integrative Biology, Oregon State University, Cordley Hall 3029, Corvallis, OR 97331 USA
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
| | - Michael J Aspinwall
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
- />Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW 2751 Australia
| | - David B Lowry
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
| | - Juan Diego Palacio-Mejía
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
| | - Tierney L Logan
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
| | - Philip A Fay
- />USDA-ARS Grassland Soil and Water Research Laboratory, Temple, TX 76502 USA
| | - Thomas E Juenger
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
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189
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Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.). BMC Genomics 2014. [PMID: 24964784 DOI: 10.1186/1471‐2164‐15‐527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light: dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. RESULTS Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. CONCLUSIONS Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses.
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190
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Johnson SM, Lim FL, Finkler A, Fromm H, Slabas AR, Knight MR. Transcriptomic analysis of Sorghum bicolor responding to combined heat and drought stress. BMC Genomics 2014; 15:456. [PMID: 24916767 PMCID: PMC4070570 DOI: 10.1186/1471-2164-15-456] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 05/27/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Abiotic stresses which include drought and heat are amongst the main limiting factors for plant growth and crop productivity. In the field, these stress types are rarely presented individually and plants are often subjected to a combination of stress types. Sorghum bicolor is a cereal crop which is grown in arid and semi-arid regions and is particularly well adapted to the hot and dry conditions in which it originates and is now grown as a crop. In order to better understand the mechanisms underlying combined stress tolerance in this important crop, we have used microarrays to investigate the transcriptional response of Sorghum subjected to heat and drought stresses imposed both individually and in combination. RESULTS Microarrays consisting of 28585 gene probes identified gene expression changes equating to ~4% and 18% of genes on the chip following drought and heat stresses respectively. In response to combined stress ~20% of probes were differentially expressed. Whilst many of these transcript changes were in common with those changed in response to heat or drought alone, the levels of 2043 specific transcripts (representing 7% of all gene probes) were found to only be changed following the combined stress treatment. Ontological analysis of these 'unique' transcripts identified a potential role for specific transcription factors including MYB78 and ATAF1, chaperones including unique heat shock proteins (HSPs) and metabolic pathways including polyamine biosynthesis in the Sorghum combined stress response. CONCLUSIONS These results show evidence for both cross-talk and specificity in the Sorghum response to combined heat and drought stress. It is clear that some aspects of the combined stress response are unique compared to those of individual stresses. A functional characterization of the genes and pathways identified here could lead to new targets for the enhancement of plant stress tolerance, which will be particularly important in the face of climate change and the increasing prevalence of these abiotic stress types.
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Affiliation(s)
- Stephanie M Johnson
- Durham Centre for Crop Improvement Technology, School of Biological and Biomedical Sciences, Durham University, South Road, DH1 3LE Durham, UK.
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191
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Breitenbach HH, Wenig M, Wittek F, Jordá L, Maldonado-Alconada AM, Sarioglu H, Colby T, Knappe C, Bichlmeier M, Pabst E, Mackey D, Parker JE, Vlot AC. Contrasting Roles of the Apoplastic Aspartyl Protease APOPLASTIC, ENHANCED DISEASE SUSCEPTIBILITY1-DEPENDENT1 and LEGUME LECTIN-LIKE PROTEIN1 in Arabidopsis Systemic Acquired Resistance. PLANT PHYSIOLOGY 2014; 165:791-809. [PMID: 24755512 PMCID: PMC4044859 DOI: 10.1104/pp.114.239665] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 04/22/2014] [Indexed: 05/19/2023]
Abstract
Systemic acquired resistance (SAR) is an inducible immune response that depends on ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1). Here, we show that Arabidopsis (Arabidopsis thaliana) EDS1 is required for both SAR signal generation in primary infected leaves and SAR signal perception in systemic uninfected tissues. In contrast to SAR signal generation, local resistance remains intact in eds1 mutant plants in response to Pseudomonas syringae delivering the effector protein AvrRpm1. We utilized the SAR-specific phenotype of the eds1 mutant to identify new SAR regulatory proteins in plants conditionally expressing AvrRpm1. Comparative proteomic analysis of apoplast-enriched extracts from AvrRpm1-expressing wild-type and eds1 mutant plants led to the identification of 12 APOPLASTIC, EDS1-DEPENDENT (AED) proteins. The genes encoding AED1, a predicted aspartyl protease, and another AED, LEGUME LECTIN-LIKE PROTEIN1 (LLP1), were induced locally and systemically during SAR signaling and locally by salicylic acid (SA) or its functional analog, benzo 1,2,3-thiadiazole-7-carbothioic acid S-methyl ester. Because conditional overaccumulation of AED1-hemagglutinin inhibited SA-induced resistance and SAR but not local resistance, the data suggest that AED1 is part of a homeostatic feedback mechanism regulating systemic immunity. In llp1 mutant plants, SAR was compromised, whereas the local resistance that is normally associated with EDS1 and SA as well as responses to exogenous SA appeared largely unaffected. Together, these data indicate that LLP1 promotes systemic rather than local immunity, possibly in parallel with SA. Our analysis reveals new positive and negative components of SAR and reinforces the notion that SAR represents a distinct phase of plant immunity beyond local resistance.
