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Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PLANTS 2020; 9:plants9050591. [PMID: 32384671 PMCID: PMC7285221 DOI: 10.3390/plants9050591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Alessia Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
- Correspondence: ; Tel.: +39-081-253-9492
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Ruocco N, Bertocci I, Munari M, Musco L, Caramiello D, Danovaro R, Zupo V, Costantini M. Morphological and molecular responses of the sea urchin Paracentrotus lividus to highly contaminated marine sediments: The case study of Bagnoli-Coroglio brownfield (Mediterranean Sea). MARINE ENVIRONMENTAL RESEARCH 2020; 154:104865. [PMID: 32056706 DOI: 10.1016/j.marenvres.2019.104865] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
Marine sediments store complex mixtures of compounds, including heavy metals, organotins and a large array of other contaminants. Sediment quality monitoring, characterization and management are priorities, due to potential impacts of the above compounds on coastal waters and their biota, especially in cases of pollutants released during dredging activities. Harbours and marinas, as well as estuaries and bays, where limited exchanges of water occurr, the accumulation of toxic compounds poses major concerns for human and environmental health. Here we report the effects of highly contaminated sediments from the site of national interest Bagnoli-Coroglio (Tyrrhenian Sea, Western Mediterranean) on the sea urchin Paracentrotus lividus, considered a good model for ecotoxicological studies. Adult sea urchins were reared one month in aquaria in the presence of contaminated sediment that was experimentally subject to different patterns of re-suspension events (mimicking the effect of natural storms occurring in the field), crossed with O2 enrichment versus natural gas exchanges in the water. The development of embryos deriving from adult urchins exposed to such experimental conditions was followed until the pluteus stage, checking the power of contaminated sediment to induce morphological malformations and its eventual buffering by high oxygenation. Real-Time qPCR analysis revealed that the expression of several genes (among the fifty analyzed, involved in different functional processes) was targeted by contaminated sediments more than those exposed in oxygen-enriched condition. Our findings have biological and ecological relevance in terms of assessing the actual impact on local organisms of chronic environmental contamination by heavy metals and polycyclic aromatic hydrocarbons affecting the Bagnoli-Coroglio area, and of exploring enhanced sediment and water oxygenation as a promising tool to mitigate the effects of contamination in future environmental restoration actions.
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Affiliation(s)
- Nadia Ruocco
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Iacopo Bertocci
- Department of Biology, University of Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn,Villa Comunale, 80121, Naples, Italy
| | - Marco Munari
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn,Villa Comunale, 80121, Naples, Italy
| | - Luigi Musco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn,Villa Comunale, 80121, Naples, Italy
| | - Davide Caramiello
- Unit Marine Resources for Research, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy
| | - Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy; Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Valerio Zupo
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Maria Costantini
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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Barbosa Dos Santos I, Park SW. Versatility of Cyclophilins in Plant Growth and Survival: A Case Study in Arabidopsis. Biomolecules 2019; 9:biom9010020. [PMID: 30634678 PMCID: PMC6358970 DOI: 10.3390/biom9010020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/22/2018] [Accepted: 01/02/2019] [Indexed: 11/16/2022] Open
Abstract
Cyclophilins (CYPs) belong to a peptidyl-prolyl cis-trans isomerase family, and were first characterized in mammals as a target of an immunosuppressive drug, cyclosporin A, preventing proinflammatory cytokine production. In Arabidopsis, 29 CYPs and CYP-like proteins are found across all subcellular compartments, involved in various physiological processes including transcriptional regulation, organogenesis, photosynthetic and hormone signaling pathways, stress adaptation and defense responses. These important but diverse activities of CYPs must be reflected by their versatility as cellular and molecular modulators. However, our current knowledge regarding their mode of actions is still far from complete. This review will briefly revisit recent progresses on the roles and mechanisms of CYPs in Arabidopsis studies, and information gaps within, which help understanding the phenotypic and environmental plasticity of plants.
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Affiliation(s)
| | - Sang-Wook Park
- Department of Entomology and Plant Pathology Auburn University, Auburn, AL 36849, USA.
