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Elakhdar A, El-Naggar AA, Kubo T, Kumamaru T. Genome-wide transcriptomic and functional analyses provide new insights into the response of spring barley to drought stress. PHYSIOLOGIA PLANTARUM 2023; 175:e14089. [PMID: 38148212 DOI: 10.1111/ppl.14089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/22/2023] [Accepted: 10/27/2023] [Indexed: 12/28/2023]
Abstract
Drought is a major abiotic stress that impairs the physiology and development of plants, ultimately leading to crop yield losses. Drought tolerance is a complex quantitative trait influenced by multiple genes and metabolic pathways. However, molecular intricacies and subsequent morphological and physiological changes in response to drought stress remain elusive. Herein, we combined morpho-physiological and comparative RNA-sequencing analyses to identify core drought-induced marker genes and regulatory networks in the barley cultivar 'Giza134'. Based on field trials, drought-induced declines occurred in crop growth rate, relative water content, leaf area duration, flag leaf area, concentration of chlorophyll (Chl) a, b and a + b, net photosynthesis, and yield components. In contrast, the Chl a/b ratio, stoma resistance, and proline concentration increased significantly. RNA-sequence analysis identified a total of 2462 differentially expressed genes (DEGs), of which 1555 were up-regulated and 907 were down-regulated in response to water-deficit stress (WD). Comparative transcriptomics analysis highlighted three unique metabolic pathways (carbohydrate metabolism, iron ion binding, and oxidoreductase activity) as containing genes differentially expressed that could mitigate water stress. Our results identified several drought-induced marker genes belonging to diverse physiochemical functions like chlorophyll concentration, photosynthesis, light harvesting, gibberellin biosynthetic, iron homeostasis as well as Cis-regulatory elements. These candidate genes can be utilized to identify gene-associated markers to develop drought-resilient barley cultivars over a short period of time. Our results provide new insights into the understanding of water stress response mechanisms in barley.
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Affiliation(s)
- Ammar Elakhdar
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ahmed A El-Naggar
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | - Takahiko Kubo
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Toshihiro Kumamaru
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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2
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Khan MIR, Palakolanu SR, Chopra P, Rajurkar AB, Gupta R, Iqbal N, Maheshwari C. Improving drought tolerance in rice: Ensuring food security through multi-dimensional approaches. PHYSIOLOGIA PLANTARUM 2021; 172:645-668. [PMID: 33006143 DOI: 10.1111/ppl.13223] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 05/27/2023]
Abstract
Drought has been highly prevalent around the world especially in Sub-Saharan Africa and South-East Asian countries. Consistent climatic instabilities and unpredictable rainfall patterns are further worsening the situation. Rice is a C3 staple cereal and an important food crop for the majority of the world's population and drought stress is one of the major growth retarding threats for rice that slashes down grain quality and yield. Drought deteriorates rice productivity and induces various acclimation responses that aids in stress mitigation. However, the complexity of traits associated with drought tolerance has made the understanding of drought stress-induced responses in rice a challenging process. An integrative understanding based on physiological adaptations, omics, transgenic and molecular breeding approaches successively backed up to developing drought stress-tolerant rice. The review represents a step forward to develop drought-resilient rice plants by exploiting the knowledge that collaborates with omics-based developments with integrative efforts to ensure the compilation of all the possible strategies undertaken to develop drought stress-tolerant rice.
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Affiliation(s)
| | - Sudhakar R Palakolanu
- Cell, Molecular Biology and Genetic Engineering Group, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Ashish B Rajurkar
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Ravi Gupta
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Chirag Maheshwari
- Agricultural Energy and Power Division, ICAR-Central Institute of Agricultural Engineering, Bhopal, India
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3
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Yuan L, Xie S, Nie L, Zheng Y, Wang J, Huang J, Zhao M, Zhu S, Hou J, Chen G, Wang C. Comparative Proteomics Reveals Cold Acclimation Machinery Through Enhanced Carbohydrate and Amino Acid Metabolism in Wucai ( Brassica Campestris L.). PLANTS (BASEL, SWITZERLAND) 2019; 8:E474. [PMID: 31698739 PMCID: PMC6918420 DOI: 10.3390/plants8110474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 05/30/2023]
Abstract
Limited information is available on the cold acclimation of non-heading Chinese cabbage (NHCC) under low temperatures. In this study, the isobaric tags for relative and absolute quantification (iTRAQ) were used to illustrate the molecular machinery of cold acclimation. Compared to the control (Cont), altogether, 89 differentially expressed proteins (DEPs) were identified in wucai leaves responding to low temperatures (LT). Among these proteins, 35 proteins were up-regulated ((and 54 were down-regulated). These differentially expressed proteins were categorized as having roles in carbohydrate metabolism, photosynthesis and energy metabolism, oxidative defense, amino acid metabolism, metabolic progress, cold regulation, methylation progress, and signal transduction. The fructose, glucose, and sucrose were dramatically increased in response to cold acclimation. It was firstly reported that aspartate, serine, glutamate, proline, and threonine were significantly accumulated under low temperatures. Results of quantitative real-time PCR analysis of nine DEPs displayed that the transcriptional expression patterns of six genes were consistent with their protein expression abundance. Our results demonstrated that wucai acclimated to low temperatures through regulating the expression of several crucial proteins. Additionally, carbohydrate and amino acid conversion played indispensable and vital roles in improving cold assimilation in wucai.
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Affiliation(s)
- Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Shilei Xie
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Libing Nie
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Yushan Zheng
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Jie Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Ju Huang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
| | - Mengru Zhao
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Shidong Zhu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
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A single segment substitution line population for identifying traits relevant to drought tolerance and avoidance. Genomics 2019; 114:476-481. [PMID: 31678150 DOI: 10.1016/j.ygeno.2019.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
A population of chromosome segment substitution lines was developed using KDML105 as the recurrent parent and one of DH212 (IR68586-F2-CA-143) or DH103 (IR68586-F2-CA-31) as the donor parent. The donor parents are part of a doubled haploid population from a cross between CT9993, an upland japonica accession, and IR62266, a lowland indica accession. Multiple QTL that are relevant to drought avoidance, drought tolerance and yield traits under drought stress were mapped in this doubled haploid population and the segments selected for the chromosome segment substitution lines were chosen to capture these QTL. The chromosome segment substitution line population was phenotyped under irrigated and mild drought stress conditions, which identified that many yield traits under drought stress had been introduced into the chromosome segment substitution lines.
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Smita S, Katiyar A, Lenka SK, Dalal M, Kumar A, Mahtha SK, Yadav G, Chinnusamy V, Pandey DM, Bansal KC. Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis. Funct Integr Genomics 2019; 20:29-49. [PMID: 31286320 DOI: 10.1007/s10142-019-00697-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/31/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Abiotic stress tolerance is a complex trait regulated by multiple genes and gene networks in plants. A range of abiotic stresses are known to limit rice productivity. Meta-transcriptomics has emerged as a powerful approach to decipher stress-associated molecular network in model crops. However, retaining specificity of gene expression in tolerant and susceptible genotypes during meta-transcriptome analysis is important for understanding genotype-dependent stress tolerance mechanisms. Addressing this aspect, we describe here "abiotic stress tolerant" (ASTR) genes and networks specifically and differentially expressing in tolerant rice genotypes in response to different abiotic stress conditions. We identified 6,956 ASTR genes, key hub regulatory genes, transcription factors, and functional modules having significant association with abiotic stress-related ontologies and cis-motifs. Out of the 6956 ASTR genes, 73 were co-located within the boundary of previously identified abiotic stress trait-related quantitative trait loci. Functional annotation of 14 uncharacterized ASTR genes is proposed using multiple computational methods. Around 65% of the top ASTR genes were found to be differentially expressed in at least one of the tolerant genotypes under different stress conditions (cold, salt, drought, or heat) from publicly available RNAseq data comparison. The candidate ASTR genes specifically associated with tolerance could be utilized for engineering rice and possibly other crops for broad-spectrum tolerance to abiotic stresses.
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Affiliation(s)
- Shuchi Smita
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amit Katiyar
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- ICMR-AIIMS Computational Genomics Center, Div. of I.S.R.M., Indian Council of Medical Research, Ansari Nagar, New Delhi, 110029, India
| | - Sangram Keshari Lenka
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India
| | - Monika Dalal
- ICAR-National Research Center on Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
| | - Amish Kumar
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjeet Kumar Mahtha
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Viswanathan Chinnusamy
- ICAR-Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Dev Mani Pandey
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kailash Chander Bansal
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India.
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India.
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6
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Sircar S, Parekh N. Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach. PLoS One 2019; 14:e0216068. [PMID: 31059518 PMCID: PMC6502313 DOI: 10.1371/journal.pone.0216068] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Drought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress. RESULTS Co-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as 'seed' genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up- and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signalling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signalling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signalling, calcium signalling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions. CONCLUSION Currently, a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community. In this study, a computational approach integrating information from various resources such as gene co-expression networks, protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes.