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Affiliation(s)
- Heiko H Breitenbach
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Marion Wenig
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Finni Wittek
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Lucia Jordá
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Ana M Maldonado-Alconada
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Hakan Sarioglu
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Thomas Colby
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Claudia Knappe
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Marlies Bichlmeier
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Elisabeth Pabst
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - David Mackey
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - Jane E Parker
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
| | - A Corina Vlot
- Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology (H.H.B., M.W., F.W., C.K., M.B., E.P., A.C.V.), and Research Unit Protein Science (H.S.), 85764 Neuherberg, Germany;Max-Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions (L.J., J.E.P., A.C.V.) and Mass Spectrometry Unit (T.C.), 50829 Cologne, Germany;John Innes Centre, Norwich NR4 7UH, United Kingdom (A.M.M.-A.); andOhio State University, Department of Horticulture and Crop Science and Department of Molecular Genetics, Columbus, Ohio 43210 (D.M.)
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Ding Y, Virlouvet L, Liu N, Riethoven JJ, Fromm M, Avramova Z. Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana. BMC PLANT BIOLOGY 2014; 14:141. [PMID: 24885787 PMCID: PMC4081654 DOI: 10.1186/1471-2229-14-141] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/12/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND Pre-exposing plants to diverse abiotic stresses may alter their physiological and transcriptional responses to a subsequent stress, suggesting a form of "stress memory". Arabidopsis thaliana plants that have experienced multiple exposures to dehydration stress display transcriptional behavior suggesting "memory" from an earlier stress. Genes that respond to a first stress by up-regulating or down-regulating their transcription but in a subsequent stress provide a significantly different response define the 'memory genes' category. Genes responding similarly to each stress form the 'non-memory' category. It is unknown whether such memory responses exists in other Angiosperm lineages and whether memory is an evolutionarily conserved response to repeated dehydration stresses. RESULTS Here, we determine the transcriptional responses of maize (Zea mays L.) plants that have experienced repeated exposures to dehydration stress in comparison with plants encountering the stress for the first time. Four distinct transcription memory response patterns similar to those displayed by A. thaliana were revealed. The most important contribution is the evidence that monocot and eudicot plants, two lineages that have diverged 140 to 200 M years ago, display similar abilities to 'remember' a dehydration stress and to modify their transcriptional responses, accordingly. The highly sensitive RNA-Seq analyses allowed to identify genes that function similarly in the two lineages, as well as genes that function in species-specific ways. Memory transcription patterns indicate that the transcriptional behavior of responding genes under repeated stresses is different from the behavior during an initial dehydration stress, suggesting that stress memory is a complex phenotype resulting from coordinated responses of multiple signaling pathways. CONCLUSIONS Structurally related genes displaying the same memory responses in the two species would suggest conservation of the genes' memory during the evolution of plants' dehydration stress response systems. On the other hand, divergent transcription memory responses by genes encoding similar functions would suggest occurrence of species-specific memory responses. The results provide novel insights into our current knowledge of how plants respond to multiple dehydration stresses, as compared to a single exposure, and may serve as a reference platform to study the functions of memory genes in adaptive responses to water deficit in monocot and eudicot plants.
