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Tyczewska A, Twardowski T, Woźniak-Gientka E. Agricultural biotechnology for sustainable food security. Trends Biotechnol 2023; 41:331-341. [PMID: 36710131 PMCID: PMC9881846 DOI: 10.1016/j.tibtech.2022.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/29/2022] [Accepted: 12/21/2022] [Indexed: 01/30/2023]
Abstract
Of late, global food security has been under threat by the coronavirus disease 2019 (COVID-19) pandemic and the recent military conflict in Eastern Europe. This article presents the objectives of the Sustainable Development Goals and the European Green Deal related to achieving food security and sustainable development in European Union (EU) agriculture, taking the aforementioned threats into account. In addition, it discusses the future of plant agricultural biotechnology and artificial intelligence (AI) systems, considering their potential for reaching the goal of food security. Paradoxically, the present challenging situation may allow politicians and stakeholders of the EU to realize opportunities and use the potential of the biotechnology sector.
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Affiliation(s)
- Agata Tyczewska
- Laboratory of Animal Model Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Tomasz Twardowski
- Bioeconomy and Sustainable Development Team, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Ewa Woźniak-Gientka
- Bioeconomy and Sustainable Development Team, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
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2
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Lee JS, Sung YJ, Sim SJ. Kinetic analysis of microalgae cultivation utilizing 3D-printed real-time monitoring system reveals potential of biological CO 2 conversion. BIORESOURCE TECHNOLOGY 2022; 364:128014. [PMID: 36155817 DOI: 10.1016/j.biortech.2022.128014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
The microalgae-based bioconversion process is a promising carbon utilization technology because it can upgrade CO2 into valuable substances, but a multiplex monitoring system required for process control to maximize biomass productivity has not been well established. Herein, a 3D printed real-time optical density monitoring device (RTOMD) combined platform was presented. This platform enables precise kinetics analysis by maintaining high accuracy (over 95 %) under raucous outdoor conditions. Through RTOMD-based high-frequency measurements, it was observed that maximum biomass productivity of 4.497 g L-1 d-1 was reached, which greatly exceeds the requirements for a feasible microalgae process. We discovered that the CO2 fixation efficiency could be achieved to 70.75 %, indicating the potential of a bioconversion process to realize a carbon-neutral society. Consequently, the RTOMD system can contribute to promoting microalgae cultivation as an attractive carbon mitigation technology based on an improved understanding of the photosynthetic CO2 fixation kinetics.
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Affiliation(s)
- Jeong Seop Lee
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Young Joon Sung
- Department of Chemical and Biological Engineering, Sookmyung Women's University, 100 Cheongpa-ro 47-gil, Yongsan-gu, Seoul, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.
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3
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MicroRNA398: A Master Regulator of Plant Development and Stress Responses. Int J Mol Sci 2022; 23:ijms231810803. [PMID: 36142715 PMCID: PMC9502370 DOI: 10.3390/ijms231810803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/04/2022] [Accepted: 09/12/2022] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in plant development and stress responses, and a growing number of studies suggest that miRNAs are promising targets for crop improvement because they participate in the regulation of diverse, important agronomic traits. MicroRNA398 (miR398) is a conserved miRNA in plants and has been shown to control multiple stress responses and plant growth in a variety of species. There are many studies on the stress response and developmental regulation of miR398. To systematically understand its function, it is necessary to summarize the evolution and functional roles of miR398 and its target genes. In this review, we analyze the evolution of miR398 in plants and outline its involvement in abiotic and biotic stress responses, in growth and development and in model and non-model plants. We summarize recent functional analyses, highlighting the role of miR398 as a master regulator that coordinates growth and diverse responses to environmental factors. We also discuss the potential for fine-tuning miR398 to achieve the goal of simultaneously improving plant growth and stress tolerance.
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4
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Abdulhafiz F. Plant Cell Culture Technologies: A promising alternatives to Produce High-Value Secondary Metabolites. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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5
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Altman A, Shennan S, Odling-Smee J. Ornamental plant domestication by aesthetics-driven human cultural niche construction. TRENDS IN PLANT SCIENCE 2022; 27:124-138. [PMID: 34629220 DOI: 10.1016/j.tplants.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/17/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Unlike plants that were domesticated to secure food, the domestication and breeding of ornamental plants are driven by aesthetic values. Here, we examine the major elements of the extended evolutionary synthesis (EES) theory that bridges the gap between the biology of ornamental plant domestication and the sociocultural motivations behind it. We propose that it involves specific elements of cumulative cultural evolution (CCE), plant gene-human culture coevolution (PGHCC), and niche construction (NC). Moreover, ornamental plant domestication represents an aesthetics-driven dimension of human niche construction that coevolved with socioeconomic changes and the adoption of new scientific technologies. Initially functioning as symbolic and aesthetic assets, ornamental plants became globally marketed material commodities as a result of the co-dependence of human CCE and prestige-competition motivations.
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Affiliation(s)
- Arie Altman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel; Institute of Archaeology, University College of London, WC1H 0PY, London, UK.
| | - Stephen Shennan
- Institute of Archaeology, University College of London, WC1H 0PY, London, UK
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6
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Long-Term Dynamic of Cold Stress during Heading and Flowering Stage and Its Effects on Rice Growth in China. ATMOSPHERE 2022. [DOI: 10.3390/atmos13010103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Short episodes of low-temperature stress during reproductive stages can cause significant crop yield losses, but our understanding of the dynamics of extreme cold events and their impact on rice growth and yield in the past and present climate remains limited. In this study, by analyzing historical climate, phenology and yield component data, the spatial and temporal variability of cold stress during the rice heading and flowering stages and its impact on rice growth and yield in China was characterized. The results showed that cold stress was unevenly distributed throughout the study region, with the most severe events observed in the Yunnan Plateau with altitudes higher than 1800 m. With the increasing temperature, a significant decreasing trend in cold stress was observed across most of the three ecoregions after the 1970s. However, the phenological-shift effects with the prolonged growing period during the heading and flowering stages have slowed down the cold stress decreasing trend and led to an underestimation of the magnitude of cold stress events. Meanwhile, cold stress during heading and flowering will still be a potential threat to rice production. The cold stress-induced yield loss is related to both the intensification of extreme cold stress and the contribution of related components to yield in the three regions.
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Amaro Bittencourt G, Porto de Souza Vandenberghe L, Valladares-Diestra K, Wedderhoff Herrmann L, Fátima Murawski de Mello A, Sarmiento Vásquez Z, Grace Karp S, Ricardo Soccol C. Soybean hulls as carbohydrate feedstock for medium to high-value biomolecule production in biorefineries: A review. BIORESOURCE TECHNOLOGY 2021; 339:125594. [PMID: 34311407 DOI: 10.1016/j.biortech.2021.125594] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Soybean is one of the major world crops, with an annual production of 359 million tons. Each ton of processed soybean generates 50-80 kg of soybean hulls (SHs), representing 5-8% of the whole seed. Due to environmental concerns and great economic potential, the search of SHs re-use solutions are deeply discussed. The lignocellulosic composition of SHs has attracted the attention of the scientific and productive sector. Recently, some studies have reported the use of SHs in the production of medium to high value-added molecules, with potential applications in food and feed, agriculture, bioenergy, and other segments. This review presents biotechnological approaches and processes for the management and exploitation of SHs, including pre-treatment methods and fermentation techniques, for the production of different biomolecules. Great potentialities and innovations were found concerning SH exploration and valorisation of the soybean chain under a biorefinery and circular bioeconomy optic.