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Affiliation(s)
- Sanchari Sircar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Nita Parekh
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
- * E-mail:
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7
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Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach. Sci Rep 2017; 7:42131. [PMID: 28181537 PMCID: PMC5299611 DOI: 10.1038/srep42131] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/30/2016] [Indexed: 12/14/2022] Open
Abstract
Traditional cultivars of rice in India exhibit tolerance to drought stress due to their inherent genetic variations. Here we present comparative physiological and transcriptome analyses of two contrasting cultivars, drought tolerant Dhagaddeshi (DD) and susceptible IR20. Microarray analysis revealed several differentially expressed genes (DEGs) exclusively in DD as compared to IR20 seedlings exposed to 3 h drought stress. Physiologically, DD seedlings showed higher cell membrane stability and differential ABA accumulation in response to dehydration, coupled with rapid changes in gene expression. Detailed analyses of metabolic pathways enriched in expression data suggest interplay of ABA dependent along with secondary and redox metabolic networks that activate osmotic and detoxification signalling in DD. By co-localization of DEGs with QTLs from databases or published literature for physiological traits of DD and IR20, candidate genes were identified including those underlying major QTL qDTY1.1 in DD. Further, we identified previously uncharacterized genes from both DD and IR20 under drought conditions including OsWRKY51, OsVP1 and confirmed their expression by qPCR in multiple rice cultivars. OsFBK1 was also functionally validated in susceptible PB1 rice cultivar and Arabidopsis for providing drought tolerance. Some of the DEGs mapped to the known QTLs could thus, be of potential significance for marker-assisted breeding.
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8
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Merewitz E, Xu Y, Huang B. Differentially Expressed Genes Associated with Improved Drought Tolerance in Creeping Bentgrass Overexpressing a Gene for Cytokinin Biosynthesis. PLoS One 2016; 11:e0166676. [PMID: 27855226 PMCID: PMC5113972 DOI: 10.1371/journal.pone.0166676] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 11/02/2016] [Indexed: 12/03/2022] Open
Abstract
Transformation with an isopentenyl transferase (ipt) gene controlling cytokinin (CK) synthesis has been shown to enhance plant drought tolerance. The objective of this study was to identify differentially-expressed genes (DEGs) in creeping bentgrass (Agrostis stolonifera) overexpressing ipt compared to non-transgenic plants. The ipt transgene was controlled by a senescence-activated promoter (SAG12). Both a null transformed line (NT) and SAG12-ipt plants were exposed to drought stress in an environmentally-controlled growth chamber until the soil water content declined to approximately 5% and leaf relative water content declined to 47%, which were both significantly below the well-watered controls. RNA was extracted from leaf samples of both well-watered and drought-stressed plants. Eight sets of subtractive hybridizations were performed for detection of up-regulated and down-regulated genes due to the presence of the transgene and due to drought stress in both NT and transgenic plants. Sequencing analysis revealed the identity of 252 DEGs due to either the transgene and drought stress. Sequencing analysis of 170 DEGs identified genes encoding for proteins that were related to energy production, metabolism, stress defense, signaling, protein synthesis and transport, and membrane transport could play major roles in the improved drought tolerance by overexpressing ipt in creeping bentgrass.
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Affiliation(s)
- Emily Merewitz
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, 48824, United States of America
| | - Yi Xu
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, United States of America
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, United States of America
- * E-mail:
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9
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Divided Infringement in the Limelight of the Patent Battle Field. Trends Biotechnol 2016; 34:771-773. [PMID: 27262507 DOI: 10.1016/j.tibtech.2016.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 11/23/2022]
Abstract
Diagnostic patents usually comprise multiple steps and can be jointly implemented by different parties. However, in the USA, joint implementation may render diagnostic patents unenforceable in light of recent court opinions. Here, I explain how inappropriate claim drafting may render a diagnostic patent vulnerable to joint implementation.
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Prince SJ, Joshi T, Mutava RN, Syed N, Joao Vitor MDS, Patil G, Song L, Wang J, Lin L, Chen W, Shannon JG, Valliyodan B, Xu D, Nguyen HT. Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:65-78. [PMID: 26475188 DOI: 10.1016/j.plantsci.2015.08.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 08/17/2015] [Accepted: 08/22/2015] [Indexed: 05/20/2023]
Abstract
Drought stress causes significant yield losses in major oil seed crops, such as soybean [Glycine max (L.) Merr]. Few soybean lines have been identified as canopy-wilting tolerant; however, the molecular mechanism conferring tolerance is not fully understood. To understand the biological process, a whole genome transcriptome analysis was performed for leaf tissues of two contrasting soybean lines: drought-susceptible (DS) Pana and drought-tolerant (DT) PI 567690. A pairwise comparison of the DS and DT lines under drought and control conditions detected 1914 and 670 genes with a greater than two-fold change in expression under drought conditions. Pairwise treatment comparison and gene enrichment analysis on the DT line showed the down-regulation of genes associated with protein binding, hydrolase activity, carbohydrate/lipid metabolism, xyloglucan endo-transglycosylases associated with cell-wall, apoplast, and chlorophyll a/b binding proteins. On the other hand, genes that were associated with the biotic stress response, ion binding and transport, the oxido-reductive process and electron carrier activity were up-regulated. Gene enrichment analysis detected UDP glucuronosyl transferase activity-encoding genes to be differentially expressed in PI 567690 under drought stress conditions. We found valuable SNPs variation in aquaporin genes of the DT line that are conserved in known slower canopy-wilting lines, this should facilitate marker-assisted selection in soybeans with improved drought tolerance.
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Affiliation(s)
- Silvas J Prince
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Trupti Joshi
- Department of Computer Science, Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Raymond N Mutava
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Naeem Syed
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, United Kingdom
| | | | - Gunvant Patil
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Li Song
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - JiaoJiao Wang
- Department of Computer Science, Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Li Lin
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Wei Chen
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - J Grover Shannon
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Department of Computer Science, Informatics Institute, University of Missouri, Columbia, MO 65211, USA; School of Human and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, United Kingdom
| | - Henry T Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA.
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11
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Qiao G, Wen XP, Zhang T. Molecular cloning and characterization of the light-harvesting chlorophyll a/b gene from the pigeon pea (Cajanus cajan). Appl Biochem Biotechnol 2015; 177:1447-55. [PMID: 26329890 DOI: 10.1007/s12010-015-1825-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/23/2015] [Indexed: 11/29/2022]
Abstract
Light-harvesting chlorophyll a/b-binding proteins (LHCB) have been implicated in the stress response. In this study, a gene encoding LHCB in the pigeon pea was cloned and characterized. Based on the sequence of a previously obtained 327 bp Est, a full-length 793 bp cDNA was cloned using the rapid amplification of cDNA ends (RACE) method. It was designated CcLHCB1 and encoded a 262 amino acid protein. The calculated molecular weight of the CcLHCB1 protein was 27.89 kDa, and the theoretical isoelectric point was 5.29. Homology search and sequence multi-alignment demonstrated that the CcLHCB1 protein sequence shared a high identity with LHCB from other plants. Bioinformatics analysis revealed that CcLHCB1 was a hydrophobic protein with three transmembrane domains. By fluorescent quantitative real-time polymerase chain reaction (PCR), CcLHCB1 mRNA transcripts were detectable in different tissues (leaf, stem, and root), with the highest level found in the leaf. The expression of CcLHCB1 mRNA in the leaves was up-regulated by drought stimulation and AM inoculation. Our results provide the basis for a better understanding of the molecular organization of LCHB and might be useful for understanding the interaction between plants and microbes in the future.
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Affiliation(s)
- Guang Qiao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region and Ministry of Education, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, China
| | - Xiao-Peng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region and Ministry of Education, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, China.
| | - Ting Zhang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region and Ministry of Education, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, China
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12
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Nouri MZ, Moumeni A, Komatsu S. Abiotic Stresses: Insight into Gene Regulation and Protein Expression in Photosynthetic Pathways of Plants. Int J Mol Sci 2015; 16:20392-416. [PMID: 26343644 PMCID: PMC4613210 DOI: 10.3390/ijms160920392] [Citation(s) in RCA: 65] [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: 06/25/2015] [Revised: 08/13/2015] [Accepted: 08/21/2015] [Indexed: 01/05/2023] Open
Abstract
Global warming and climate change intensified the occurrence and severity of abiotic stresses that seriously affect the growth and development of plants,especially, plant photosynthesis. The direct impact of abiotic stress on the activity of photosynthesis is disruption of all photosynthesis components such as photosystem I and II, electron transport, carbon fixation, ATP generating system and stomatal conductance. The photosynthetic system of plants reacts to the stress differently, according to the plant type, photosynthetic systems (C₃ or C₄), type of the stress, time and duration of the occurrence and several other factors. The plant responds to the stresses by a coordinate chloroplast and nuclear gene expression. Chloroplast, thylakoid membrane, and nucleus are the main targets of regulated proteins and metabolites associated with photosynthetic pathways. Rapid responses of plant cell metabolism and adaptation to photosynthetic machinery are key factors for survival of plants in a fluctuating environment. This review gives a comprehensive view of photosynthesis-related alterations at the gene and protein levels for plant adaptation or reaction in response to abiotic stress.
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Affiliation(s)
- Mohammad-Zaman Nouri
- Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization (AREEO), Amol 46191-91951, Iran.
| | - Ali Moumeni
- Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization (AREEO), Amol 46191-91951, Iran.