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Abstract
Transcriptome analysis reflects the status quo of transcribed genetic code present in the form of mRNA, which helps to infer biological processes and unravel metabolic status. Despite the increasing adoption of RNA-Seq technique in recent years, transcriptome analysis using the microarray platform remains the gold standard technique, which offers a simpler, more cost-effective, and efficient method for high-throughput gene expression profiling. In this chapter, we described a streamlined transcriptomic analyses pipeline employed to study developing rice grains that can also be applied to other tissue samples and species. We described a novel RNA extraction method that obviates the problem introduced by high-starch content during rice grain development that usually leads to reduction in RNA yield and quality. The detailed procedure of microarray analysis involved in cDNA synthesis, cRNA labeling, microarray hybridization, slide scanning, feature extraction to QC validation has been described. The description of a newly developed Indica- and Japonica-specific microarray slides developed from the genome information of subpopulation to study gene expression of 60,000 genes has been highlighted. The downstream bioinformatics analyses including expression QTL mapping and gene regulatory network analyses were mentioned.
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Sahebi M, Hanafi MM, Rafii MY, Mahmud TMM, Azizi P, Osman M, Abiri R, Taheri S, Kalhori N, Shabanimofrad M, Miah G, Atabaki N. Improvement of Drought Tolerance in Rice ( Oryza sativa L.): Genetics, Genomic Tools, and the WRKY Gene Family. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3158474. [PMID: 30175125 PMCID: PMC6106855 DOI: 10.1155/2018/3158474] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/14/2018] [Accepted: 07/05/2018] [Indexed: 11/17/2022]
Abstract
Drought tolerance is an important quantitative trait with multipart phenotypes that are often further complicated by plant phenology. Different types of environmental stresses, such as high irradiance, high temperatures, nutrient deficiencies, and toxicities, may challenge crops simultaneously; therefore, breeding for drought tolerance is very complicated. Interdisciplinary researchers have been attempting to dissect and comprehend the mechanisms of plant tolerance to drought stress using various methods; however, the limited success of molecular breeding and physiological approaches suggests that we rethink our strategies. Recent genetic techniques and genomics tools coupled with advances in breeding methodologies and precise phenotyping will likely reveal candidate genes and metabolic pathways underlying drought tolerance in crops. The WRKY transcription factors are involved in different biological processes in plant development. This zinc (Zn) finger protein family, particularly members that respond to and mediate stress responses, is exclusively found in plants. A total of 89 WRKY genes in japonica and 97 WRKY genes in O. nivara (OnWRKY) have been identified and mapped onto individual chromosomes. To increase the drought tolerance of rice (Oryza sativa L.), research programs should address the problem using a multidisciplinary strategy, including the interaction of plant phenology and multiple stresses, and the combination of drought tolerance traits with different genetic and genomics approaches, such as microarrays, quantitative trait loci (QTLs), WRKY gene family members with roles in drought tolerance, and transgenic crops. This review discusses the newest advances in plant physiology for the exact phenotyping of plant responses to drought to update methods of analysing drought tolerance in rice. Finally, based on the physiological/morphological and molecular mechanisms found in resistant parent lines, a strategy is suggested to select a particular environment and adapt suitable germplasm to that environment.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamed M. Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - M. Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - T. M. M. Mahmud
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamad Osman
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Rambod Abiri
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Nahid Kalhori
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - M. Shabanimofrad
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Gous Miah
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Narges Atabaki
- Iran Azad University of Tehran Science & Reserach Branch, Hesarak, Tehran 1477893855, Iran
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Ruocco N, Maria Fedele A, Costantini S, Romano G, Ianora A, Costantini M. New inter-correlated genes targeted by diatom-derived polyunsaturated aldehydes in the sea urchin Paracentrotus lividus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:355-362. [PMID: 28437727 DOI: 10.1016/j.ecoenv.2017.04.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
The marine environment is continually subjected to the action of stressors (including natural toxins), which represent a constant danger for benthic communities. In the present work using network analysis we identified ten genes on the basis of associated functions (FOXA, FoxG, GFI-1, nodal, JNK, OneCut/Hnf6, TAK1, tcf4, TCF7, VEGF) in the sea urchin Paracentrotus lividus, having key roles in different processes, such as embryonic development and asymmetry, cell fate specification, cell differentiation and morphogenesis, and skeletogenesis. These genes are correlated with three HUB genes, Foxo, Jun and HIF1A. Real Time qPCR revealed that during sea urchin embryonic development the expression levels of these genes were modulated by three diatom-derived polyunsaturated aldehydes (PUAs), decadienal, heptadienal and octadienal. Our findings show how changes in gene expression levels may be used as an early indicator of stressful conditions in the marine environment. The identification of key genes and the molecular pathways in which they are involved represents a fundamental tool in understanding how marine organisms try to afford protection against toxicants, to avoid deleterious consequences and irreversible damages. The genes identified in this work as targets for PUAs can be considered as possible biomarkers to detect exposure to different environmental pollutants.