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Affiliation(s)
- Gustavo Amaro Bittencourt
- Federal University of Paraná, Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, 81531-980 Curitiba, Paraná, Brazil
| | - Luciana Porto de Souza Vandenberghe
- Federal University of Paraná, Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, 81531-980 Curitiba, Paraná, Brazil.
| | - Kim Valladares-Diestra
- Federal University of Paraná, Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, 81531-980 Curitiba, Paraná, Brazil
| | - Leonardo Wedderhoff Herrmann
- Federal University of Paraná, Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, 81531-980 Curitiba, Paraná, Brazil
| | - Ariane Fátima Murawski de Mello
- Federal University of Paraná, Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, 81531-980 Curitiba, Paraná, Brazil
| | - Zulma Sarmiento Vásquez
- Federal University of Paraná, Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, 81531-980 Curitiba, Paraná, Brazil
| | - Susan Grace Karp
- Federal University of Paraná, Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, 81531-980 Curitiba, Paraná, Brazil
| | - Carlos Ricardo Soccol
- Federal University of Paraná, Department of Bioprocess Engineering and Biotechnology, Centro Politécnico, 81531-980 Curitiba, Paraná, Brazil
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8
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Neves J, Sampaio M, Séneca A, Pereira S, Pissarra J, Pereira C. Abiotic Stress Triggers the Expression of Genes Involved in Protein Storage Vacuole and Exocyst-Mediated Routes. Int J Mol Sci 2021; 22:ijms221910644. [PMID: 34638986 PMCID: PMC8508612 DOI: 10.3390/ijms221910644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 12/20/2022] Open
Abstract
Adverse conditions caused by abiotic stress modulate plant development and growth by altering morphological and cellular mechanisms. Plants’ responses/adaptations to stress often involve changes in the distribution and sorting of specific proteins and molecules. Still, little attention has been given to the molecular mechanisms controlling these rearrangements. We tested the hypothesis that plants respond to stress by remodelling their endomembranes and adapting their trafficking pathways. We focused on the molecular machinery behind organelle biogenesis and protein trafficking under abiotic stress conditions, evaluating their effects at the subcellular level, by looking at ultrastructural changes and measuring the expression levels of genes involved in well-known intracellular routes. The results point to a differential response of the endomembrane system, showing that the genes involved in the pathway to the Protein Storage Vacuole and the exocyst-mediated routes are upregulated. In contrast, the ones involved in the route to the Lytic Vacuole are downregulated. These changes are accompanied by morphological alterations of endomembrane compartments. The data obtained demonstrate that plants’ response to abiotic stress involves the differential expression of genes related to protein trafficking machinery, which can be connected to the activation/deactivation of specific intracellular sorting pathways and lead to alterations in the cell ultrastructure.
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Affiliation(s)
- João Neves
- Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal; (J.N.); (M.S.); (A.S.); (S.P.); (J.P.)
| | - Miguel Sampaio
- Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal; (J.N.); (M.S.); (A.S.); (S.P.); (J.P.)
- GreenUPorto-Sustainable Agrifood Production Research Centre, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal
| | - Ana Séneca
- Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal; (J.N.); (M.S.); (A.S.); (S.P.); (J.P.)
- GreenUPorto-Sustainable Agrifood Production Research Centre, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal
| | - Susana Pereira
- Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal; (J.N.); (M.S.); (A.S.); (S.P.); (J.P.)
- GreenUPorto-Sustainable Agrifood Production Research Centre, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal
| | - José Pissarra
- Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal; (J.N.); (M.S.); (A.S.); (S.P.); (J.P.)
- GreenUPorto-Sustainable Agrifood Production Research Centre, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal
| | - Cláudia Pereira
- Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal; (J.N.); (M.S.); (A.S.); (S.P.); (J.P.)
- GreenUPorto-Sustainable Agrifood Production Research Centre, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal
- Correspondence:
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9
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Fincheira P, Tortella G, Seabra AB, Quiroz A, Diez MC, Rubilar O. Nanotechnology advances for sustainable agriculture: current knowledge and prospects in plant growth modulation and nutrition. PLANTA 2021; 254:66. [PMID: 34491441 DOI: 10.1007/s00425-021-03714-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 08/29/2021] [Indexed: 05/27/2023]
Abstract
Advances in nanotechnology make it an important tool for improving agricultural production. Strong evidence supports the role of nanomaterials as nutrients or nanocarriers for the controlled release of fertilizers to improve plant growth. Scientific research shows that nanotechnology applied in plant sciences is smart technology. Excessive application of mineral fertilizers has produced a harmful impact on the ecosystem. Furthermore, the projected increase in the human population by 2050 has led to the search for alternatives to ensure food security. Nanotechnology is a promising strategy to enhance crop productivity while minimizing fertilizer inputs. Nanofertilizers can contribute to the slow and sustainable release of nutrients to improve the efficiency of nutrient use in plants. Nanomaterial properties (i.e., size, morphology and charge) and plant physiology are crucial factors that influence the impact on plant growth. An important body of scientific research highlights the role of carbon nanomaterials, metal nanoparticles and metal oxide nanoparticles to improve plant development through the modulation of physiological and metabolic processes. Modulating nutrient concentrations, photosynthesis processes and antioxidant enzyme activities have led to increases in shoot length, root development, photosynthetic pigments and fruit yield. In parallel, nanocarriers (nanoclays, nanoparticles of hydroxyapatite, mesoporous silica and chitosan) have been shown to be an important tool for the controlled and sustainable release of conventional fertilizers to improve plant nutrition; however, the technical advances in nanofertilizers need to be accompanied by modernization of the regulations and legal frameworks to allow wider commercialization of these elements. Nanofertilizers are a promising strategy to improve plant development and nutrition, but their application in sustainable agriculture remains a great challenge. The present review summarizes the current advance of research into nanofertilizers, and their future prospects.
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Affiliation(s)
- Paola Fincheira
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA-BIOREN), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile.
| | - Gonzalo Tortella
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA-BIOREN), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile
- Departamento de Ingeniería Química, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - Amedea B Seabra
- Center for Natural and Human Sciences, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Andrés Quiroz
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA-BIOREN), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - María Cristina Diez
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA-BIOREN), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile
- Departamento de Ingeniería Química, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - Olga Rubilar
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA-BIOREN), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile
- Departamento de Ingeniería Química, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
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Harfouche AL, Petousi V, Meilan R, Sweet J, Twardowski T, Altman A. Promoting Ethically Responsible Use of Agricultural Biotechnology. TRENDS IN PLANT SCIENCE 2021; 26:546-559. [PMID: 33483266 DOI: 10.1016/j.tplants.2020.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 05/28/2023]
Abstract
Growing global demands for food, bioenergy, and specialty products, along with the threat posed by various environmental changes, present substantial challenges for agricultural production. Agricultural biotechnology offers a promising avenue for meeting these challenges; however, ethical and sociocultural concerns must first be addressed, to ensure widespread public trust and uptake. To be effective, we need to develop solutions that are ethically responsible, socially responsive, relevant to people of different cultural and social backgrounds, and conveyed to the public in a convincing and straightforward manner. Here, we highlight how ethical approaches, principled decision-making strategies, citizen-stakeholder participation, effective science communication, and bioethics education should be used to guide responsible use of agricultural biotechnology.