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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13
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Aneja B, Yadav NR, Kumar N, Yadav RC. Hsp transcript induction is correlated with physiological changes under drought stress in Indian mustard. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2015; 21:305-16. [PMID: 26261395 PMCID: PMC4524871 DOI: 10.1007/s12298-015-0305-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 05/28/2023]
Abstract
Brassica juncea is an important oilseed crop and drought stress is major abiotic stress that limits its growth and productivity. RH0116 (drought tolerant) and RH8812 (drought sensitive) genotypes were undertaken to study some of the physiological parameters and hsp gene expression related to stress tolerance under drought stress conditions. Differential response in terms of seed germination, electrolyte leakage, RWC, osmotic potential was observed in the selected genotypes. In vitro seed germination studies using PEG stress treatments indicated reduced seed germination with increasing levels of stress treatment. Electrolyte leakage increased, whereas, relative water content and osmotic potential decreased in stressed seedlings. Expression of hsp gene was found to be upregulated during drought stress as the transcripts were present only in the stressed plants and disappeared upon rehydration. The drought tolerant variety showed higher transcript accumulation as compared to the sensitive variety. The study showed that drought induced changes in gene expression in two contrasting genotypes were consistent with the physiological response.
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Affiliation(s)
- Bharti Aneja
- />Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125 004 India
| | - Neelam R. Yadav
- />Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125 004 India
| | - Neeraj Kumar
- />Department of Botany and Plant Physiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125 004 India
| | - Ram C. Yadav
- />Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125 004 India
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14
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Proteomic analysis of upland rice (Oryza sativa L.) exposed to intermittent water deficit. Protein J 2014; 33:221-30. [PMID: 24652039 DOI: 10.1007/s10930-014-9554-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Rice is the most important crop consumed all over the world. In Brazil, irrigated rice covers 50 % of the rice producing area and is responsible for 75 % of the national production. Upland rice covers most of the remaining area, and is therefore, a very important production system in the country. In the present study, we have used the drought tolerant upland rice variety Três Meses Antigo to investigate the proteomic changes that occur during drought stress. Plants were submitted to drought by the reposition of 50 % of the water lost daily. Twenty days after the beginning of the drought stress period, leaves were harvested and used for protein extraction. The 2D maps obtained from treated and control plants revealed 408 reproducible spots, 44 of which were identified by mass spectrometry, including 15 differential proteins. Several unaltered proteins were also identified (39 spots) and were mainly involved in photosynthesis. Taken together, the results obtained suggest that the tolerant upland rice up-regulates anti-oxidant and energy production related proteins in order to cope with water deficit.
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15
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ZHANG JI, CRUZ DE CARVALHO MARIAH, TORRES‐JEREZ IVONE, KANG YUN, ALLEN STACYN, HUHMAN DAVIDV, TANG YUHONG, MURRAY JEREMY, SUMNER LLOYDW, UDVARDI MICHAELK. Global reprogramming of transcription and metabolism in
M
edicago truncatula
during progressive drought and after rewatering. PLANT, CELL & ENVIRONMENT 2014; 37:2553-76. [PMID: 24661137 PMCID: PMC4260174 DOI: 10.1111/pce.12328] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 03/14/2014] [Accepted: 03/16/2014] [Indexed: 05/18/2023]
Affiliation(s)
- JI‐YI ZHANG
- Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA
| | | | - IVONE TORRES‐JEREZ
- Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA
| | - YUN KANG
- Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA
| | - STACY N. ALLEN
- Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA
| | - DAVID V. HUHMAN
- Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA
| | - YUHONG TANG
- Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA
| | - JEREMY MURRAY
- Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA
| | - LLOYD W. SUMNER
- Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA
| | - MICHAEL K. UDVARDI
- Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA
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16
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Thu NBA, Hoang XLT, Doan H, Nguyen TH, Bui D, Thao NP, Tran LSP. Differential expression analysis of a subset of GmNAC genes in shoots of two contrasting drought-responsive soybean cultivars DT51 and MTD720 under normal and drought conditions. Mol Biol Rep 2014. [PMID: 24985975 DOI: 10.1007/s11105-014-0825-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
NAC transcription factors are known to be involved in regulation of plant responses to drought stress. In this study, the expression of 23 drought-responsive GmNAC genes was assessed in the shoot tissues of DT51 and MTD720, the two soybean varieties with contrasting drought-responsive phenotypes, by real-time quantitative PCR (RT-qPCR) under normal and drought conditions. Results indicated that expression profile of GmNAC genes was genotype-dependent, and six GmNACs (GmNAC019, 043, 062, 085, 095 and 101) had higher transcript levels in the shoots of the drought-tolerant DT51 in comparison with the drought-sensitive MTD720 under drought. Our study suggests a positive correlation between the higher drought tolerance degree of DT51 versus MTD720 and the up-regulation of at least these six drought-responsive GmNACs in the shoot tissues. Furthermore, on the basis of our analysis, three genes, GmNAC043, 085 and 101, were identified as promising candidates for development of drought-tolerant soybean cultivars by genetic engineering.
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Affiliation(s)
- Nguyen Binh Anh Thu
- School of Biotechnology, International University, Vietnam National University HCMC, Block 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
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17
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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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18
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Sheth BP, Thaker VS. Plant systems biology: insights, advances and challenges. PLANTA 2014; 240:33-54. [PMID: 24671625 DOI: 10.1007/s00425-014-2059-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/06/2014] [Indexed: 05/20/2023]
Abstract
Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.
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Affiliation(s)
- Bhavisha P Sheth
- Department of Biosciences, Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Saurashtra University, Rajkot, 360005, Gujarat, India,
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19
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Liu Y, Liu M, Li X, Cao B, Ma X. Identification of differentially expressed genes in leaf of Reaumuria soongorica under PEG-induced drought stress by digital gene expression profiling. PLoS One 2014; 9:e94277. [PMID: 24736242 PMCID: PMC3988058 DOI: 10.1371/journal.pone.0094277] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/14/2014] [Indexed: 12/17/2022] Open
Abstract
Reaumuria soongorica (Pall.) Maxim., a resurrection semi-shrub, is a typical constructive and dominant species in desert ecosystems in northwestern China. However, the gene expression characteristics of R. soongorica under drought stress have not been elucidated. Digital gene expression analysis was performed using Illumina technique to investigate differentially expressed genes (DEGs) between control and PEG-treated samples of R. soongorica. A total of 212,338 and 211,052 distinct tags were detected in the control and PEG-treated libraries, respectively. A total of 1,325 genes were identified as DEGs, 379 (28.6%) of which were up-regulated and 946 (71.4%) were down-regulated in response to drought stress. Functional annotation analysis identified numerous drought-inducible genes with various functions in response to drought stress. A number of regulatory proteins, functional proteins, and proteins induced by other stress factors in R. soongorica were identified. Alteration in the regulatory proteins (transcription factors and protein kinase) may be involved in signal transduction. Functional proteins, including flavonoid biosynthetic proteins, late embryogenesis abundant (LEA) proteins, small heat shock proteins (sHSP), and aquaporin and proline transporter may play protective roles in response to drought stress. Flavonoids, LEA proteins and sHSP function as reactive oxygen species scavenger or molecular chaperone. Aquaporin and proline transporters regulate the distribution of water and proline throughout the whole plant. The tolerance ability of R. soongorica may be gained through effective signal transduction and enhanced protection of functional proteins to reestablish cellular homeostasis. DEGs obtained in this study may provide useful insights to help further understand the drought-tolerant mechanism of R. soongorica.
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Affiliation(s)
- Yubing Liu
- Shapotou Desert Research & Experiment Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P. R. China
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P. R. China
- * E-mail:
| | - Meiling Liu
- Shapotou Desert Research & Experiment Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P. R. China
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P. R. China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinrong Li
- Shapotou Desert Research & Experiment Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P. R. China
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P. R. China
| | - Bo Cao
- Shapotou Desert Research & Experiment Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P. R. China
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P. R. China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, P. R. China
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20
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Fonseca C, Planchon S, Pinheiro C, Renaut J, Ricardo CP, Oliveira MM, Batista R. Maize IgE binding proteins: each plant a different profile? Proteome Sci 2014; 12:17. [PMID: 24650160 PMCID: PMC3999935 DOI: 10.1186/1477-5956-12-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 03/11/2014] [Indexed: 01/06/2023] Open
Abstract
Background Allergies are nearly always triggered by protein molecules and the majority of individuals with documented immunologic reactions to foods exhibit IgE hypersensitivity reactions. In this study we aimed to understand if natural differences, at proteomic level, between maize populations, may induce different IgE binding proteins profiles among maize-allergic individuals. We also intended to deepen our knowledge on maize IgE binding proteins. Results In order to accomplish this goal we have used proteomic tools (SDS-PAGE and 2-D gel electrophoresis followed by western blot) and tested plasma IgE reactivity from four maize-allergic individuals against four different protein fractions (albumins, globulins, glutelins and prolamins) of three different maize cultivars. We have observed that maize cultivars have different proteomes that result in different IgE binding proteins profiles when tested against plasma from maize-allergic individuals. We could identify 19 different maize IgE binding proteins, 11 of which were unknown to date. Moreover, we found that most (89.5%) of the 19 identified potential maize allergens could be related to plant stress. Conclusions These results lead us to conclude that, within each species, plant allergenic potential varies with genotype. Moreover, considering the stress-related IgE binding proteins identified, we hypothesise that the environment, particularly stress conditions, may alter IgE binding protein profiles of plant components.