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Affiliation(s)
- Yong Ding
- University of Science & Technology of China, 443 Huangshang Road, Hefei, Anhui 230027, China
- University of Nebraska School of Biological Sciences, 1901 Vine Street, Lincoln 68588, USA
| | - Laetitia Virlouvet
- University of Nebraska Center for Biotechnology and Center for Plant Science Innovation, 1901 Vine Street, Lincoln 68588, USA
| | - Ning Liu
- University of Nebraska School of Biological Sciences, 1901 Vine Street, Lincoln 68588, USA
| | - Jean-Jack Riethoven
- University of Nebraska School of Biological Sciences, 1901 Vine Street, Lincoln 68588, USA
- University of Nebraska Center for Biotechnology and Center for Plant Science Innovation, 1901 Vine Street, Lincoln 68588, USA
| | - Michael Fromm
- University of Nebraska Center for Biotechnology and Center for Plant Science Innovation, 1901 Vine Street, Lincoln 68588, USA
| | - Zoya Avramova
- University of Nebraska School of Biological Sciences, 1901 Vine Street, Lincoln 68588, USA
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193
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Kissoudis C, van de Wiel C, Visser RGF, van der Linden G. Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk. FRONTIERS IN PLANT SCIENCE 2014; 5:207. [PMID: 24904607 PMCID: PMC4032886 DOI: 10.3389/fpls.2014.00207] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/28/2014] [Indexed: 05/18/2023]
Abstract
Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops.
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194
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Zhang X, Lu G, Long W, Zou X, Li F, Nishio T. Recent progress in drought and salt tolerance studies in Brassica crops. BREEDING SCIENCE 2014; 64:60-73. [PMID: 24987291 PMCID: PMC4031111 DOI: 10.1270/jsbbs.64.60] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 03/19/2014] [Indexed: 05/19/2023]
Abstract
Water deficit imposed by either drought or salinity brings about severe growth retardation and yield loss of crops. Since Brassica crops are important contributors to total oilseed production, it is urgently needed to develop tolerant cultivars to ensure yields under such adverse conditions. There are various physiochemical mechanisms for dealing with drought and salinity in plants at different developmental stages. Accordingly, different indicators of tolerance to drought or salinity at the germination, seedling, flowering and mature stages have been developed and used for germplasm screening and selection in breeding practices. Classical genetic and modern genomic approaches coupled with precise phenotyping have boosted the unravelling of genes and metabolic pathways conferring drought or salt tolerance in crops. QTL mapping of drought and salt tolerance has provided several dozen target QTLs in Brassica and the closely related Arabidopsis. Many drought- or salt-tolerant genes have also been isolated, some of which have been confirmed to have great potential for genetic improvement of plant tolerance. It has been suggested that molecular breeding approaches, such as marker-assisted selection and gene transformation, that will enhance oil product security under a changing climate be integrated in the development of drought- and salt-tolerant Brassica crops.
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Affiliation(s)
- Xuekun Zhang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
| | - Guangyuan Lu
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
| | - Weihua Long
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences,
Nanjing 210014,
China
| | - Xiling Zou
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
| | - Feng Li
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute,
CAAS, Wuhan 430062,
China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University,
Sendai, Miyagi 981-8555,
Japan
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195
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Sperdouli I, Moustakas M. A better energy allocation of absorbed light in photosystem II and less photooxidative damage contribute to acclimation of Arabidopsis thaliana young leaves to water deficit. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:587-93. [PMID: 24709149 DOI: 10.1016/j.jplph.2013.11.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 05/23/2023]
Abstract
Water deficit stress promotes excitation pressure and photooxidative damage due to an imbalance between light capture and energy use. Young leaves (YL) of Arabidopsis thaliana plants acclimate better to the onset of water deficit (OnsWD) than do mature leaves (ML). To obtain a better understanding of this differential response, we evaluated whether YL and ML of A. thaliana exposed to the OnsWD, mild water deficit (MiWD) and moderate water deficit (MoWD), show differences in their photosynthetic performance, and whether photosynthetic acclimation correlates with leaf developmental stage. Water deficit (WD) resulted in greater photooxidative damage in ML compared to YL, but the latter could not be protected under the OnsWD or MiWD, but only under MoWD. YL of A. thaliana with signs of photosynthetic acclimation under MoWD retained higher maximum quantum yield (Fv/Fm) and decreased reactive oxygen species (ROS) formation. YL under MoWD, show a reduced excitation pressure and a better balance between light capture and photochemical energy use, which contributed to their photoprotection, but only under low light intensity (LL, 130μmolphotonsm(-2)s(-1)) and not under high light (HL, 1200μmolphotonsm(-2)s(-1)). In conclusion, leaf developmental stage was correlated with photo-oxidative damage and a differential allocation of absorbed light energy in photosystem II (PSII) of Arabidopsis leaves under WD.