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Affiliation(s)
- Nadia Ruocco
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy; Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, Pozzuoli, Naples 80078, Italy
| | - Anna Maria Fedele
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Susan Costantini
- Unità di Farmacologia Sperimentale, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, 80131 Napoli, Italy
| | - Giovanna Romano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Adrianna Ianora
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Maria Costantini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
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Analysis of environmental stress factors using an artificial growth system and plant fitness optimization. BIOMED RESEARCH INTERNATIONAL 2015; 2015:292543. [PMID: 25874206 PMCID: PMC4385635 DOI: 10.1155/2015/292543] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/04/2014] [Accepted: 11/13/2014] [Indexed: 11/18/2022]
Abstract
The environment promotes evolution. Evolutionary processes represent environmental adaptations over long time scales; evolution of crop genomes is not inducible within the relatively short time span of a human generation. Extreme environmental conditions can accelerate evolution, but such conditions are often stress inducing and disruptive. Artificial growth systems can be used to induce and select genomic variation by changing external environmental conditions, thus, accelerating evolution. By using cloud computing and big-data analysis, we analyzed environmental stress factors for Pleurotus ostreatus by assessing, evaluating, and predicting information of the growth environment. Through the indexing of environmental stress, the growth environment can be precisely controlled and developed into a technology for improving crop quality and production.
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Ma X, Sukiran NL, Ma H, Su Z. Moderate drought causes dramatic floral transcriptomic reprogramming to ensure successful reproductive development in Arabidopsis. BMC PLANT BIOLOGY 2014; 14:164. [PMID: 24928551 PMCID: PMC4067085 DOI: 10.1186/1471-2229-14-164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 05/29/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Drought is a major constraint that leads to extensive losses to agricultural yield worldwide. The potential yield is largely determined during inflorescence development. However, to date, most investigations on plant response to drought have focused on vegetative development. This study describes the morphological changes of reproductive development and the comparison of transcriptomes under various drought conditions. RESULTS The plants grown were studied under two drought conditions: minimum for successful reproduction (45-50% soil water content, moderate drought, MD) and for survival (30-35%, severe drought, SD). MD plants can produce similar number of siliques on the main stem and similar number of seeds per silique comparing with well-water plants. The situation of SD plants was much worse than MD plants. The transcriptomes of inflorescences were further investigated at molecular level using microarrays. Our results showed more than four thousands genes with differential expression under severe drought and less than two thousand changed under moderate drought condition (with 2-fold change and q-value < 0.01). We found a group of genes with increased expression as the drought became more severe, suggesting putative adaptation to the dehydration. Interestingly, we also identified genes with alteration only under the moderate but not the severe drought condition, indicating the existence of distinct sets of genes responsive to different levels of water availability. Further cis-element analyses of the putative regulatory sequences provided more information about the underlying mechanisms for reproductive responses to drought, suggesting possible novel candidate genes that protect those developing flowers under drought stress. CONCLUSIONS Different pathways may be activated in response to moderate and severe drought in reproductive tissues, potentially helping plant to maximize its yield and balance the resource consumption between vegetative and reproductive development under dehydration stresses.