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Affiliation(s)
| | | | | | | | | | | | - Rita Batista
- National Health Institute Dr, Ricardo Jorge, Av, Padre Cruz, 1649-016 Lisboa, Portugal.
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21
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Kumar D, Datta R, Sinha R, Ghosh A, Chattopadhyay S. Proteomic profiling of γ-ECS overexpressed transgenic Nicotiana in response to drought stress. PLANT SIGNALING & BEHAVIOR 2014; 9:e29246. [PMID: 25763614 PMCID: PMC4203497 DOI: 10.4161/psb.29246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 05/29/2023]
Abstract
The contribution of Glutathione (GSH) in drought stress tolerance is an established fact. However, the proteins which are directly or indirectly related to the increased level of GSH in response to drought stress are yet to be known. To explore this, here, transgenic tobacco plants (NtGp11) overexpressing gamma-glutamylcysteine synthetase (γ-ECS) was tested for tolerance against drought stress. NtGp11 conferred tolerance to drought stress by increased germination rate, water retention, water recovery, chlorophyll, and proline content compared with wild-type plants. Semi-quantitative RT-PCR analysis revealed that the transcript levels of stress-responsive genes were higher in NtGp11 compared with wild-type in response to drought stress. Two-dimensional gel electrophoresis (2-DE) coupled with MALDI TOF-TOF MS/MS analysis has been used to identify 43 differentially expressed proteins in response to drought in wild-type and NtGp11 plants. The results demonstrated the up-accumulation of 58.1% of proteins among which 36%, 24%, and 20% of them were related to stress and defense, carbon metabolism and energy metabolism categories, respectively. Taken together, our results demonstrated that GSH plays an important role in combating drought stress in plants by inducing stress related genes and proteins like HSP70, chalcone synthase, glutathione peroxidase, thioredoxin peroxidase, ACC oxidase, and heme oxygenase I.
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Affiliation(s)
- Deepak Kumar
- Plant Biology Laboratory; Drug Development/Diagnostics and Biotechnology Division; CSIR-Indian Institute of Chemical Biology; Kolkata, India
| | - Riddhi Datta
- Plant Biology Laboratory; Drug Development/Diagnostics and Biotechnology Division; CSIR-Indian Institute of Chemical Biology; Kolkata, India
| | - Ragini Sinha
- Plant Biology Laboratory; Drug Development/Diagnostics and Biotechnology Division; CSIR-Indian Institute of Chemical Biology; Kolkata, India
| | - Aparupa Ghosh
- Plant Biology Laboratory; Drug Development/Diagnostics and Biotechnology Division; CSIR-Indian Institute of Chemical Biology; Kolkata, India
| | - Sharmila Chattopadhyay
- Plant Biology Laboratory; Drug Development/Diagnostics and Biotechnology Division; CSIR-Indian Institute of Chemical Biology; Kolkata, India
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22
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Des Marais DL, Hernandez KM, Juenger TE. Genotype-by-Environment Interaction and Plasticity: Exploring Genomic Responses of Plants to the Abiotic Environment. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135806] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David L. Des Marais
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712;
| | - Kyle M. Hernandez
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712;
| | - Thomas E. Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712;
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
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23
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Sanchez DH. Physiological and biotechnological implications of transcript-level variation under abiotic stress. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:925-930. [PMID: 24033916 DOI: 10.1111/plb.12075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/09/2013] [Indexed: 06/02/2023]
Abstract
The discovery of genes that can be used to increase plant tolerance to environmental stress has practical implications for agriculture, since knowledge at the molecular level can potentially be translated from model plants to crops or from tolerant to sensitive cultivars. For more than a decade, researchers have attempted to identify transcriptional and metabolic pathways involved in stress tolerance using functional genomics tools. In some cases, promising results were obtained when a clear causal link was found between transcripts and tolerance/sensitivity to stress. However, recent reports question the global translational power of functional genomics for biotechnological applications, as one of the main limitations seems to be the large variability in gene expression. Transcript-level variability under stress has not been considered of interest in the scientific literature because it is intuitively obvious, but most reports seem to naively overlook the consequences. Here, three case situations are reviewed (variability between genotypes, variability due to environmental interactions and variability between stressors) in support of the concept that inherent transcript-level variation in biological systems may limit our knowledge of environmental plant tolerance and of functional genomics in molecular stress physiology.
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Affiliation(s)
- D H Sanchez
- Laboratory of Plant Genetics-Sciences III, University of Geneva, Geneva, Switzerland
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24
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Insight into differential responses of upland and paddy rice to drought stress by comparative expression profiling analysis. Int J Mol Sci 2013; 14:5214-38. [PMID: 23459234 PMCID: PMC3634487 DOI: 10.3390/ijms14035214] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 01/30/2013] [Accepted: 02/05/2013] [Indexed: 12/13/2022] Open
Abstract
In this study, the drought responses of two genotypes, IRAT109 and Zhenshan 97 (ZS97), representing upland and paddy rice, respectively, were systematically compared at the morphological, physiological and transcriptional levels. IRAT109 has better performance in traits related to drought avoidance, such as leaf rolling, root volumes, the ratio of leaf water loss and relative conductivity. At the transcriptional level, more genes were induced by drought in IRAT109 at the early drought stage, but more genes had dynamic expression patterns in ZS97 at different drought degrees. Under drought conditions, more genes related to reproductive development and establishment of localization were repressed in IRAT109, but more genes involved in degradation of cellular components were induced in ZS97. By checking the expression patterns of 36 drought-responsive genes (located in 14 quantitative trail loci [QTL] intervals) in ZS97, IRAT109 and near isogenic lines (NILs) of the QTL intervals, we found that more than half of these genes had their expression patterns or expression levels changed in the NILs when compared to that in ZS97 or IRAT109. Our results may provide valuable information for dissecting the genetic bases of traits related to drought resistance, as well as for narrowing the candidate genes for the traits.
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25
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Polyphasic chlorophyll a fluorescence kinetics and leaf protein analyses to track dynamics of photosynthetic performance in mulberry during progressive drought. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 119:71-83. [DOI: 10.1016/j.jphotobiol.2012.12.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 10/12/2012] [Accepted: 12/17/2012] [Indexed: 12/30/2022]
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26
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Zhang J, Li D, Zou D, Luo F, Wang X, Zheng Y, Li X. A cotton gene encoding a plasma membrane aquaporin is involved in seedling development and in response to drought stress. Acta Biochim Biophys Sin (Shanghai) 2013. [PMID: 23178915 DOI: 10.1093/abbs/gms096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cotton (Gossypium hirsutum), the most important textile crop worldwide, often encounters abiotic stress such as drought and waterlog during its growth season (summer), and its productivity is significantly limited by adverse factors. To investigate the molecular adaptation mechanisms of this plant species to abiotic stress, a gene encoding the plasma membrane intrinsic protein (PIP) was isolated in cotton, and designated as GhPIP2;7. Quantitative reverse transcriptase polymerase chain reaction analysis indicated that GhPIP2;7 was preferentially expressed in cotyledons and leaves, and its expression was up-regulated in leaves after drought treatments. Strong expression of GUS gene driven by GhPIP2;7 promoter was detected in leaves of 5- to 10-day-old transgenic Arabidopsis seedlings, but GUS activity gradually became weak as the seedlings further developed. GhPIP2;7 promoter activity was also remarkably induced by mannitol treatment. Furthermore, yeast cells over-expressing GhPIP2;7 displayed relatively higher drought tolerance, compared with controls. Over-expression of GhPIP2;7 in Arabidopsis enhanced plant tolerance to drought stress. Collectively, these data suggested that GhPIP2;7 gene may be involved in leaf development and in response to drought stress.
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Affiliation(s)
- Jie Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
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Cal AJ, Liu D, Mauleon R, Hsing YIC, Serraj R. Transcriptome profiling of leaf elongation zone under drought in contrasting rice cultivars. PLoS One 2013; 8:e54537. [PMID: 23372737 PMCID: PMC3553057 DOI: 10.1371/journal.pone.0054537] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/13/2012] [Indexed: 11/19/2022] Open
Abstract
Inhibition of leaf elongation and expansion is one of the earliest responses of rice to water deficit. Despite this sensitivity, a great deal of genetic variation exists in the extant of leaf elongation rate (LER) reduction in response to declining soil moisture. We analyzed global gene expression in the leaf elongation zone under drought in two rice cultivars with disparate LER sensitivities to water stress. We found little overlap in gene regulation between the two varieties under moderate drought; however, the transcriptional response to severe drought was more conserved. In response to moderate drought, we found several genes related to secondary cell wall deposition that were down regulated in Moroberekan, an LER tolerant variety, but up-regulated in LER sensitive variety IR64.
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Affiliation(s)
- Andrew J Cal
- International Rice Research Institute, Los Baños, Philippines.