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Affiliation(s)
- Antoine L Harfouche
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy.
| | - Vasiliki Petousi
- Department of Sociology, University of Crete, Gallos Campus, 74100 Rethymno, Greece
| | - Richard Meilan
- Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, USA
| | - Jeremy Sweet
- Sweet Environmental Consultants, 6 Green Street, Willingham, CB24 5JA Cambridge, UK
| | - Tomasz Twardowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Zygmunta Noskowskiego Street 12/14, 61-704 Poznan, Poland
| | - Arie Altman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Faculty of Agricultural, Food, and Environmental Quality Sciences, PO Box 12, Rehovot 76100, Israel; The Lester and Sally Entin Faculty of Humanities, Unit of Culture Research, Tel Aviv University, PO Box 39040, Tel Aviv 6997801, Israel.
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11
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Burjoski V, Reddy ASN. The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status. Int J Mol Sci 2021; 22:2845. [PMID: 33799602 PMCID: PMC7999938 DOI: 10.3390/ijms22062845] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/25/2021] [Accepted: 03/10/2021] [Indexed: 12/28/2022] Open
Abstract
RNAs transmit information from DNA to encode proteins that perform all cellular processes and regulate gene expression in multiple ways. From the time of synthesis to degradation, RNA molecules are associated with proteins called RNA-binding proteins (RBPs). The RBPs play diverse roles in many aspects of gene expression including pre-mRNA processing and post-transcriptional and translational regulation. In the last decade, the application of modern techniques to identify RNA-protein interactions with individual proteins, RNAs, and the whole transcriptome has led to the discovery of a hidden landscape of these interactions in plants. Global approaches such as RNA interactome capture (RIC) to identify proteins that bind protein-coding transcripts have led to the identification of close to 2000 putative RBPs in plants. Interestingly, many of these were found to be metabolic enzymes with no known canonical RNA-binding domains. Here, we review the methods used to analyze RNA-protein interactions in plants thus far and highlight the understanding of plant RNA-protein interactions these techniques have provided us. We also review some recent protein-centric, RNA-centric, and global approaches developed with non-plant systems and discuss their potential application to plants. We also provide an overview of results from classical studies of RNA-protein interaction in plants and discuss the significance of the increasingly evident ubiquity of RNA-protein interactions for the study of gene regulation and RNA biology in plants.
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Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA;
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12
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Fincheira P, Quiroz A, Tortella G, Diez MC, Rubilar O. Current advances in plant-microbe communication via volatile organic compounds as an innovative strategy to improve plant growth. Microbiol Res 2021; 247:126726. [PMID: 33640574 DOI: 10.1016/j.micres.2021.126726] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/25/2021] [Accepted: 02/10/2021] [Indexed: 12/18/2022]
Abstract
Volatile organic compounds (VOCs) emitted by microorganisms have demonstrated an important role to improve growth and tolerance against abiotic stress on plants. Most studies have used Arabidopsis thaliana as a model plant, extending to other plants of commercial interest in the last years. Interestingly, the microbial VOCs are characterized by its biodegradable structure, quick action, absence of toxic substances, and acts at lower concentration to regulate plant physiological changes. These compounds modulate plant physiological processes such as phytohormone pathways, photosynthesis, nutrient acquisition, and metabolisms. Besides, the regulation of gene expression associated with cell components, biological processes, and molecular function are triggered by microbial VOCs. Otherwise, few studies have reported the important role of VOCs for confer plant tolerance to abiotic stress, such as drought and salinity. Although VOCs have shown an efficient action to enhance the plant growth under controlled conditions, there are still great challenges for their greenhouse or field application. Therefore, in this review, we summarize the current knowledge about the technical procedures, study cases, and physiological mechanisms triggered by microbial VOCs to finally discuss the challenges of its application in agriculture.
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Affiliation(s)
- Paola Fincheira
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, Chile.
| | - Andrés Quiroz
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, Chile; Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - Gonzalo Tortella
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, Chile; Departamento de Ingeniería Química, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - María Cristina Diez
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, Chile; Departamento de Ingeniería Química, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - Olga Rubilar
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, Chile; Departamento de Ingeniería Química, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
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Gómez-Candón D, Bellvert J, Royo C. Performance of the Two-Source Energy Balance (TSEB) Model as a Tool for Monitoring the Response of Durum Wheat to Drought by High-Throughput Field Phenotyping. FRONTIERS IN PLANT SCIENCE 2021; 12:658357. [PMID: 33936143 PMCID: PMC8085348 DOI: 10.3389/fpls.2021.658357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/22/2021] [Indexed: 05/08/2023]
Abstract
The current lack of efficient methods for high throughput field phenotyping is a constraint on the goal of increasing durum wheat yields. This study illustrates a comprehensive methodology for phenotyping this crop's water use through the use of the two-source energy balance (TSEB) model employing very high resolution imagery. An unmanned aerial vehicle (UAV) equipped with multispectral and thermal cameras was used to phenotype 19 durum wheat cultivars grown under three contrasting irrigation treatments matching crop evapotranspiration levels (ETc): 100%ETc treatment meeting all crop water requirements (450 mm), 50%ETc treatment meeting half of them (285 mm), and a rainfed treatment (122 mm). Yield reductions of 18.3 and 48.0% were recorded in the 50%ETc and rainfed treatments, respectively, in comparison with the 100%ETc treatment. UAV flights were carried out during jointing (April 4th), anthesis (April 30th), and grain-filling (May 22nd). Remotely-sensed data were used to estimate: (1) plant height from a digital surface model (H, R 2 = 0.95, RMSE = 0.18m), (2) leaf area index from multispectral vegetation indices (LAI, R 2 = 0.78, RMSE = 0.63), and (3) actual evapotranspiration (ETa) and transpiration (T) through the TSEB model (R 2 = 0.50, RMSE = 0.24 mm/h). Compared with ground measurements, the four traits estimated at grain-filling provided a good prediction of days from sowing to heading (DH, r = 0.58-0.86), to anthesis (DA, r = 0.59-0.85) and to maturity (r = 0.67-0.95), grain-filling duration (GFD, r = 0.54-0.74), plant height (r = 0.62-0.69), number of grains per spike (NGS, r = 0.41-0.64), and thousand kernel weight (TKW, r = 0.37-0.42). The best trait to estimate yield, DH, DA, and GFD was ETa at anthesis or during grain filling. Better forecasts for yield-related traits were recorded in the irrigated treatments than in the rainfed one. These results show a promising perspective in the use of energy balance models for the phenotyping of large numbers of durum wheat genotypes under Mediterranean conditions.
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Affiliation(s)
- David Gómez-Candón
- Efficient Use of Water in Agriculture Program, Institute of Agrifood Research and Technology (IRTA), Fruitcentre, PCiTAL, Parc Científic i Tecnològic Agroalimentari de Gardeny, Lleida, Spain
- *Correspondence: David Gómez-Candón
| | - Joaquim Bellvert
- Efficient Use of Water in Agriculture Program, Institute of Agrifood Research and Technology (IRTA), Fruitcentre, PCiTAL, Parc Científic i Tecnològic Agroalimentari de Gardeny, Lleida, Spain
| | - Conxita Royo
- Sustainable Field Crops Program, Institute of Agrifood Research and Technology (IRTA), Lleida, Spain
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The application of artificial neural networks in modeling and predicting the effects of melatonin on morphological responses of citrus to drought stress. PLoS One 2020; 15:e0240427. [PMID: 33052940 PMCID: PMC7556499 DOI: 10.1371/journal.pone.0240427] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/25/2020] [Indexed: 12/21/2022] Open
Abstract
Drought stress as one of the most devastating abiotic stresses affects agricultural and horticultural productivity in many parts of the world. The application of melatonin can be considered as a promising approach for alleviating the negative impact of drought stress. Modeling of morphological responses to drought stress can be helpful to predict the optimal condition for improving plant productivity. The objective of the current study is modeling and predicting morphological responses (leaf length, number of leaves/plants, crown diameter, plant height, and internode length) of citrus to drought stress, based on four input variables including melatonin concentrations, days after applying treatments, citrus species, and level of drought stress, using different Artificial Neural Networks (ANNs) including Generalized Regression Neural Network (GRNN), Radial basis function (RBF), and Multilayer Perceptron (MLP). The results indicated a higher accuracy of GRNN as compared to RBF and MLP. The great accordance between the experimental and predicted data of morphological responses for both training and testing processes support the excellent efficiency of developed GRNN models. Also, GRNN was connected to Non-dominated Sorting Genetic Algorithm-II (NSGA-II) to optimize input variables for obtaining the best morphological responses. Generally, the validation experiment showed that ANN-NSGA-II can be considered as a promising and reliable computational tool for studying and predicting plant morphological and physiological responses to drought stress.