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Affiliation(s)
- Ilektra Sperdouli
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Michael Moustakas
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece.
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196
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Genome-wide identification, evolution and expression analysis of the grape (Vitis vinifera L.) zinc finger-homeodomain gene family. Int J Mol Sci 2014; 15:5730-48. [PMID: 24705465 PMCID: PMC4013592 DOI: 10.3390/ijms15045730] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/15/2014] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Plant zinc finger-homeodomain (ZHD) genes encode a family of transcription factors that have been demonstrated to play an important role in the regulation of plant growth and development. In this study, we identified a total of 13 ZHD genes (VvZHD) in the grape genome that were further classified into at least seven groups. Genome synteny analysis revealed that a number of VvZHD genes were present in the corresponding syntenic blocks of Arabidopsis, indicating that they arose before the divergence of these two species. Gene expression analysis showed that the identified VvZHD genes displayed distinct spatiotemporal expression patterns, and were differentially regulated under various stress conditions and hormone treatments, suggesting that the grape VvZHDs might be also involved in plant response to a variety of biotic and abiotic insults. Our work provides insightful information and knowledge about the ZHD genes in grape, which provides a framework for further characterization of their roles in regulation of stress tolerance as well as other aspects of grape productivity.
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197
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Hichri I, Muhovski Y, Žižková E, Dobrev PI, Franco-Zorrilla JM, Solano R, Lopez-Vidriero I, Motyka V, Lutts S. The Solanum lycopersicum Zinc Finger2 cysteine-2/histidine-2 repressor-like transcription factor regulates development and tolerance to salinity in tomato and Arabidopsis. PLANT PHYSIOLOGY 2014; 164:1967-90. [PMID: 24567191 PMCID: PMC3982756 DOI: 10.1104/pp.113.225920] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 02/19/2014] [Indexed: 05/07/2023]
Abstract
The zinc finger superfamily includes transcription factors that regulate multiple aspects of plant development and were recently shown to regulate abiotic stress tolerance. Cultivated tomato (Solanum lycopersicum Zinc Finger2 [SIZF2]) is a cysteine-2/histidine-2-type zinc finger transcription factor bearing an ERF-associated amphiphilic repression domain and binding to the ACGTCAGTG sequence containing two AGT core motifs. SlZF2 is ubiquitously expressed during plant development, and is rapidly induced by sodium chloride, drought, and potassium chloride treatments. Its ectopic expression in Arabidopsis (Arabidopsis thaliana) and tomato impaired development and influenced leaf and flower shape, while causing a general stress visible by anthocyanin and malonyldialdehyde accumulation. SlZF2 enhanced salt sensitivity in Arabidopsis, whereas SlZF2 delayed senescence and improved tomato salt tolerance, particularly by maintaining photosynthesis and increasing polyamine biosynthesis, in salt-treated hydroponic cultures (125 mm sodium chloride, 20 d). SlZF2 may be involved in abscisic acid (ABA) biosynthesis/signaling, because SlZF2 is rapidly induced by ABA treatment and 35S::SlZF2 tomatoes accumulate more ABA than wild-type plants. Transcriptome analysis of 35S::SlZF2 revealed that SlZF2 both increased and reduced expression of a comparable number of genes involved in various physiological processes such as photosynthesis, polyamine biosynthesis, and hormone (notably ABA) biosynthesis/signaling. Involvement of these different metabolic pathways in salt stress tolerance is discussed.