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Peng S, Jiang H, Zhang S, Chen L, Li X, Korpelainen H, Li C. Transcriptional profiling reveals sexual differences of the leaf transcriptomes in response to drought stress in Populus yunnanensis. TREE PHYSIOLOGY 2012; 32:1541-1555. [PMID: 23148036 DOI: 10.1093/treephys/tps110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Populus yunnanensis Dode., a native dioecious woody plant species in Southwest China, plays an important role in commercial forestry and environmental protection. In natural habitats, female P. yunnanensis trees are extremely rare while males are dominant in population. Our previous physiological studies in the species have revealed sex-dependent difference in response to drought stress, and females suffer greater negative effects than males. However, the molecular basis of sex-related differences during drought stress has been poorly characterized. We use the Illumina-Solexa platform to sequence the leaf transcriptomes derived from male and female P. yunnanensis trees grown in normal condition and drought stress. In total, 22,235 transcripts were identified in this study and 6039 genes were differentially expressed (DEGs) during drought stress. Majority of the DEGs were identified in males (92%, 5539); thus, males had greater remodeling of the leaf transcriptome in response to drought compared with females. Furthermore, many genes involved in hormone biosynthesis, photosynthesis and reactive oxygen species (ROS) scavenging enzyme system had more transcript changes in males than in females during drought stress, while these genes exhibited higher transcript alteration in females than in males in normal condition. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis of 15 selected genes suggested that during drought treatment the up-regulated DEGs had a quicker increment in their transcript abundances in females than that in males. The sexual differences of gene transcription coincide with the sexual different adaptation of P. yunnanensis in the present natural habitats.
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Affiliation(s)
- Shuming Peng
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu 610041, China
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Xia Y, Ning Z, Bai G, Li R, Yan G, Siddique KHM, Baum M, Guo P. Allelic variations of a light harvesting chlorophyll a/b-binding protein gene (Lhcb1) associated with agronomic traits in barley. PLoS One 2012; 7:e37573. [PMID: 22662173 PMCID: PMC3360778 DOI: 10.1371/journal.pone.0037573] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 04/21/2012] [Indexed: 11/19/2022] Open
Abstract
Light-harvesting chlorophyll a/b-binding protein (LHCP) is one of the most abundant chloroplast proteins in plants. Its main function is to collect and transfer light energy to photosynthetic reaction centers. However, the roles of different LHCPs in light-harvesting antenna systems remain obscure. Exploration of nucleotide variation in the genes encoding LHCP can facilitate a better understanding of the functions of LHCP. In this study, nucleotide variations in Lhcb1, a LHCP gene in barley, were investigated across 292 barley accessions collected from 35 different countries using EcoTILLING technology, a variation of the Targeting Induced Local Lesions In Genomes (TILLING). A total of 23 nucleotide variations were detected including three insert/deletions (indels) and 20 single nucleotide polymorphisms (SNPs). Among them, 17 SNPs were in the coding region with nine missense changes. Two SNPs with missense changes are predicted to be deleterious to protein function. Seventeen SNP formed 31 distinguishable haplotypes in the barley collection. The levels of nucleotide diversity in the Lhcb1 locus differed markedly with geographic origins and species of accessions. The accessions from Middle East Asia exhibited the highest nucleotide and haplotype diversity. H. spontaneum showed greater nucleotide diversity than H. vulgare. Five SNPs in Lhcb1 were significantly associated with at least one of the six agronomic traits evaluated, namely plant height, spike length, number of grains per spike, thousand grain weight, flag leaf area and leaf color, and these SNPs may be used as potential markers for improvement of these barley traits.
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Affiliation(s)
- Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, China
| | - Zhengxiang Ning
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, China
| | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service, Manhattan, Kansas, United States of America
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Guijun Yan
- The Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Kadambot H. M. Siddique
- The Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas, Aleppo, Syria
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
- * E-mail:
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Manavalan LP, Chen X, Clarke J, Salmeron J, Nguyen HT. RNAi-mediated disruption of squalene synthase improves drought tolerance and yield in rice. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:163-75. [PMID: 21926092 PMCID: PMC3245457 DOI: 10.1093/jxb/err258] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
About one-third of the world's rice area is in rain-fed lowlands and most are prone to water shortage. The identification of genes imparting tolerance to drought in the model cereal plant, rice, is an attractive strategy to engineer improved drought tolerance not only rice but other cereals as well. It is demonstrated that RNAi-mediated disruption of a rice farnesyltransferase/squalene synthase (SQS) by maize squalene synthase improves drought tolerance at both the vegetative and reproductive stages. Twenty-day-old seedlings of wild type (Nipponbare) and seven independent events of transgenic RNAi lines showed no difference in morphology. When subjected to water stress for a period of 32 d under growth chamber conditions, transgenic positives showed delayed wilting, conserved more soil water, and improved recovery. When five independent events along with wild-type plants were subjected to drought at the reproductive stage under greenhouse conditions, the transgenic plants lost water more slowly compared with the wild type, through reduced stomatal conductance and the retention of high leaf relative water content (RWC). After 28 d of slow progressive soil drying, transgenic plants recovered better and flowered earlier than wild-type plants. The yield of water-stressed transgenic positive plants ranged from 14-39% higher than wild-type plants. When grown in plates with Yoshida's nutrient solution with 1.2% agar, transgenic positives from three independent events showed increased root length and an enhanced number of lateral roots. The RNAi-mediated inactivation produced reduced stomatal conductance and subsequent drought tolerance.
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Affiliation(s)
| | - Xi Chen
- Syngenta Biotechnology Inc, Research Triangle Park, NC-27709, USA
| | - Joseph Clarke
- Syngenta Biotechnology Inc, Research Triangle Park, NC-27709, USA
| | - John Salmeron
- Syngenta Biotechnology Inc, Research Triangle Park, NC-27709, USA
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO-65211, USA
- To whom correspondence should be addressed. E-mail:
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Todaka D, Nakashima K, Shinozaki K, Yamaguchi-Shinozaki K. Toward understanding transcriptional regulatory networks in abiotic stress responses and tolerance in rice. RICE (NEW YORK, N.Y.) 2012; 5:6. [PMID: 24764506 PMCID: PMC3834508 DOI: 10.1186/1939-8433-5-6] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 03/08/2012] [Indexed: 05/18/2023]
Abstract
Abiotic stress causes loss of crop production. Under abiotic stress conditions, expression of many genes is induced, and their products have important roles in stress responses and tolerance. Progress has been made in understanding the biological roles of regulons in abiotic stress responses in rice. A number of transcription factors (TFs) regulate stress-responsive gene expression. OsDREB1s and OsDREB2s were identified as abiotic-stress responsive TFs that belong to the AP2/ERF family. Similar to Arabidopsis, these DREB regulons were most likely not involved in the abscisic acid (ABA) pathway. OsAREBs such as OsAREB1 were identified as key components in ABA-dependent transcriptional networks in rice. OsNAC/SNACs including OsNAC6 were characterized as factors that regulate expression of genes important for abiotic stress responses in rice. Here, we review on the rice abiotic-stress responses mediated by transcriptional networks, with the main focus on TFs that function in abiotic stress responses and confer stress tolerance in rice.
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Affiliation(s)
- Daisuke Todaka
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Kazuo Nakashima
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Kazuo Shinozaki
- RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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Chen J, Chang SX, Anyia AO. Gene discovery in cereals through quantitative trait loci and expression analysis in water-use efficiency measured by carbon isotope discrimination. PLANT, CELL & ENVIRONMENT 2011; 34:2009-23. [PMID: 21752030 DOI: 10.1111/j.1365-3040.2011.02397.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Drought continues to be a major constraint on cereal production in many areas, and the frequency of drought is likely to increase in most arid and semi-arid regions under future climate change scenarios. Considerable research and breeding efforts have been devoted to investigating crop responses to drought at various levels and producing drought-resistant genotypes. Plant physiology has provided new insights to yield improvement in drought-prone environments. Crop performance could be improved through increases in water use, water-use efficiency (WUE) and harvest index. Greater WUE can be achieved by coordination between photosynthesis and transpiration. Carbon isotope discrimination (Δ(13) C) has been demonstrated to be a simple but reliable measure of WUE, and negative correlation between them has been used to indirectly estimate WUE under selected environments. New tools, such as quantitative trait loci (QTL) mapping and gene expression profiling, are playing vital roles in dissecting drought resistance-related traits. The combination of gene expression and association mapping could help identify candidate genes underlying the QTL of interest and complement map-based cloning and marker-assisted selection. Eventually, improved cultivars can be produced through genetic engineering. Future efficient and effective breeding progress in cereals under targeted drought environments will come from the integrated knowledge of physiology and genomics.