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15
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Dai L, Li J, Harmens H, Zheng X, Zhang C. Melatonin enhances drought resistance by regulating leaf stomatal behaviour, root growth and catalase activity in two contrasting rapeseed (Brassica napus L.) genotypes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 149:86-95. [PMID: 32058897 DOI: 10.1016/j.plaphy.2020.01.039] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/31/2020] [Indexed: 05/23/2023]
Abstract
Two contrasting rapeseed (Brassica napus L.) genotypes, Qinyou 8 (drought-sensitive) and Q2 (drought-tolerant), were studied under drought stress with or without pretreatment with melatonin to (i) explore whether melatonin enhances drought resistance by regulating root growth and (ii) determine the relationship between the belowground and aboveground responses to melatonin under drought stress. Results show that the light-saturated rate of photosynthesis (Pn), stomatal conductance (gs), water use efficiency (WUE) and chlorophyll content were decreased by drought for Qinyou 8, whereas drought only decreased Pn and chlorophyll content for Q2. Drought decreased actual photochemical efficiency in saturated light (Fv'/Fm'), actual photochemical efficiency (PhiPSⅡ), quenching of photochemical efficiency (qL) and electron transport rate (ETR) in Qinyou 8. However drought only decreased Fv'/Fm' and qL in Q2. Drought increased malondialdehyde (MDA) and hydrogen peroxide (H2O2) contents in the roots of both genotypes. Melatonin had no significant additional effects on root guaiacol peroxidase (POD) and superoxide dismutase (SOD) activities, but enhanced root catalase (CAT) activity of droughted plants further. Melatonin promoted taproot and lateral root growth under drought stress. Melatonin also promoted stomatal opening resulting in enhanced photosynthesis in the two genotypes. The two mechanisms induced by melatonin synergistically enhance drought resistance of rapeseed as indicated by enhanced gas exchange parameters under melatonin pretreatment. The findings provide evidence for a physiological role of melatonin in improving drought resistance, especially in belowground parts.
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Affiliation(s)
- Lulu Dai
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Haidian Distract, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan Disctrict, Beijing, 100049, China
| | - Jun Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Harry Harmens
- UK Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Xiaodong Zheng
- College of Horticulture, Qingdao Agricultural University, Changcheng Road 700, Chengyang District, Qingdao, 266109, China
| | - Chunlei Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Jameel A, Noman M, Liu W, Ahmad N, Wang F, Li X, Li H. Tinkering Cis Motifs Jigsaw Puzzle Led to Root-Specific Drought-Inducible Novel Synthetic Promoters. Int J Mol Sci 2020; 21:E1357. [PMID: 32085397 PMCID: PMC7072871 DOI: 10.3390/ijms21041357] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
Following an in-depth transcriptomics-based approach, we first screened out and analyzed (in silico) cis motifs in a group of 63 drought-inducible genes (in soybean). Six novel synthetic promoters (SynP14-SynP19) were designed by concatenating 11 cis motifs, ABF, ABRE, ABRE-Like, CBF, E2F-VARIANT, G-box, GCC-Box, MYB1, MYB4, RAV1-A, and RAV1-B (in multiple copies and various combination) with a minimal 35s core promoter and a 222 bp synthetic intron sequence. In order to validate their drought-inducibility and root-specificity, the designed synthetic assemblies were transformed in soybean hairy roots to drive GUS gene using pCAMBIA3301. Through GUS histochemical assay (after a 72 h 6% PEG6000 treatment), we noticed higher glucuronidase activity in transgenic hairy roots harboring SynP15, SynP16, and SynP18. Further screening through GUS fluorometric assay flaunted SynP16 as the most appropriate combination of efficient drought-responsive cis motifs. Afterwards, we stably transformed SynP15, SynP16, and SynP18 in Arabidopsis and carried out GUS staining as well as fluorometric assays of the transgenic plants treated with simulated drought stress. Consistently, SynP16 retained higher transcriptional activity in Arabidopsis roots in response to drought. Thus the root-specific drought-inducible synthetic promoters designed using stimulus-specific cis motifs in a definite fashion could be exploited in developing drought tolerance in soybean and other crops as well. Moreover, the rationale of design extends our knowledge of trial-and-error based cis engineering to construct synthetic promoters for transcriptional upgradation against other stresses.
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Affiliation(s)
| | | | | | | | | | - Xiaowei Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, China; (A.J.); (M.N.); (W.L.); (N.A.)
| | - Haiyan Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, China; (A.J.); (M.N.); (W.L.); (N.A.)
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Liebsch D, Palatnik JF. MicroRNA miR396, GRF transcription factors and GIF co-regulators: a conserved plant growth regulatory module with potential for breeding and biotechnology. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:31-42. [PMID: 31726426 DOI: 10.1016/j.pbi.2019.09.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 05/23/2023]
Abstract
Multicellular life relies on complex regulatory mechanisms ensuring proper growth and development. In plants, these mechanisms construct a body plan that is both reproducible, and highly flexible for adaptation to different environmental conditions. A crucial regulatory module - consisting of microRNA miR396, GROWTH REGULATING FACTORS (GRFs) and GRF-INTERACTING FACTORS (GIFs) - has been shown to control growth of multiple tissues and organs in a variety of species. Especially in the last few years, research has expanded our knowledge of miR396-GRF/GIF function to crops, where it affects agronomically important traits, and highlighted its role in coordinating growth with endogenous and environmental factors. Special properties make the miR396-GRF/GIF system highly efficient in growth regulation and a promising target for improving plant yield.
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Affiliation(s)
- Daniela Liebsch
- IBR (Instituto de Biologia Molecular y Celular de Rosario), UNR/CONICET, Ocampo y Esmeralda s/n, 2000 Rosario, Argentina.
| | - Javier F Palatnik
- IBR (Instituto de Biologia Molecular y Celular de Rosario), UNR/CONICET, Ocampo y Esmeralda s/n, 2000 Rosario, Argentina; Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, Argentina.
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18
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Resources, Collaborators, and Neighbors: The Three-Pronged Challenge in the Implementation of Bioeconomy Regions. SUSTAINABILITY 2019. [DOI: 10.3390/su11247235] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the last decade, the bioeconomy has become increasingly important and visible in international policy agendas, with several strategies being recently developed. The implementation of bio-based technologies mostly takes place on a regional scale. Therefore, from a regional perspective, a key question revolves around what main challenges are associated with technological developments that could catalyze the implementation of sustainable bioeconomy regions. In this study, a cross-cutting analysis was carried out to determine these challenges. First, interviews were conducted with industry practitioners and scientists working in the bioeconomy field. These interviews were supplemented with a literature review to determine the status quo of bioeconomy strategies and their implementation, particularly on a regional level. A multidisciplinary workshop was then organized to identify the most relevant challenges in the short- and mid-term associated with establishing bioeconomy regions. The results show that there is a three-pronged challenge in innovative technological development from a regional perspective: (1) Resources: The establishment of sustainable regional feedstock strategies and supplies for supporting the bio-industrial sector; (2) collaborators: The establishment of a regional “critical mass” by fostering supply chain clusters and networks; and (3) neighbors: Understanding the local dynamics of societal trends and preferences and social acceptance of bio-technologies and their representative bio-based products.