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Affiliation(s)
- Xuan Ma
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
- Intercollege Graduate Program in Cell and Developmental Biology, the Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Noor Liyana Sukiran
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
- Current address: School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Institute of Genetics, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zhao Su
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
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Ali A, Ali Z, Quraishi UM, Kazi AG, Malik RN, Sher H, Mujeeb-Kazi A. Integrating Physiological and Genetic Approaches for Improving Drought Tolerance in Crops. EMERGING TECHNOLOGIES AND MANAGEMENT OF CROP STRESS TOLERANCE 2014. [PMID: 0 DOI: 10.1016/b978-0-12-800875-1.00014-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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Tuberosa R. Phenotyping for drought tolerance of crops in the genomics era. Front Physiol 2012; 3:347. [PMID: 23049510 PMCID: PMC3446691 DOI: 10.3389/fphys.2012.00347] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 08/09/2012] [Indexed: 12/11/2022] Open
Abstract
Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.
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Affiliation(s)
- Roberto Tuberosa
- Department of Agroenvironmental Science and Technology, University of BolognaBologna, Italy
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Mir RR, Zaman-Allah M, Sreenivasulu N, Trethowan R, Varshney RK. Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:625-45. [PMID: 22696006 PMCID: PMC3405239 DOI: 10.1007/s00122-012-1904-9] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/18/2012] [Indexed: 05/19/2023]
Abstract
Drought is one of the most serious production constraint for world agriculture and is projected to worsen with anticipated climate change. Inter-disciplinary scientists have been trying to understand and dissect the mechanisms of plant tolerance to drought stress using a variety of approaches; however, success has been limited. Modern genomics and genetic approaches coupled with advances in precise phenotyping and breeding methodologies are expected to more effectively unravel the genes and metabolic pathways that confer drought tolerance in crops. This article discusses the most recent advances in plant physiology for precision phenotyping of drought response, a vital step before implementing the genetic and molecular-physiological strategies to unravel the complex multilayered drought tolerance mechanism and further exploration using molecular breeding approaches for crop improvement. Emphasis has been given to molecular dissection of drought tolerance by QTL or gene discovery through linkage and association mapping, QTL cloning, candidate gene identification, transcriptomics and functional genomics. Molecular breeding approaches such as marker-assisted backcrossing, marker-assisted recurrent selection and genome-wide selection have been suggested to be integrated in crop improvement strategies to develop drought-tolerant cultivars that will enhance food security in the context of a changing and more variable climate.
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Affiliation(s)
- Reyazul Rouf Mir
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324 India
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu (SKUAST-J), Chatha, Jammu, 180 009 India
| | - Mainassara Zaman-Allah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324 India
- Department of Biology, Faculty of Sciences, University of Maradi, BP 465, Maradi, Niger
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Richard Trethowan
- Plant Breeding Institute, University of Sydney, PMB11, Camden, NSW 2570 Australia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324 India
- CGIAR-Generation Challenge Programme (GCP), c/o CIMMYT, Int APDO Postal 6-641, 06600 Mexico, DF Mexico
- School of Plant Biology (M084), Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
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Avin-Wittenberg T, Tzin V, Angelovici R, Less H, Galili G. Deciphering energy-associated gene networks operating in the response of Arabidopsis plants to stress and nutritional cues. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:954-66. [PMID: 22288575 DOI: 10.1111/j.1365-313x.2012.04926.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants need to continuously adjust their transcriptome in response to various stresses that lead to inhibition of photosynthesis and the deprivation of cellular energy. This adjustment is triggered in part by a coordinated re-programming of the energy-associated transcriptome to slow down photosynthesis and activate other energy-promoting gene networks. Therefore, understanding the stress-related transcriptional networks of genes belonging to energy-associated pathways is of major importance for engineering stress tolerance. In a bioinformatics approach developed by our group, termed 'gene coordination', we previously divided genes encoding for enzymes and transcription factors in Arabidopsis thaliana into three clusters, displaying altered coordinated transcriptional behaviors in response to multiple biotic and abiotic stresses (Plant Cell, 23, 2011, 1264). Enrichment analysis indicated further that genes controlling energy-associated metabolism operate as a compound network in response to stress. In the present paper, we describe in detail the network association of genes belonging to six central energy-associated pathways in each of these three clusters described in our previous paper. Our results expose extensive stress-associated intra- and inter-pathway interactions between genes from these pathways, indicating that genes encoding proteins involved in energy-associated metabolism are expressed in a highly coordinated manner. We also provide examples showing that this approach can be further utilized to elucidate candidate genes for stress tolerance and functions of isozymes.