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Affiliation(s)
- Jing Chen
- Department of Renewable Resources, 442 Earth Sciences Building, University of Alberta, Edmonton, Alberta, Canada
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Kang Y, Han Y, Torres-Jerez I, Wang M, Tang Y, Monteros M, Udvardi M. System responses to long-term drought and re-watering of two contrasting alfalfa varieties. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:871-89. [PMID: 21838776 DOI: 10.1111/j.1365-313x.2011.04738.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Systems analysis of two alfalfa varieties, Wisfal (Medicago sativa ssp. falcata var. Wisfal) and Chilean (M. sativa ssp. sativa var. Chilean), with contrasting tolerance/sensitivity to drought revealed common and divergent responses to drought stress. At a qualitative level, molecular, biochemical, and physiological responses to drought stress were similar in the two varieties, indicating that they employ the same strategies to cope with drought. However, quantitative differences in responses at all levels were revealed that may contribute to greater drought tolerance in Wisfal. These included lower stomatal density and conductance in Wisfal; delayed leaf senescence compared with Chilean; greater root growth following a drought episode, and greater accumulation of osmolytes, including raffinose and galactinol, and flavonoid antioxidants in roots and/or shoots of Wisfal. Genes encoding transcription factors and other regulatory proteins, and genes involved in the biosynthesis of osmolytes and (iso)flavonoids were differentially regulated between the two varieties and represent potential targets for improving drought tolerance in alfalfa in the future.
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Affiliation(s)
- Yun Kang
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
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Sharoni AM, Nuruzzaman M, Satoh K, Moumeni A, Attia K, Venuprasad R, Serraj R, Kumar A, Leung H, Islam AKMR, Kikuchi S. Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. Mol Genet Genomics 2011; 287:1-19. [PMID: 22102215 PMCID: PMC3249189 DOI: 10.1007/s00438-011-0659-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 11/07/2011] [Indexed: 11/26/2022]
Abstract
The AP2/EREBP genes play various roles in developmental processes and in stress-related responses in plants. Genome-wide microarrays based on the gene expression profiles of the AP2/EREBP family were analyzed under conditions of normal growth and drought stress. The preferential expression of fifteen genes was observed in specific tissues, suggesting that these genes may play important roles in vegetative and reproductive stages of growth. A large number of redundant genes were differentially expressed following phytohormone treatments (NAA, GA3, KT, SA, JA, and ABA). To investigate the gene expression responses in the root, leaf, and panicle of three rice genotypes, two drought stress conditions were applied using the fraction of transpirable soil water (FTSW) under severe (0.2 FTSW), mild (0.5 FTSW), and control (1.0 FTSW) conditions. Following treatment, transcriptomic analysis using a 44-K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from two near-isogenic lines, IR77298-14-1-2-B-10 (drought tolerant) and IR77298-14-1-2-B-13 (drought susceptible), under drought stress conditions. The majority of the genes that were activated in the IR77298-14-1-2-B-10 line were members of the AP2/EREBP gene family. Non-redundant genes (sixteen) were found in the drought-tolerant line, and four genes were selected as candidate novel reference genes because of their higher expression levels in IR77298-14-1-2-B-10. Most of the genes in the AP2, B3, and B5 subgroups were involved in the panicle under severe stress conditions, but genes from the B1 and B2 subgroups were down-regulated in the root. Of the four subfamilies, RAV exhibited the highest number of up-regulated genes (80%) in the panicle under severe stress conditions in the drought-tolerant line compared to Minghui 63 under normal conditions, and the gene structures of the RAV subfamily may be involved in the response to drought stress in the flowering stage. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis.
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Affiliation(s)
- Akhter Most Sharoni
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
- Department of Botany, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Mohammed Nuruzzaman
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
| | - Kouji Satoh
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
| | - Ali Moumeni
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
| | - Kotb Attia
- Graduate School of Science and Technology, Niigata University, Ikarashi-2, Niigata, 950-2181 Japan
- Centre of Excellence in Biotechnology Research, King Saud University, Riyadh, 11451 Kingdom of Saudi Arabia
| | - Ramiah Venuprasad
- Africa Rice Center (AfricaRice), Ibadan Station, c/o IITA, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Rachid Serraj
- Diversification and Sustainable Intensification of Production Systems Program (DSIPSP), International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5466, Aleppo, Syria
| | - Arvind Kumar
- Plant Breeding, Genetics and Biotechnology Division (PBGB), International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines
| | - Hei Leung
- Plant Breeding, Genetics and Biotechnology Division (PBGB), International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines
| | | | - Shoshi Kikuchi
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
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Wang D, Pan Y, Zhao X, Zhu L, Fu B, Li Z. Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice. BMC Genomics 2011; 12:149. [PMID: 21406116 PMCID: PMC3070656 DOI: 10.1186/1471-2164-12-149] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 03/16/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements. RESULTS There were 5,284 genes detected to be differentially expressed under drought stress. Most of these genes were tissue- or stage-specific regulated by drought. The tissue-specific down-regulated genes showed distinct function categories as photosynthesis-related genes prevalent in leaf, and the genes involved in cell membrane biogenesis and cell wall modification over-presented in root and young panicle. In a drought environment, several genes, such as GA2ox, SAP15, and Chitinase III, were regulated in a reciprocal way in two tissues at the same development stage. A total of 261 transcription factor genes were detected to be differentially regulated by drought stress. Most of them were also regulated in a tissue- or stage-specific manner. A cis-element containing special CGCG box was identified to over-present in the upstream of 55 common induced genes, and it may be very important for rice plants responding to drought environment. CONCLUSIONS Genome-wide gene expression profiling revealed that most of the drought differentially expressed genes (DEGs) were under temporal and spatial regulation, suggesting a crosstalk between various development cues and environmental stimuli. The identification of the differentially regulated DEGs, including TF genes and unique candidate cis-element for drought responsiveness, is a very useful resource for the functional dissection of the molecular mechanism in rice responding to environment stress.
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Affiliation(s)
- Di Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
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36
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Qian G, Ping JJ, Zhang Z, Luo SY, Li XY, Yang MZ, Zhang D. [Molecular cloning and protein structure prediction of barley (Hordeum vulgare L.) Dhn6 gene and its expression pattern under dehydration conditions]. YI CHUAN = HEREDITAS 2011; 33:270-7. [PMID: 21402536 DOI: 10.3724/sp.j.1005.2011.00270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Dehydrins (DHNs), proteins with protective functions encoded by the late embryogenesis abundant (LEA), are differentially up-regulated at the transcriptional level under environmental stresses such as water deficit, salinity, and low temperature or in response to ABA. Data involving protein structure and expression of dehydrins could elucidate their functional roles under dehydration conditions in plants. Dhn6 gene of 1767 bp with an intron (92 bp) in six-rowed barley, a member of LEA D11, was cloned into pMD18-T vector in the present study. It shared 93.18% identity with Hordeum vulgare ssp. vulgare (GenBank accession: AF043091), encoding a protein composed of 523 amino acid residues with the predicted molecular weight of 49.68 kDa and the theoretical isoelectric point of 8.04. Analyses of domain and structure indicated that the protein was dominantly composed of 83% hydrophillic amino acid residues, with numerous imperative curls and three loosed helixes. Three-dimensional measurement revealed that the water-soluble lipid-associating protein was attributed to its twisted cable formed by reverse paralleled chains. Moreover, the putative amphipathic α-helices formed by K-segments might play roles in protecting membrane structure in barley. Significantly, relatively high accumulations of Dhn6 gene were detected after 8 h of water deficit by real-time quantitative RT-PCR. These results possibly suggested that the accumulation of Dhn6 gene could be critical for resistant dehydration in plants.
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Affiliation(s)
- Gang Qian
- Department of Cell Biology and Genetics, Zunyi Medical College, and Department of Interventional Radiology, the Affiliated Hospital of Zunyi Medical College, Zunyi 563000, China.
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Yu H, Tu K, Xie L, Li YY. DigOut: viewing differential expression genes as outliers. J Bioinform Comput Biol 2010; 8 Suppl 1:161-75. [PMID: 21155026 DOI: 10.1142/s0219720010005208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 08/25/2010] [Accepted: 09/10/2010] [Indexed: 01/03/2023]
Abstract
With regards to well-replicated two-conditional microarray datasets, the selection of differentially expressed (DE) genes is a well-studied computational topic, but for multi-conditional microarray datasets with limited or no replication, the same task is not properly addressed by previous studies. This paper adopts multivariate outlier analysis to analyze replication-lacking multi-conditional microarray datasets, finding that it performs significantly better than the widely used limit fold change (LFC) model in a simulated comparative experiment. Compared with the LFC model, the multivariate outlier analysis also demonstrates improved stability against sample variations in a series of manipulated real expression datasets. The reanalysis of a real non-replicated multi-conditional expression dataset series leads to satisfactory results. In conclusion, a multivariate outlier analysis algorithm, like DigOut, is particularly useful for selecting DE genes from non-replicated multi-conditional gene expression dataset.
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Affiliation(s)
- Hui Yu
- Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China.
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38
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Cohen D, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D, Hummel I. Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics 2010; 11:630. [PMID: 21073700 PMCID: PMC3091765 DOI: 10.1186/1471-2164-11-630] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 11/12/2010] [Indexed: 12/18/2022] Open
Abstract
Background Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from other Populus species. Results Using a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought. Conclusions In poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.