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19
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Harfouche AL, Jacobson DA, Kainer D, Romero JC, Harfouche AH, Scarascia Mugnozza G, Moshelion M, Tuskan GA, Keurentjes JJ, Altman A. Accelerating Climate Resilient Plant Breeding by Applying Next-Generation Artificial Intelligence. Trends Biotechnol 2019; 37:1217-1235. [DOI: 10.1016/j.tibtech.2019.05.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/18/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
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20
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Dalal A, Bourstein R, Haish N, Shenhar I, Wallach R, Moshelion M. Dynamic Physiological Phenotyping of Drought-Stressed Pepper Plants Treated With "Productivity-Enhancing" and "Survivability-Enhancing" Biostimulants. FRONTIERS IN PLANT SCIENCE 2019; 10:905. [PMID: 31379898 PMCID: PMC6654182 DOI: 10.3389/fpls.2019.00905] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/26/2019] [Indexed: 05/02/2023]
Abstract
The improvement of crop productivity under abiotic stress is one of the biggest challenges faced by the agricultural scientific community. Despite extensive research, the research-to-commercial transfer rate of abiotic stress-resistant crops remains very low. This is mainly due to the complexity of genotype × environment interactions and in particular, the ability to quantify the dynamic plant physiological response profile to a dynamic environment. Most existing phenotyping facilities collect information using robotics and automated image acquisition and analysis. However, their ability to directly measure the physiological properties of the whole plant is limited. We demonstrate a high-throughput functional phenotyping system (HFPS) that enables comparing plants' dynamic responses to different ambient conditions in dynamic environments due to its direct and simultaneous measurement of yield-related physiological traits of plants under several treatments. The system is designed as one-to-one (1:1) plant-[sensors+controller] units, i.e., each individual plant has its own personalized sensor, controller and irrigation valves that enable (i) monitoring water-relation kinetics of each plant-environment response throughout the plant's life cycle with high spatiotemporal resolution, (ii) a truly randomized experimental design due to multiple independent treatment scenarios for every plant, and (iii) reduction of artificial ambient perturbations due to the immobility of the plants or other objects. In addition, we propose two new resilience-quantifying-related traits that can also be phenotyped using the HFPS: transpiration recovery rate and night water reabsorption. We use the HFPS to screen the effects of two commercial biostimulants (a seaweed extract -ICL-SW, and a metabolite formula - ICL-NewFo1) on Capsicum annuum under different irrigation regimes. Biostimulants are considered an alternative approach to improving crop productivity. However, their complex mode of action necessitates cost-effective pre-field phenotyping. The combination of two types of treatment (biostimulants and drought) enabled us to evaluate the precision and resolution of the system in investigating the effect of biostimulants on drought tolerance. We analyze and discuss plant behavior at different stages, and assess the penalty and trade-off between productivity and resilience. In this test case, we suggest a protocol for the screening of biostimulants' physiological mechanisms of action.
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Affiliation(s)
- Ahan Dalal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ronny Bourstein
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Department of Soil and Water Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Nadav Haish
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Itamar Shenhar
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Rony Wallach
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Department of Soil and Water Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Menachem Moshelion
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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21
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Gosa SC, Lupo Y, Moshelion M. Quantitative and comparative analysis of whole-plant performance for functional physiological traits phenotyping: New tools to support pre-breeding and plant stress physiology studies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:49-59. [PMID: 31003611 DOI: 10.1016/j.plantsci.2018.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/14/2018] [Accepted: 05/14/2018] [Indexed: 05/18/2023]
Abstract
Plants are autotrophic organisms in which there are linear relationships between the rate at which organic biomass is accumulated and many ambient parameters such as water, nutrients, CO2 and solar radiation. These linear relationships are the result of good feedback regulation between a plants sensing of the environment and the optimization of its performance response. In this review, we suggest that continuous monitoring of the plant physiological profile in response to changing ambient conditions could be a useful new phenotyping tool, allowing the characterization and comparison of different levels of functional phenotypes and productivity. This functional physiological phenotyping (FPP) approach can be integrated into breeding programs, which are facing difficulties in selecting plants that perform well under abiotic stress. Moreover, high-throughput FPP will increase the efficiency of the selection of traits that are closely related to environmental interactions (such as plant water status, water-use efficiency, stomatal conductance, etc.) thanks to its high resolution and dynamic measurements. One of the important advantages of FPP is, its simplicity and effectiveness and compatibility with experimental methods that use load-cell lysimeters and ambient sensors. In the future, this platform could help with phenotyping of complex physiological traits, beneficial for yield gain to enhance functional breeding approaches and guide in crop modeling.
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Affiliation(s)
- Sanbon Chaka Gosa
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Yaniv Lupo
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Menachem Moshelion
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
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22
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Abstract
Designing the expression cassettes with desired properties remains the most important consideration of gene engineering technology. One of the challenges for predictive gene expression is the modeling of synthetic gene switches to regulate one or more target genes which would directly respond to specific chemical, environmental, and physiological stimuli. Assessment of natural promoter, high-throughput sequencing, and modern biotech inventory aided in deciphering the structure of cis elements and molding the native cis elements into desired synthetic promoter. Synthetic promoters which are molded by rearrangement of cis motifs can greatly benefit plant biotechnology applications. This review gives a glimpse of the manual in vivo gene regulation through synthetic promoters. It summarizes the integrative design strategy of synthetic promoters and enumerates five approaches for constructing synthetic promoters. Insights into the pattern of cis regulatory elements in the pursuit of desirable "gene switches" to date has also been reevaluated. Joint strategies of bioinformatics modeling and randomized biochemical synthesis are addressed in an effort to construct synthetic promoters for intricate gene regulation.
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23
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Towards Food Security: Current State and Future Prospects of Agrobiotechnology. Trends Biotechnol 2018; 36:1219-1229. [PMID: 30262405 DOI: 10.1016/j.tibtech.2018.07.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 11/20/2022]
Abstract
The consistent increase in the global population, estimated to reach 9 billion people by 2050, poses a serious challenge for the achievement of global food security. Therefore, the need to feed an increasing world population and to respond adequately to the effects of climate change must be urgently considered. Progress may be achieved by applying knowledge of molecular and genetic mechanisms to create and/or improve agricultural and industrial processes. We highlight the importance of crops (wheat, maize, rice, rapeseed, and soybean) to the development of sustainable agriculture and agrobiotechnology in the EU and discuss possible solutions for ensuring food security, while also considering their social acceptance.