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Affiliation(s)
- Imène Hichri
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université Catholique de Louvain, B–1348 Louvain-la-Neuve, Belgium (I.H., S.L.)
- Département Sciences du Vivant, Centre Wallon de Recherches Agronomiques, B–5030 Gembloux, Belgium (Y.M.)
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic (E.Z., P.I.D., V.M.)
- and Genomics Unit (J.M.F-Z., I.L.-V.) and Departamento de Genética Molecular de Plantas (R.S.), Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Yordan Muhovski
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université Catholique de Louvain, B–1348 Louvain-la-Neuve, Belgium (I.H., S.L.)
- Département Sciences du Vivant, Centre Wallon de Recherches Agronomiques, B–5030 Gembloux, Belgium (Y.M.)
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic (E.Z., P.I.D., V.M.)
- and Genomics Unit (J.M.F-Z., I.L.-V.) and Departamento de Genética Molecular de Plantas (R.S.), Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Eva Žižková
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université Catholique de Louvain, B–1348 Louvain-la-Neuve, Belgium (I.H., S.L.)
- Département Sciences du Vivant, Centre Wallon de Recherches Agronomiques, B–5030 Gembloux, Belgium (Y.M.)
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic (E.Z., P.I.D., V.M.)
- and Genomics Unit (J.M.F-Z., I.L.-V.) and Departamento de Genética Molecular de Plantas (R.S.), Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Petre I. Dobrev
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université Catholique de Louvain, B–1348 Louvain-la-Neuve, Belgium (I.H., S.L.)
- Département Sciences du Vivant, Centre Wallon de Recherches Agronomiques, B–5030 Gembloux, Belgium (Y.M.)
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic (E.Z., P.I.D., V.M.)
- and Genomics Unit (J.M.F-Z., I.L.-V.) and Departamento de Genética Molecular de Plantas (R.S.), Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Jose Manuel Franco-Zorrilla
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université Catholique de Louvain, B–1348 Louvain-la-Neuve, Belgium (I.H., S.L.)
- Département Sciences du Vivant, Centre Wallon de Recherches Agronomiques, B–5030 Gembloux, Belgium (Y.M.)
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic (E.Z., P.I.D., V.M.)
- and Genomics Unit (J.M.F-Z., I.L.-V.) and Departamento de Genética Molecular de Plantas (R.S.), Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Roberto Solano
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université Catholique de Louvain, B–1348 Louvain-la-Neuve, Belgium (I.H., S.L.)
- Département Sciences du Vivant, Centre Wallon de Recherches Agronomiques, B–5030 Gembloux, Belgium (Y.M.)
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic (E.Z., P.I.D., V.M.)
- and Genomics Unit (J.M.F-Z., I.L.-V.) and Departamento de Genética Molecular de Plantas (R.S.), Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Irene Lopez-Vidriero
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université Catholique de Louvain, B–1348 Louvain-la-Neuve, Belgium (I.H., S.L.)
- Département Sciences du Vivant, Centre Wallon de Recherches Agronomiques, B–5030 Gembloux, Belgium (Y.M.)
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic (E.Z., P.I.D., V.M.)
- and Genomics Unit (J.M.F-Z., I.L.-V.) and Departamento de Genética Molecular de Plantas (R.S.), Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Vaclav Motyka
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université Catholique de Louvain, B–1348 Louvain-la-Neuve, Belgium (I.H., S.L.)
- Département Sciences du Vivant, Centre Wallon de Recherches Agronomiques, B–5030 Gembloux, Belgium (Y.M.)
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic (E.Z., P.I.D., V.M.)