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Affiliation(s)
- David Cohen
- INRA, Nancy Université, UMR1137 Ecologie et Ecophysiologie Forestières, IFR 110 EFABA, F-54280 Champenoux, France
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Ray S, Dansana PK, Giri J, Deveshwar P, Arora R, Agarwal P, Khurana JP, Kapoor S, Tyagi AK. Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Funct Integr Genomics 2010; 11:157-78. [PMID: 20821243 DOI: 10.1007/s10142-010-0187-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2010] [Revised: 08/10/2010] [Accepted: 08/16/2010] [Indexed: 01/04/2023]
Abstract
Water-deficit stress is detrimental for rice growth, development, and yield. Transcriptome analysis of 1-week-old rice (Oryza sativa L. var. IR64) seedling under water-deficit stress condition using Affymetrix 57 K GeneChip® has revealed 1,563 and 1,746 genes to be up- and downregulated, respectively. In an effort to amalgamate data across laboratories, we identified 5,611 differentially expressing genes under varying extrinsic water-deficit stress conditions in six vegetative and one reproductive stage of development in rice. Transcription factors (TFs) involved in ABA-dependent and ABA-independent pathways have been found to be upregulated during water-deficit stress. Members of zinc-finger TFs namely, C₂H₂, C₂C₂, C₃H, LIM, PHD, WRKY, ZF-HD, and ZIM, along with TF families like GeBP, jumonji, MBF1 and ULT express differentially under water-deficit conditions. NAC (NAM, ATAF and CUC) TF family emerges to be a potential key regulator of multiple abiotic stresses. Among the 12 TF genes that are co-upregulated under water-deficit, salt and cold stress conditions, five belong to the NAC TF family. We identified water-deficit stress-responsive genes encoding key enzymes involved in biosynthesis of osmoprotectants like polyols and sugars; amino acid and quaternary ammonium compounds; cell wall loosening and structural components; cholesterol and very long chain fatty acid; cytokinin and secondary metabolites. Comparison of genes responsive to water-deficit stress conditions with genes preferentially expressed during panicle and seed development revealed a significant overlap of transcriptome alteration and pathways.
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Affiliation(s)
- Swatismita Ray
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
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Gong P, Zhang J, Li H, Yang C, Zhang C, Zhang X, Khurram Z, Zhang Y, Wang T, Fei Z, Ye Z. Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:3563-75. [PMID: 20643807 PMCID: PMC2921197 DOI: 10.1093/jxb/erq167] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Revised: 05/14/2010] [Accepted: 05/17/2010] [Indexed: 05/18/2023]
Abstract
To unravel the molecular mechanisms of drought responses in tomato, gene expression profiles of two drought-tolerant lines identified from a population of Solanum pennellii introgression lines, and the recurrent parent S. lycopersicum cv. M82, a drought-sensitive cultivar, were investigated under drought stress using tomato microarrays. Around 400 genes identified were responsive to drought stress only in the drought-tolerant lines. These changes in genes expression are most likely caused by the two inserted chromosome segments of S. pennellii, which possibly contain drought-tolerance quantitative trait loci (QTLs). Among these genes are a number of transcription factors and signalling proteins which could be global regulators involved in the tomato responses to drought stress. Genes involved in organism growth and development processes were also specifically regulated by drought stress, including those controlling cell wall structure, wax biosynthesis, and plant height. Moreover, key enzymes in the pathways of gluconeogenesis (fructose-bisphosphate aldolase), purine and pyrimidine nucleotide biosynthesis (adenylate kinase), tryptophan degradation (aldehyde oxidase), starch degradation (beta-amylase), methionine biosynthesis (cystathionine beta-lyase), and the removal of superoxide radicals (catalase) were also specifically affected by drought stress. These results indicated that tomato plants could adapt to water-deficit conditions through decreasing energy dissipation, increasing ATP energy provision, and reducing oxidative damage. The drought-responsive genes identified in this study could provide further information for understanding the mechanisms of drought tolerance in tomato.
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Affiliation(s)
- Pengjuan Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Changxian Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chanjuan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziaf Khurram
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 and USDA Robert W Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Zhibiao Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- To whom correspondence should be addressed: E-mail:
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41
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Wang L, Li P, Brutnell TP. Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct Genomics 2010; 9:118-28. [PMID: 20130067 DOI: 10.1093/bfgp/elp057] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Ultra high-throughput sequencing (UHTS) technologies offer the potential to interrogate transcriptomes in detail that has traditionally been restricted to single gene surveys. For instance, it is now possible to globally define transcription start sites, polyadenylation signals, alternative splice sites and generate quantitative data on gene transcript accumulation in single tissues or cell types. These technologies are thus paving the way for whole genome transcriptomics and will undoubtedly lead to novel insights into plant development and biotic and abiotic stress responses. However, several challenges exist to making this technology broadly accessible to the plant research community. These include the current need for a computationally intensive analysis of data sets, a lack of standardized alignment and formatting procedures and a relatively small number of analytical software packages to interpret UHTS outputs. In this review we summarize recent findings from UHTS and discuss potential opportunities and challenges for broad adoption of these technologies in the plant science community.
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Affiliation(s)
- Lin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
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42
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Gao F, Zhang H, Wang H, Gao H, Li Z. Comparative transcriptional profiling under drought stress between upland and lowland rice (Oryza sativa L.) using cDNA-AFLP. Sci Bull (Beijing) 2009. [DOI: 10.1007/s11434-009-0524-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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43
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Foito A, Byrne SL, Shepherd T, Stewart D, Barth S. Transcriptional and metabolic profiles of Lolium perenne L. genotypes in response to a PEG-induced water stress. PLANT BIOTECHNOLOGY JOURNAL 2009; 7:719-32. [PMID: 19702648 DOI: 10.1111/j.1467-7652.2009.00437.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Metabolic profiling was carried out in the forage grass Lolium perenne L. (perennial ryegrass) to uncover mechanisms involved in the plants response to water stress. When leaf and root materials from two genotypes, with a contrasting water stress response, were analysed by GC-MS, a clear difference in the metabolic profiles of the leaf tissue under water stress was observed. Differences were principally due to a reduction in fatty acid levels in the more susceptible Cashel genotype and an increase in sugars and compatible solutes in the more tolerant PI 462336 genotype. Sugars with a significant increase included: raffinose, trehalose, glucose, fructose and maltose. Increasing the ability of perennial ryegrass to accumulate these sugars in response to a water deficit may lead to more tolerant varieties. The metabolomics approach was combined with a transcriptomics approach in the water stress tolerant genotype PI 462336, which has identified perennial ryegrass genes regulated under water stress.
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Affiliation(s)
- Alexandre Foito
- Teagasc, Crops Biosciences Centre, Oak Park, Carlow, Ireland
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44
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Degenkolbe T, Do PT, Zuther E, Repsilber D, Walther D, Hincha DK, Köhl KI. Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. PLANT MOLECULAR BIOLOGY 2009; 69:133-53. [PMID: 18931976 PMCID: PMC2709230 DOI: 10.1007/s11103-008-9412-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 09/27/2008] [Indexed: 05/19/2023]
Abstract
Understanding the molecular basis of plant performance under water-limiting conditions will help to breed crop plants with a lower water demand. We investigated the physiological and gene expression response of drought-tolerant (IR57311 and LC-93-4) and drought-sensitive (Nipponbare and Taipei 309) rice (Oryza sativa L.) cultivars to 18 days of drought stress in climate chamber experiments. Drought stressed plants grew significantly slower than the controls. Gene expression profiles were measured in leaf samples with the 20 K NSF oligonucleotide microarray. A linear model was fitted to the data to identify genes that were significantly regulated under drought stress. In all drought stressed cultivars, 245 genes were significantly repressed and 413 genes induced. Genes differing in their expression pattern under drought stress between tolerant and sensitive cultivars were identified by the genotype x environment (G x E) interaction term. More genes were significantly drought regulated in the sensitive than in the tolerant cultivars. Localizing all expressed genes on the rice genome map, we checked which genes with a significant G x E interaction co-localized with published quantitative trait loci regions for drought tolerance. These genes are more likely to be important for drought tolerance in an agricultural environment. To identify the metabolic processes with a significant G x E effect, we adapted the analysis software MapMan for rice. We found a drought stress induced shift toward senescence related degradation processes that was more pronounced in the sensitive than in the tolerant cultivars. In spite of higher growth rates and water use, more photosynthesis related genes were down-regulated in the tolerant than in the sensitive cultivars.