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24
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Butt H, Jamil M, Wang JY, Al-Babili S, Mahfouz M. Engineering plant architecture via CRISPR/Cas9-mediated alteration of strigolactone biosynthesis. BMC PLANT BIOLOGY 2018; 18:174. [PMID: 30157762 PMCID: PMC6116466 DOI: 10.1186/s12870-018-1387-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 08/07/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Precision plant genome engineering holds much promise for targeted improvement of crop traits via unprecedented single-base level control over the genetic material. Strigolactones (SLs) are a key determinant of plant architecture, known for their role in inhibiting shoot branching (tillering). RESULTS We used CRISPR/Cas9 in rice (Oryza sativa) for targeted disruption of CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7), which controls a key step in SL biosynthesis. The ccd7 mutants exhibited a striking increase in tillering, combined with a reduced height, which could be rescued by application of the synthetic SL analog GR24. Striga germination assays and liquid chromatography-mass spectrometry analysis showed that root exudates of ccd7 mutants were also SL deficient. CONCLUSIONS Taken together, our results show the potential and feasibility of the use of the CRISPR/Cas9 system for targeted engineering of plant architecture and for elucidating the molecular underpinnings of architecture-related traits.
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Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Muhammad Jamil
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Jian You Wang
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Salim Al-Babili
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
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Zhang M, Li G, Zhou Q, Pan D, Zhu M, Xiao R, Zhang Y, Wu G, Wan Y, Shen Y. Boosted Electrochemical Immunosensing of Genetically Modified Crop Markers Using Nanobody and Mesoporous Carbon. ACS Sens 2018; 3:684-691. [PMID: 29457451 DOI: 10.1021/acssensors.8b00011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The problems of environmental security and the potential risks of human health caused by transgenic crops have attracted much attention. Recent studies reveal 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Agrobacterium sp. strain CP4 protein (CP4-EPSPS), which shows very high resistance to herbicide glyphosate, is a typical biomarker of genetically modified (GM) crops. For this reason, it is highly anticipated to devise a sensitive and convenient strategy to detect CP4-EPSPS protein in crops. Herein, we report a simple electrochemical immunosensor by coupling nanobody, ordered mesoporous carbon (OMC), and thionine (Th). As a capture agent, the nanobody was screened out from an immunized Bactrian camel, and exhibited superior properties with respect to conventional antibody, such as higher stability and stronger heat resistance. Moreover, OMC offered an effective platform with high surface area, electrical conductivity, and biocompatibility, which greatly facilitated the assembly of redox probe Th, and further coupling of large amount of capture nanobodies. As a result, the CP4-EPSPS protein could be determined with high sensitivity and efficiency by differential pulse voltammetry (DPV) in a wide linear range from 0.001 to 100 ng·mL-1 with a low detection limit of 0.72 pg·mL-1, which was more than 3 orders of magnitude lower than those of previously reported works. As an example, the proposed electrochemical immunosensor was successfully applied to spiked samples, demonstrating its great potential in CP4-EPSPS screening and detection.
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Affiliation(s)
- Mingming Zhang
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 210009, China
- Center of Clinical Laboratory Medicine of Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, China
| | - Guanghui Li
- Shanghai Novamab Biopharmaceuticals Co., Ltd., Shanghai 201203, China
| | - Qing Zhou
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 210009, China
| | - Deng Pan
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 210009, China
| | - Min Zhu
- Shanghai Novamab Biopharmaceuticals Co., Ltd., Shanghai 201203, China
| | - Runyu Xiao
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yuanjian Zhang
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 210009, China
| | - Guoqiu Wu
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 210009, China
- Center of Clinical Laboratory Medicine of Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yakun Wan
- Shanghai Novamab Biopharmaceuticals Co., Ltd., Shanghai 201203, China
| | - Yanfei Shen
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 210009, China
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Loeschcke A, Dienst D, Wewer V, Hage-Hülsmann J, Dietsch M, Kranz-Finger S, Hüren V, Metzger S, Urlacher VB, Gigolashvili T, Kopriva S, Axmann IM, Drepper T, Jaeger KE. The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis. PLoS One 2017; 12:e0189816. [PMID: 29281679 PMCID: PMC5744966 DOI: 10.1371/journal.pone.0189816] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/01/2017] [Indexed: 11/18/2022] Open
Abstract
Cyclic triterpenes constitute one of the most diverse groups of plant natural products. Besides the intriguing biochemistry of their biosynthetic pathways, plant triterpenes exhibit versatile bioactivities, including antimicrobial effects against plant and human pathogens. While prokaryotes have been extensively used for the heterologous production of other classes of terpenes, the synthesis of cyclic triterpenes, which inherently includes the two-step catalytic formation of the universal linear precursor 2,3-oxidosqualene, is still a major challenge. We thus explored the suitability of the metabolically versatile photosynthetic α-proteobacterium Rhodobacter capsulatus SB1003 and cyanobacterium Synechocystis sp. PCC 6803 as alternative hosts for biosynthesis of cyclic plant triterpenes. Therefore, 2,3-oxidosqualene production was implemented and subsequently combined with different cyclization reactions catalyzed by the representative oxidosqualene cyclases CAS1 (cycloartenol synthase), LUP1 (lupeol synthase), THAS1 (thalianol synthase) and MRN1 (marneral synthase) derived from model plant Arabidopsis thaliana. While successful accumulation of 2,3-oxidosqualene could be detected by LC-MS analysis in both hosts, cyclase expression resulted in differential production profiles. CAS1 catalyzed conversion to only cycloartenol, but expression of LUP1 yielded lupeol and a triterpenoid matching an oxidation product of lupeol, in both hosts. In contrast, THAS1 expression did not lead to cyclic product formation in either host, whereas MRN1-dependent production of marnerol and hydroxymarnerol was observed in Synechocystis but not in R. capsulatus. Our findings thus indicate that 2,3-oxidosqualene cyclization in heterologous phototrophic bacteria is basically feasible but efficient conversion depends on both the respective cyclase enzyme and individual host properties. Therefore, photosynthetic α-proteo- and cyanobacteria are promising alternative candidates for providing new bacterial access to the broad class of triterpenes for biotechnological applications.
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Affiliation(s)
- Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Dennis Dienst
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vera Wewer
- Cluster of Excellence on Plant Sciences (CEPLAS)
- MS Platform, Department of Biology, University of Cologne, Cologne, Germany
| | - Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Maximilian Dietsch
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sarah Kranz-Finger
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute of Biochemistry II, Department of Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vanessa Hüren
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sabine Metzger
- Cluster of Excellence on Plant Sciences (CEPLAS)
- MS Platform, Department of Biology, University of Cologne, Cologne, Germany
| | - Vlada B. Urlacher
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute of Biochemistry II, Department of Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tamara Gigolashvili
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Botanical Institute, University of Cologne, Cologne, Germany
| | - Stanislav Kopriva
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Botanical Institute, University of Cologne, Cologne, Germany
| | - Ilka M. Axmann
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- * E-mail: (IMA); (TD)
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
- * E-mail: (IMA); (TD)
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute of Bio- and Geosciences (IBG-1), Forschungszentrum Jülich, Jülich, Germany
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Rasche F, Blagodatskaya E, Emmerling C, Belz R, Musyoki MK, Zimmermann J, Martin K. A preview of perennial grain agriculture: knowledge gain from biotic interactions in natural and agricultural ecosystems. Ecosphere 2017. [DOI: 10.1002/ecs2.2048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute); University of Hohenheim; 70593 Stuttgart Germany
| | - Evgenia Blagodatskaya
- Department of Soil Science of Temperate Ecosystems; Georg-August University Göttingen; 37077 Göttingen Germany
| | | | - Regina Belz
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute); University of Hohenheim; 70593 Stuttgart Germany
| | - Mary K. Musyoki
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute); University of Hohenheim; 70593 Stuttgart Germany
| | - Judith Zimmermann
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute); University of Hohenheim; 70593 Stuttgart Germany
| | - Konrad Martin
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute); University of Hohenheim; 70593 Stuttgart Germany
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Dalal A, Attia Z, Moshelion M. To Produce or to Survive: How Plastic Is Your Crop Stress Physiology? FRONTIERS IN PLANT SCIENCE 2017; 8:2067. [PMID: 29259613 PMCID: PMC5723404 DOI: 10.3389/fpls.2017.02067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/17/2017] [Indexed: 05/08/2023]
Abstract
Abiotic stress causes major crop losses and is considered a greater challenge than biotic stress. Comparisons of the number of published articles and patents regarding these different types of stresses, and the number of commercially released crops designed to tolerate different types of stresses, revealed a huge gap in the bench-to-field transfer rate of abiotic stress-tolerant crops, as compared to crops designed to tolerate biotic stress. These differences underscore the complexity of abiotic stress-response mechanisms. Here, we suggest that breeding programs favoring yield-related quantitative physiological traits (QPTs; e.g., photosynthesis rate or stomatal conductance) have canalized those QPTs at their highest levels. This has affected the sensitivity of those QPTs to changing environmental conditions and those traits have become less plastic. We also suggest that breeding pressure has had an asymmetric impact on different QPTs, depending on their sensitivity to environmental conditions and their interactions with other QPTs. We demonstrate this asymmetric impact on the regulation of whole-plant water balance, showing how plastic membrane water content, stomatal conductance and leaf hydraulic conductance interact to canalize whole-organ water content. We suggest that a QPT's plasticity is itself an important trait and that understanding this plasticity may help us to develop yield-optimized crops.