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Affiliation(s)
- Tamar Avin-Wittenberg
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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Li B, Ding L, Li W, Story MD, Pace BS. Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation. BMC Genomics 2012; 13:153. [PMID: 22537182 PMCID: PMC3353202 DOI: 10.1186/1471-2164-13-153] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 04/26/2012] [Indexed: 12/14/2022] Open
Abstract
Background The fetal and adult globin genes in the human β-globin cluster on chromosome 11 are sequentially expressed to achieve normal hemoglobin switching during human development. The pharmacological induction of fetal γ-globin (HBG) to replace abnormal adult sickle βS-globin is a successful strategy to treat sickle cell disease; however the molecular mechanism of γ-gene silencing after birth is not fully understood. Therefore, we performed global gene expression profiling using primary erythroid progenitors grown from human peripheral blood mononuclear cells to characterize gene expression patterns during the γ-globin to β-globin (γ/β) switch observed throughout in vitro erythroid differentiation. Results We confirmed erythroid maturation in our culture system using cell morphologic features defined by Giemsa staining and the γ/β-globin switch by reverse transcription-quantitative PCR (RT-qPCR) analysis. We observed maximal γ-globin expression at day 7 with a switch to a predominance of β-globin expression by day 28 and the γ/β-globin switch occurred around day 21. Expression patterns for transcription factors including GATA1, GATA2, KLF1 and NFE2 confirmed our system produced the expected pattern of expression based on the known function of these factors in globin gene regulation. Subsequent gene expression profiling was performed with RNA isolated from progenitors harvested at day 7, 14, 21, and 28 in culture. Three major gene profiles were generated by Principal Component Analysis (PCA). For profile-1 genes, where expression decreased from day 7 to day 28, we identified 2,102 genes down-regulated > 1.5-fold. Ingenuity pathway analysis (IPA) for profile-1 genes demonstrated involvement of the Cdc42, phospholipase C, NF-Kβ, Interleukin-4, and p38 mitogen activated protein kinase (MAPK) signaling pathways. Transcription factors known to be involved in γ-and β-globin regulation were identified. The same approach was used to generate profile-2 genes where expression was up-regulated over 28 days in culture. IPA for the 2,437 genes with > 1.5-fold induction identified the mitotic roles of polo-like kinase, aryl hydrocarbon receptor, cell cycle control, and ATM (Ataxia Telangiectasia Mutated Protein) signaling pathways; transcription factors identified included KLF1, GATA1 and NFE2 among others. Finally, profile-3 was generated from 1,579 genes with maximal expression at day 21, around the time of the γ/β-globin switch. IPA identified associations with cell cycle control, ATM, and aryl hydrocarbon receptor signaling pathways. Conclusions The transcriptome analysis completed with erythroid progenitors grown in vitro identified groups of genes with distinct expression profiles, which function in metabolic pathways associated with cell survival, hematopoiesis, blood cells activation, and inflammatory responses. This study represents the first report of a transcriptome analysis in human primary erythroid progenitors to identify transcription factors involved in hemoglobin switching. Our results also demonstrate that the in vitro liquid culture system is an excellent model to define mechanisms of global gene expression and the DNA-binding protein and signaling pathways involved in globin gene regulation.