- and Genomics Unit (J.M.F-Z., I.L.-V.) and Departamento de Genética Molecular de Plantas (R.S.), Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
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198
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Guo C, Guo R, Xu X, Gao M, Li X, Song J, Zheng Y, Wang X. Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1513-28. [PMID: 24510937 PMCID: PMC3967086 DOI: 10.1093/jxb/eru007] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
WRKY proteins comprise a large family of transcription factors that play important roles in plant defence regulatory networks, including responses to various biotic and abiotic stresses. To date, no large-scale study of WRKY genes has been undertaken in grape (Vitis vinifera L.). In this study, a total of 59 putative grape WRKY genes (VvWRKY) were identified and renamed on the basis of their respective chromosome distribution. A multiple sequence alignment analysis using all predicted grape WRKY genes coding sequences, together with those from Arabidopsis thaliana and tomato (Solanum lycopersicum), indicated that the 59 VvWRKY genes can be classified into three main groups (I-III). An evaluation of the duplication events suggested that several WRKY genes arose before the divergence of the grape and Arabidopsis lineages. Moreover, expression profiles derived from semiquantitative PCR and real-time quantitative PCR analyses showed distinct expression patterns in various tissues and in response to different treatments. Four VvWRKY genes showed a significantly higher expression in roots or leaves, 55 responded to varying degrees to at least one abiotic stress treatment, and the expression of 38 were altered following powdery mildew (Erysiphe necator) infection. Most VvWRKY genes were downregulated in response to abscisic acid or salicylic acid treatments, while the expression of a subset was upregulated by methyl jasmonate or ethylene treatments.
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Affiliation(s)
- Chunlei Guo
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- * These authors contributed equally to this manuscript
| | - Rongrong Guo
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- * These authors contributed equally to this manuscript
| | - Xiaozhao Xu
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Gao
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoqin Li
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyang Song
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
| | - Xiping Wang
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- To whom correspondence should be addressed. E-mail:
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199
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Liu N, Fromm M, Avramova Z. H3K27me3 and H3K4me3 chromatin environment at super-induced dehydration stress memory genes of Arabidopsis thaliana. MOLECULAR PLANT 2014; 7:502-13. [PMID: 24482435 DOI: 10.1093/mp/ssu001] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Pre-exposure to a stress may alter the plant's cellular, biochemical, and/or transcriptional responses during future encounters as a 'memory' from the previous stress. Genes increasing transcription in response to a first dehydration stress, but producing much higher transcript levels in a subsequent stress, represent the super-induced 'transcription memory' genes in Arabidopsis thaliana. The chromatin environment (histone H3 tri-methylations of Lys 4 and Lys 27, H3K4me3, and H3K27me3) studied at five dehydration stress memory genes revealed existence of distinct memory-response subclasses that responded differently to CLF deficiency and displayed different transcriptional activities during the watered recovery periods. Among the most important findings is the novel aspect of the H3K27me3 function observed at specific dehydration stress memory genes. In contrast to its well-known role as a chromatin repressive mechanism at developmentally regulated genes, H3K27me3 did not prevent transcription from the dehydration stress-responding genes. The high H3K27me3 levels present during transcriptionally inactive states did not interfere with the transition to active transcription and with H3K4me3 accumulation. H3K4me3 and H3K27me3 marks function independently and are not mutually exclusive at the dehydration stress-responding memory genes.
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Affiliation(s)
- Ning Liu
- University of Nebraska School of Biological Sciences, 1901 Vine Street, Lincoln, NE 68588, USA
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200
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Bakshi M, Oelmüller R. WRKY transcription factors: Jack of many trades in plants. PLANT SIGNALING & BEHAVIOR 2014; 9:e27700. [PMID: 24492469 PMCID: PMC4091213 DOI: 10.4161/psb.27700] [Citation(s) in RCA: 331] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/02/2014] [Accepted: 01/02/2014] [Indexed: 05/18/2023]
Abstract
WRKY transcription factors are one of the largest families of transcriptional regulators found exclusively in plants. They have diverse biological functions in plant disease resistance, abiotic stress responses, nutrient deprivation, senescence, seed and trichome development, embryogenesis, as well as additional developmental and hormone-controlled processes. WRKYs can act as transcriptional activators or repressors, in various homo- and heterodimer combinations. Here we review recent progress on the function of WRKY transcription factors in Arabidopsis and other plant species such as rice, potato, and parsley, with a special focus on abiotic, developmental, and hormone-regulated processes.
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Affiliation(s)
- Madhunita Bakshi
- Amity Institute of Microbial Technology; Amity University; Noida, UP, India
- Institute of Plant Physiology; Friedrich-Schiller-University Jena; Jena, Germany
| | - Ralf Oelmüller
- Institute of Plant Physiology; Friedrich-Schiller-University Jena; Jena, Germany
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