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Affiliation(s)
| | | | - Menachem Moshelion
- Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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Antoniou C, Chatzimichail G, Xenofontos R, Pavlou JJ, Panagiotou E, Christou A, Fotopoulos V. Melatonin systemically ameliorates drought stress-induced damage in Medicago sativa plants by modulating nitro-oxidative homeostasis and proline metabolism. J Pineal Res 2017; 62. [PMID: 28226194 DOI: 10.1111/jpi.12401] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/17/2017] [Indexed: 12/11/2022]
Abstract
Recent reports have uncovered the multifunctional role of melatonin in plant physiological responses under optimal and suboptimal environmental conditions. In this study, we explored whether melatonin pretreatment could provoke priming effects in alfalfa (Medicago sativa L.) plants subsequently exposed to prolonged drought stress (7 days), by withholding watering. Results revealed that the rhizospheric application of melatonin (10 μmol L-1 ) remarkably enhanced the drought tolerance of alfalfa plants, as evidenced by the observed plant tolerant phenotype, as well as by the higher levels of chlorophyll fluorescence and stomatal conductance, compared with nontreated drought-stressed plants. In addition, lower levels of lipid peroxidation (MDA content) as well as of both H2 O2 and NO contents in primed compared with nonprimed stressed plants suggest that melatonin pretreatment resulted in the systemic mitigation of drought-induced nitro-oxidative stress. Nitro-oxidative homeostasis was achieved by melatonin through the regulation of reactive oxygen (SOD, GR, CAT, APX) and nitrogen species (NR, NADHde) metabolic enzymes at the enzymatic and/or transcript level. Moreover, melatonin pretreatment resulted in the limitation of cellular redox disruption through the regulation of the mRNA levels of antioxidant and redox-related components (ADH, AOX, GST7, GST17), as well via osmoprotection through the regulation of proline homeostasis, at both the enzymatic (P5CS) and gene expression level (P5CS, P5CR). Overall, novel results highlight the importance of melatonin as a promising priming agent for the enhancement of plant tolerance to drought conditions through the regulation of nitro-oxidative and osmoprotective homeostasis.
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Affiliation(s)
- Chrystalla Antoniou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Giannis Chatzimichail
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Rafaella Xenofontos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Jan J Pavlou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Evangelia Panagiotou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Anastasis Christou
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Natural Recourses, Nicosia, Cyprus
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
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30
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Halperin O, Gebremedhin A, Wallach R, Moshelion M. High-throughput physiological phenotyping and screening system for the characterization of plant-environment interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:839-850. [PMID: 27868265 DOI: 10.1111/tpj.13425] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 05/09/2023]
Abstract
We present a simple and effective high-throughput experimental platform for simultaneous and continuous monitoring of water relations in the soil-plant-atmosphere continuum of numerous plants under dynamic environmental conditions. This system provides a simultaneously measured, detailed physiological response profile for each plant in the array, over time periods ranging from a few minutes to the entire growing season, under normal, stress and recovery conditions and at any phenological stage. Three probes for each pot in the array and a specially designed algorithm enable detailed water-relations characterization of whole-plant transpiration, biomass gain, stomatal conductance and root flux. They also enable quantitative calculation of the whole plant water-use efficiency and relative water content at high resolution under dynamic soil and atmospheric conditions. The system has no moving parts and can fit into many growing environments. A screening of 65 introgression lines of a wild tomato species (Solanum pennellii) crossed with cultivated tomato (S. lycopersicum), using our system and conventional gas-exchange tools, confirmed the accuracy of the system as well as its diagnostic capabilities. The use of this high-throughput diagnostic screening method is discussed in light of the gaps in our understanding of the genetic regulation of whole-plant performance, particularly under abiotic stress.
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Affiliation(s)
- Ofer Halperin
- Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Alem Gebremedhin
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Rony Wallach
- Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
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31
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Gemperline E, Keller C, Jayaraman D, Maeda J, Sussman MR, Ané JM, Li L. Examination of Endogenous Peptides in Medicago truncatula Using Mass Spectrometry Imaging. J Proteome Res 2016; 15:4403-4411. [PMID: 27726374 DOI: 10.1021/acs.jproteome.6b00471] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plant science is an important, rapidly developing area of study. Within plant science, one area of study that has grown tremendously with recent technological advances, such as mass spectrometry, is the field of plant-omics; however, plant peptidomics is relatively underdeveloped in comparison with proteomics and metabolomics. Endogenous plant peptides can act as signaling molecules and have been shown to affect cell division, development, nodulation, reproduction, symbiotic associations, and defense reactions. There is a growing need to uncover the role of endogenous peptides on a molecular level. Mass spectrometric imaging (MSI) is a valuable tool for biological analyses as it allows for the detection of thousands of analytes in a single experiment and also displays spatial information for the detected analytes. Despite the prediction of a large number of plant peptides, their detection and imaging with spatial localization and chemical specificity is currently lacking. Here we analyzed the endogenous peptides and proteins in Medicago truncatula using matrix-assisted laser desorption/ionization (MALDI)-MSI. Hundreds of endogenous peptides and protein fragments were imaged, with interesting peptide spatial distribution changes observed between plants in different developmental stages.
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Affiliation(s)
- Erin Gemperline
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dhileepkumar Jayaraman
- Department of Agronomy, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Junko Maeda
- Department of Agronomy, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
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32
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Martins PK, Mafra V, de Souza WR, Ribeiro AP, Vinecky F, Basso MF, da Cunha BADB, Kobayashi AK, Molinari HBC. Selection of reliable reference genes for RT-qPCR analysis during developmental stages and abiotic stress in Setaria viridis. Sci Rep 2016; 6:28348. [PMID: 27321675 PMCID: PMC4913262 DOI: 10.1038/srep28348] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/01/2016] [Indexed: 12/28/2022] Open
Abstract
Real-time PCR (RT-qPCR) expression analysis is a powerful analytical technique, but reliable results depend on the use of stable reference genes for proper normalization. This study proposed to test the expression stability of 13 candidate reference genes in Setaria viridis, a monocot species recently proposed as a new C4 model plant. Gene expression stability of these genes was assayed across different tissues and developmental stages of Setaria and under drought or aluminum stress. In general, our results showed Protein Kinase, RNA Binding Protein and SDH as the most stable genes. Moreover, pairwise analysis showed that two reference genes were sufficient to normalize the gene expression data under each condition. By contrast, GAPDH and ACT were the least stably expressed genes tested. Validation of suitable reference genes was carried out to profile the expression of P5CS and GolS during abiotic stress. In addition, normalization of gene expression of SuSy, involved in sugar metabolism, was assayed in the developmental dataset. This study provides a list of reliable reference genes for transcript normalization in S. viridis in different tissues and stages of development and under abiotic stresses, which will facilitate genetic studies in this monocot model plant.