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Affiliation(s)
- Thomas Degenkolbe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Phuc Thi Do
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ellen Zuther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Dirk Repsilber
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
- Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Dirk Walther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Dirk K. Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Karin I. Köhl
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
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45
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Guo P, Baum M, Grando S, Ceccarelli S, Bai G, Li R, von Korff M, Varshney RK, Graner A, Valkoun J. Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:3531-44. [PMID: 19561048 PMCID: PMC2724701 DOI: 10.1093/jxb/erp194] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Drought tolerance is a key trait for increasing and stabilizing barley productivity in dry areas worldwide. Identification of the genes responsible for drought tolerance in barley (Hordeum vulgare L.) will facilitate understanding of the molecular mechanisms of drought tolerance, and also facilitate the genetic improvement of barley through marker-assisted selection or gene transformation. To monitor the changes in gene expression at the transcriptional level in barley leaves during the reproductive stage under drought conditions, the 22K Affymetrix Barley 1 microarray was used to screen two drought-tolerant barley genotypes, Martin and Hordeum spontaneum 41-1 (HS41-1), and one drought-sensitive genotype Moroc9-75. Seventeen genes were expressed exclusively in the two drought-tolerant genotypes under drought stress, and their encoded proteins may play significant roles in enhancing drought tolerance through controlling stomatal closure via carbon metabolism (NADP malic enzyme, NADP-ME, and pyruvate dehydrogenase, PDH), synthesizing the osmoprotectant glycine-betaine (C-4 sterol methyl oxidase, CSMO), generating protectants against reactive-oxygen-species scavenging (aldehyde dehydrogenase,ALDH, ascorbate-dependent oxidoreductase, ADOR), and stabilizing membranes and proteins (heat-shock protein 17.8, HSP17.8, and dehydrin 3, DHN3). Moreover, 17 genes were abundantly expressed in Martin and HS41-1 compared with Moroc9-75 under both drought and control conditions. These genes were possibly constitutively expressed in drought-tolerant genotypes. Among them, seven known annotated genes might enhance drought tolerance through signalling [such as calcium-dependent protein kinase (CDPK) and membrane steroid binding protein (MSBP)], anti-senescence (G2 pea dark accumulated protein, GDA2), and detoxification (glutathione S-transferase, GST) pathways. In addition, 18 genes, including those encoding Delta(l)-pyrroline-5-carboxylate synthetase (P5CS), protein phosphatase 2C-like protein (PP2C), and several chaperones, were differentially expressed in all genotypes under drought; thus they were more likely to be general drought-responsive genes in barley. These results could provide new insights into further understanding of drought-tolerance mechanisms in barley.
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Affiliation(s)
- Peiguo Guo
- College of Life Science, Guangzhou University, Guangzhou 510006, China
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 5466, Aleppo, Syria
- To whom correspondence should be addressed: E-mail:
| | - Stefania Grando
- International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 5466, Aleppo, Syria
| | - Salvatore Ceccarelli
- International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 5466, Aleppo, Syria
| | - Guihua Bai
- USDA-ARS Plant Science and Entomology Research Unit, 4008 Throckmorton Hall, Manhattan, KS 66506, USA
| | - Ronghua Li
- College of Life Science, Guangzhou University, Guangzhou 510006, China
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Rajeev K. Varshney
- Applied Genomics Laboratory, GT-Biotechnology, ICRISAT, PATANCHERU-502 324, Greater Hyderabad, India
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research Head, Corrensstrasse 3, D-06466 Gatersleben, Germany
| | - Jan Valkoun
- International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 5466, Aleppo, Syria
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46
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Wang W, Meng B, Ge X, Song S, Yang Y, Yu X, Wang L, Hu S, Liu S, Yu J. Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines. Proteomics 2008; 8:4808-21. [DOI: 10.1002/pmic.200701164] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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von Korff M, Grando S, Del Greco A, This D, Baum M, Ceccarelli S. Quantitative trait loci associated with adaptation to Mediterranean dryland conditions in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:653-69. [PMID: 18618094 DOI: 10.1007/s00122-008-0787-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Accepted: 05/02/2008] [Indexed: 05/18/2023]
Abstract
The objective of the present study was to identify quantitative trait loci (QTL) influencing agronomic performance across rain fed Mediterranean environments in a recombinant inbred line (RIL) population derived from the barley cultivars ER/Apm and Tadmor. The population was tested in four locations (two in Syria and two in Lebanon) during four consecutive years. This allowed the analysis of marker main effects as well as of marker by location and marker by year within location interactions. The analysis demonstrated the significance of crossover interactions in environments with large differences between locations and between years within locations. Alleles from the parent with the higher yield potential, ER/Apm, were associated with improved performance at all markers exhibiting main effects for grain yield. The coincidence of main effect QTL for plant height and yield indicated that average yield was mainly determined by plant height, where Tadmor's taller plants, being susceptible to lodging, yielded less. However, a number of crossover interactions were detected, in particular for yield, where the Tadmor allele improved yield in the locations with more severe drought stress. The marker with the highest number of cross-over interactions for yield and yield component traits mapped close to the flowering gene Ppd-H2 and a candidate gene for drought tolerance HVA1 on chromosome 1H. Effects of these candidate genes and QTL may be involved in adaptation to severe drought as frequently occurring in the driest regions in the Mediterranean countries. Identification of QTL and genes affecting field performance of barley under drought stress is a first step towards the understanding of the genetics behind drought tolerance.
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Affiliation(s)
- M von Korff
- International Center for Agricultural Research in the Dry Areas, P.O. Box 5466, Aleppo, Syria
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48
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Witcombe JR, Hollington PA, Howarth CJ, Reader S, Steele KA. Breeding for abiotic stresses for sustainable agriculture. Philos Trans R Soc Lond B Biol Sci 2008; 363:703-16. [PMID: 17761467 PMCID: PMC2610105 DOI: 10.1098/rstb.2007.2179] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is salinized continues to increase, and the cost of inorganic N is set to rise. There is good potential for directly breeding for adaptation to low N while retaining an ability to respond to high N conditions. Breeding for drought and salinity tolerance have proven to be difficult, and the complex mechanisms of tolerance are reviewed. Marker-assisted selection for component traits of drought in rice and pearl millet and salinity tolerance in wheat has produced some positive results and the pyramiding of stable quantitative trait locuses controlling component traits may provide a solution. New genomic technologies promise to make progress for breeding tolerance to these two stresses through a more fundamental understanding of underlying processes and identification of the genes responsible. In wheat, there is a great potential of breeding genetic resistance for salinity and aluminium tolerance through the contributions of wild relatives.
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Affiliation(s)
- J R Witcombe
- CAZS Natural Resources, University of Wales, Bangor LL57 2UW, UK.
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49
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Yang G, Xing Y, Li S, Ding J, Yue B, Deng K, Li Y, Zhu Y. Molecular dissection of developmental behavior of tiller number and plant height and their relationship in rice (Oryza sativa L.). Hereditas 2007; 143:236-45. [PMID: 17362360 DOI: 10.1111/j.2006.0018-0661.01959.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Plant height and tiller number are two important characters related to yield in rice (Oriza sativa L.). Zhenshan97 x Minghui63 recombinant inbred lines were employed to dissect the genetic basis of development of plant height and tiller number using conditional and unconditional composite interval mapping approaches. The traits were normally distributed with transgressive segregation in both directions. Increasingly negative correlations were observed between tiller number and plant height at five consecutive growth stages. A total of 23 and 24 QTL were identified for tiller number and plant height, respectively. More QTL were detected by conditional mapping than by conventional mapping. Different QTL/genes apparently controlled the traits at different developmental stages. Three genomic regions were identified as putative co-located QTL, which showed opposite additive effects on tiller number and plant height. Furthermore, in the period reaching maximum tiller number, the expression of QTL for tiller number was active, whereas that of QTL for plant height was inactive. These facts provided a possible genetic explanation for the negative correlations between the traits. The research demonstrates conditional mapping to be superior to conventional mapping for this type of research. Implications of the results for hybrid rice improvement are discussed.
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Affiliation(s)
- Guohua Yang
- Key Laboratory of the Education Ministry of China for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, China
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50
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Suprunova T, Krugman T, Distelfeld A, Fahima T, Nevo E, Korol A. Identification of a novel gene (Hsdr4) involved in water-stress tolerance in wild barley. PLANT MOLECULAR BIOLOGY 2007; 64:17-34. [PMID: 17238046 DOI: 10.1007/s11103-006-9131-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 12/18/2006] [Indexed: 05/13/2023]
Abstract
Drought is one of the most severe stresses limiting plant growth and yield. Genes involved in water stress tolerance of wild barley (Hordeum spontaneoum), the progenitor of cultivated barley, were investigated using genotypes contrasting in their response to water stress. Gene expression profiles of water-stress tolerant vs. water-stress sensitive wild barley genotypes, under severe dehydration stress applied at the seedling stage, were compared using cDNA-AFLP analysis. Of the 1100 transcript-derived fragments (TDFs) amplified about 70 displayed differential expression between control and stress conditions. Eleven of them showed clear difference (up- or down-regulation) between tolerant and susceptible genotypes. These TDFs were isolated, sequenced and tested by RT-PCR. The differential expression of seven TDFs was confirmed by RT-PCR, and TDF-4 was selected as a promising candidate gene for water-stress tolerance. The corresponding gene, designated Hsdr4 (Hordeum spontaneum dehydration-responsive), was sequenced and the transcribed and flanking regions were determined. The deduced amino acid sequence has similarity to the rice Rho-GTPase-activating protein-like with a Sec14 p-like lipid-binding domain. Analysis of Hsdr4 promoter region that was isolated by screening a barley BAC library, revealed a new putative miniature inverted-repeat transposable element (MITE), and several potential stress-related binding sites for transcription factors (MYC, MYB, LTRE, and GT-1), suggesting a role of the Hsdr4 gene in plant tolerance to dehydration stress. Furthermore, the Hsdr4 gene was mapped using wild barley mapping population to the long arm of chromosome 3H between markers EBmac541 and EBmag705, within a region that previously was shown to affect osmotic adaptation in barley.
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Affiliation(s)
- Tatiana Suprunova
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel
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