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Affiliation(s)
- Biaoru Li
- Department Pediatrics, Georgia Health Sciences University, 1120 15th St, CN-4112, Augusta, GA 30912, USA
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14
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Friedel S, Usadel B, von Wirén N, Sreenivasulu N. Reverse engineering: a key component of systems biology to unravel global abiotic stress cross-talk. FRONTIERS IN PLANT SCIENCE 2012; 3:294. [PMID: 23293646 PMCID: PMC3533172 DOI: 10.3389/fpls.2012.00294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/10/2012] [Indexed: 05/18/2023]
Abstract
Understanding the global abiotic stress response is an important stepping stone for the development of universal stress tolerance in plants in the era of climate change. Although co-occurrence of several stress factors (abiotic and biotic) in nature is found to be frequent, current attempts are poor to understand the complex physiological processes impacting plant growth under combinatory factors. In this review article, we discuss the recent advances of reverse engineering approaches that led to seminal discoveries of key candidate regulatory genes involved in cross-talk of abiotic stress responses and summarized the available tools of reverse engineering and its relevant application. Among the universally induced regulators involved in various abiotic stress responses, we highlight the importance of (i) abscisic acid (ABA) and jasmonic acid (JA) hormonal cross-talks and (ii) the central role of WRKY transcription factors (TF), potentially mediating both abiotic and biotic stress responses. Such interactome networks help not only to derive hypotheses but also play a vital role in identifying key regulatory targets and interconnected hormonal responses. To explore the full potential of gene network inference in the area of abiotic stress tolerance, we need to validate hypotheses by implementing time-dependent gene expression data from genetically engineered plants with modulated expression of target genes. We further propose to combine information on gene-by-gene interactions with data from physical interaction platforms such as protein-protein or TF-gene networks.
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Affiliation(s)
- Swetlana Friedel
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Björn Usadel
- RWTH Aachen UniversityAachen, Germany
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum JülichJülich, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
- *Correspondence: Nese Sreenivasulu, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany. e-mail:
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Less H, Angelovici R, Tzin V, Galili G. Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues. THE PLANT CELL 2011; 23:1264-71. [PMID: 21487096 PMCID: PMC3101534 DOI: 10.1105/tpc.110.082867] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 03/03/2011] [Accepted: 03/12/2011] [Indexed: 05/18/2023]
Abstract
The expression pattern of any pair of genes may be negatively correlated, positively correlated, or not correlated at all in response to different stresses and even different progression stages of the stress. This makes it difficult to identify such relationships by classical statistical tools such as the Pearson correlation coefficient. Hence, dedicated bioinformatics approaches that are able to identify groups of cues in which there is a positive or negative expression correlation between pairs or groups of genes are called for. We herein introduce and discuss a bioinformatics approach, termed Gene Coordination, that is devoted to the identification of specific or multiple cues in which there is a positive or negative coordination between pairs of genes and can further incorporate additional coordinated genes to form large coordinated gene networks. We demonstrate the utility of this approach by providing a case study in which we were able to discover distinct expression behavior of the energy-associated gene network in response to distinct biotic and abiotic stresses. This bioinformatics approach is suitable to a broad range of studies that compare treatments versus controls, such as effects of various cues, or expression changes between a mutant and the control wild-type genotype.
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Affiliation(s)
| | | | | | - Gad Galili
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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Kainkaryam RM, Bruex A, Woolf PJ, Schiefelbein J. Smart pooling of mRNA samples for efficient transcript profiling. Methods Mol Biol 2011; 876:189-94. [PMID: 22576096 DOI: 10.1007/978-1-61779-809-2_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Gene expression profiling studies are commonly used to study signaling pathways and their impact on transcriptional regulation in plants. In some cases, a profiling study results in expression profiles in which most genes exhibit a small number of differentially expressed states among a large number of samples. In such instances, a pooling approach would help improve the efficiency of the profiling effort by employing fewer microarray chips and ensuring more robust measurement of transcript levels. Smart pooling involves pooling of mRNA samples in an information-efficient manner such that each sample is tested multiple times but always in pools with other samples. The resulting pooled measurements are then decoded to recover the expression profile of all samples in the study. In this protocol, we describe in detail the process of designing smart pooling experiments and decoding their results, which have been used for studying signaling in Arabidopsis root development. Heuristics are provided to select the design parameters that would ensure successful execution of smart pooling.
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