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Gupta P, Geniza M, Elser J, Al-Bader N, Baschieri R, Phillips JL, Haq E, Preece J, Naithani S, Jaiswal P. Reference genome of the nutrition-rich orphan crop chia ( Salvia hispanica) and its implications for future breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1272966. [PMID: 38162307 PMCID: PMC10757625 DOI: 10.3389/fpls.2023.1272966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Chia (Salvia hispanica L.) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.6 Mb and encodes 48,090 annotated protein-coding genes. Our analysis revealed that ~42% of the chia genome harbors repetitive content, and identified ~3 million single nucleotide polymorphisms (SNPs) and 15,380 simple sequence repeat (SSR) marker sites. By investigating the chia transcriptome, we discovered that ~44% of the genes undergo alternative splicing with a higher frequency of intron retention events. Additionally, we identified chia genes associated with important nutrient content and quality traits, such as the biosynthesis of PUFAs and seed mucilage fiber (dietary fiber) polysaccharides. Notably, this is the first report of in-silico annotation of a plant genome for protein-derived small bioactive peptides (biopeptides) associated with improving human health. To facilitate further research and translational applications of this valuable orphan crop, we have developed the Salvia genomics database (SalviaGDB), accessible at https://salviagdb.org.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Rachel Baschieri
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy Levi Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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Tan F, Hou Y, Huang X, Jia J, Yang H, Luo P. Temporal and spatial arrangement of wheat sowing date: a revolutionary strategy to accomplish Tianfu Granary. FRONTIERS IN PLANT SCIENCE 2023; 14:1240417. [PMID: 38053769 PMCID: PMC10694224 DOI: 10.3389/fpls.2023.1240417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Rapidly global urbanization and economic growth in the past several decades have resulted in a sharp contraction of arable areas worldwide. However, food supply requirements are quickly increasing due to higher living standards and larger populations. Therefore, food crises are still a major threat to human society. The conflict between farmland areas and the increasing need for essential supplies is becoming acuter in China. Therefore, we suggest that a novel strategy would address the issue, in which temporal and spatial arrangement of wheat sowing dates would be highly focused.
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Affiliation(s)
- Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Yulian Hou
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Xinyu Huang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Jia Jia
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Agricultural College, Sichuan Agricultural University, Chengdu, China
- Sichuan Long-Gao-Fei Agricultural Science and Technology Co., Ltd, Chengdu, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Agricultural College, Sichuan Agricultural University, Chengdu, China
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AHMAD M. Plant breeding advancements with "CRISPR-Cas" genome editing technologies will assist future food security. FRONTIERS IN PLANT SCIENCE 2023; 14:1133036. [PMID: 36993865 PMCID: PMC10040607 DOI: 10.3389/fpls.2023.1133036] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Genome editing techniques are being used to modify plant breeding, which might increase food production sustainably by 2050. A product made feasible by genome editing is becoming better known, because of looser regulation and widespread acceptance. The world's population and food supply would never have increased proportionally under current farming practices. The development of plants and food production has been greatly impacted by global warming and climate change. Therefore, minimizing these effects is crucial for agricultural production that is sustainable. Crops are becoming more resilient to abiotic stress because of sophisticated agricultural practices and a better understanding of the abiotic stress response mechanism. Both conventional and molecular breeding techniques have been used to create viable crop types both processes are time-consuming. Recently, plant breeders have shown an interest in genome editing approaches for genetic manipulation that use clustered regularly interspaced short palindromic repeats (CRISPR/Cas9). To ensure the security of the food supply in the future, plant kinds with desired traits must be developed. A completely new era in plant breeding has begun because of the revolution in genome editing techniques based on the CRISPR/CRISPR-associated nuclease (Cas9) systems. All plants may effectively target a particular gene or group of loci using Cas9 and single-guide RNA (sgRNA). CRISPR/Cas9 can thereby save time and labor compared to conventional breeding methods. An easy, quick, and efficient method for directly altering the genetic sequences in cells is with the CRISPR and Cas9 systems. The CRISPR-Cas9 system, which was developed from components of the earliest known bacterial immune system, allows for targeted gene breakage and gene editing in a variety of cells/RNA sequences to guide endonuclease cleavage specificity in the CRISPR-Cas9 system. Editing can be directed to practically any genomic site by altering the guide RNA (gRNA) sequence and delivering it to a target cell along with the Cas9 endonuclease. We summarize recent CRISPR/Cas9 plant research findings, investigate potential applications in plant breeding, and make predictions about likely future breakthroughs and approaches to food security through 2050.