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Affiliation(s)
- Polyana Kelly Martins
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | - Valéria Mafra
- Brazilian Bioethanol Science and Technology Laboratory/Brazilian Center of Research in Energy and Materials, Campinas, SP, 13083-100, Brazil
| | - Wagner Rodrigo de Souza
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | - Ana Paula Ribeiro
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | - Felipe Vinecky
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | - Marcos Fernando Basso
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | | | - Adilson Kenji Kobayashi
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
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Rouphael Y, Colla G, Bernardo L, Kane D, Trevisan M, Lucini L. Zinc Excess Triggered Polyamines Accumulation in Lettuce Root Metabolome, As Compared to Osmotic Stress under High Salinity. FRONTIERS IN PLANT SCIENCE 2016; 7:842. [PMID: 27375675 PMCID: PMC4901059 DOI: 10.3389/fpls.2016.00842] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/30/2016] [Indexed: 05/20/2023]
Abstract
Abiotic stresses such as salinity and metal contaminations are the major environmental stresses that adversely affect crop productivity worldwide. Crop responses and tolerance to abiotic stress are complex processes for which "-omic" approaches such as metabolomics is giving us a newest view of biological systems. The aim of the current research was to assess metabolic changes in lettuce (Lactuca sativa L.), by specifically probing the root metabolome of plants exposed to elevated isomolar concentrations of NaCl and ZnSO4. Most of the metabolites that were differentially accumulated in roots were identified for stress conditions, however the response was more intense in plants exposed to NaCl. Compounds identified in either NaCl or ZnSO4 conditions were: carbohydrates, phenolics, hormones, glucosinolates, and lipids. Our findings suggest that osmotic stress and the consequent redox imbalance play a major role in determining lettuce root metabolic response. In addition, it was identified that polyamines and polyamine conjugates were triggered as a specific response to ZnSO4. These findings help improve understanding of how plants cope with abiotic stresses. This information can be used to assist decision-making in breeding programs for improving crop tolerance to salinity and heavy metal contaminations.
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Affiliation(s)
- Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico IINaples, Italy
| | - Giuseppe Colla
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
| | - Letizia Bernardo
- Institute of Environmental and Agricultural Chemistry, Catholic University of the Sacred HeartPiacenza, Italy
| | - David Kane
- Enviresearch Ltd., Nanotechnology Centre, Newcastle UniversityNewcastle Upon Tyne, UK
| | - Marco Trevisan
- Institute of Environmental and Agricultural Chemistry, Catholic University of the Sacred HeartPiacenza, Italy
| | - Luigi Lucini
- Institute of Environmental and Agricultural Chemistry, Catholic University of the Sacred HeartPiacenza, Italy
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Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era. BMC Genomics 2016; 17:408. [PMID: 27229151 PMCID: PMC4882841 DOI: 10.1186/s12864-016-2734-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 05/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. Results Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. Conclusion This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2734-y) contains supplementary material, which is available to authorized users.
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Negin B, Moshelion M. The advantages of functional phenotyping in pre-field screening for drought-tolerant crops. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 44:107-118. [PMID: 32480550 DOI: 10.1071/fp16156] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/10/2016] [Indexed: 06/11/2023]
Abstract
Increasing worldwide demand for food, feed and fuel presents a challenge in light of limited resources and climatic challenges. Breeding for stress tolerance and drought tolerance, in particular, is one the most challenging tasks facing breeders. The comparative screening of immense numbers of plant and gene candidates and their interactions with the environment represents a major bottleneck in this process. We suggest four key components to be considered in pre-field screens (phenotyping) for complex traits under drought conditions: (i) where, when and under which conditions to phenotype; (ii) which traits to phenotype; (iii) how to phenotype (which method); and (iv) how to translate collected data into knowledge that can be used to make practical decisions. We describe some common pitfalls, including inadequate phenotyping methods, incorrect terminology and the inappropriate use of non-relevant traits as markers for drought tolerance. We also suggest the use of more non-imaging, physiology-based, high-throughput phenotyping systems, which, used in combination with soil-plant-atmosphere continuum (SPAC) measurements and fitting models of plant responses to continuous and fluctuating environmental conditions, should be further investigated in order to serve as a phenotyping tool to better understand and characterise plant stress response. In the future, we assume that many of today's phenotyping challenges will be solved by technology and automation, leaving us with the main challenge of translating large amounts of accumulated data into meaningful knowledge and decision making tools.
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Affiliation(s)
- Boaz Negin
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Menachem Moshelion
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
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Buller RM, Connell ND, Morse SS, Campbell M, Tait RC. Strengthening the role of the IBC in the 21st century. ENSURING NATIONAL BIOSECURITY 2016. [PMCID: PMC7149545 DOI: 10.1016/b978-0-12-801885-9.00013-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The US government (USG) has not fully implemented a robust system to evaluate dual-use research (DUR). In particular, the USG has failed to effectively fund, support, and expand the role of the local Institutional Biosafety Committee in the oversight of DUR and in the changing scientific landscape; a comprehensive education program for all in life sciences research with regard to the dual-use dilemma has not been forthcoming; and finally, there has been no systematic evaluation of the impact of USG policy, regulations, and guidance on an institution’s cost structure and on scientific discovery. We detail our judgments on current USG DUR policy and provide recommendations for future oversight of DUR from our perspective as senior administrators and laboratory scientists charged with the responsibility of conducting life-sciences research in an era of increasing regulatory requirements and decreasing federal support.
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Barabaschi D, Tondelli A, Desiderio F, Volante A, Vaccino P, Valè G, Cattivelli L. Next generation breeding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:3-13. [PMID: 26566820 DOI: 10.1016/j.plantsci.2015.07.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/10/2015] [Accepted: 07/11/2015] [Indexed: 05/18/2023]
Abstract
The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. The sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Re-sequencing allows the identification of an unlimited number of markers as well as the analysis of germplasm allelic diversity based on allele mining approaches. High throughput marker technologies coupled with advanced phenotyping platforms provide new opportunities for discovering marker-trait associations which can sustain genomic-assisted breeding. The availability of genome sequencing information is enabling genome editing (site-specific mutagenesis), to obtain gene sequences desired by breeders. This review illustrates how next generation sequencing-derived information can be used to tailor genomic tools for different breeders' needs to revolutionize crop improvement.
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Affiliation(s)
- Delfina Barabaschi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Alessandro Tondelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Andrea Volante
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Rice Research Unit, SS 11 to Torino Km 2.5, 13100 Vercelli, Italy
| | - Patrizia Vaccino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Research Unit for Cereal Selection in Continental areas, via R. Forlani, e, 26866 S. Angelo Lodigiano, Italy
| | - Giampiero Valè
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Rice Research Unit, SS 11 to Torino Km 2.5, 13100 Vercelli, Italy
| | - Luigi Cattivelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy.
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