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Affiliation(s)
- M. AHMAD
- Department of Plant Sciences, University of Nebraska, Lincoln, NE, United States
- Department of Genetics and Plant Breeding, Sheri-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Srinagar, India
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Van Vu T, Das S, Hensel G, Kim JY. Genome editing and beyond: what does it mean for the future of plant breeding? PLANTA 2022; 255:130. [PMID: 35587292 PMCID: PMC9120101 DOI: 10.1007/s00425-022-03906-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/26/2022] [Indexed: 05/04/2023]
Abstract
Genome editing offers revolutionized solutions for plant breeding to sustain food production to feed the world by 2050. Therefore, genome-edited products are increasingly recognized via more relaxed legislation and community adoption. The world population and food production are disproportionally growing in a manner that would have never matched each other under the current agricultural practices. The emerging crisis is more evident with the subtle changes in climate and the running-off of natural genetic resources that could be easily used in breeding in conventional ways. Under these circumstances, affordable CRISPR-Cas-based gene-editing technologies have brought hope and charged the old plant breeding machine with the most energetic and powerful fuel to address the challenges involved in feeding the world. What makes CRISPR-Cas the most powerful gene-editing technology? What are the differences between it and the other genetic engineering/breeding techniques? Would its products be labeled as "conventional" or "GMO"? There are so many questions to be answered, or that cannot be answered within the limitations of our current understanding. Therefore, we would like to discuss and answer some of the mentioned questions regarding recent progress in technology development. We hope this review will offer another view on the role of CRISPR-Cas technology in future of plant breeding for food production and beyond.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, km 02, Pham Van Dong Road, Co Nhue 1, Bac Tu Liem, Hanoi, 11917, Vietnam
| | - Swati Das
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225, Düsseldorf, Germany.
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371, Olomouc, Czech Republic.
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Lombardi M, De Gara L, Loreto F. Determinants of root system architecture for future-ready, stress-resilient crops. PHYSIOLOGIA PLANTARUM 2021; 172:2090-2097. [PMID: 33905535 PMCID: PMC8360026 DOI: 10.1111/ppl.13439] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/19/2021] [Accepted: 04/19/2021] [Indexed: 06/02/2023]
Abstract
Climate change hampers food safety and food security. Crop breeding has been boosting superior quantity traits such as yield, but roots have often been overlooked in spite of their role in the whole plant physiology. New evidence is emerging on the relevance of root system architecture in coping with the environment. Here, we review determinants of root system architecture, mainly based on studies on Arabidopsis, and we discuss how breeding for appropriate root architecture may help obtain plants that are better adapted or resilient to abiotic and biotic stresses, more productive, and more efficient for soil and water use. We also highlight recent advances in phenotyping high-tech platforms and genotyping techniques that may further help to understand the mechanisms of root development and how roots control relationships between plants and soil. An integrated approach is proposed that combines phenotyping and genotyping information via bioinformatic analyses and reveals genetic control of root system architecture, paving the way for future research on plant breeding.
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Affiliation(s)
- Marco Lombardi
- Department of Science and Technology for Humans and the EnvironmentCampus Bio‐Medico University of RomeVia Alvaro del Portillo 21Rome00128Italy
- Department of Biology, Agriculture, and Food SciencesNational Research Council of Italy (CNR‐DISBA)Piazzale Aldo Moro 7Rome00185Italy
| | - Laura De Gara
- Department of Science and Technology for Humans and the EnvironmentCampus Bio‐Medico University of RomeVia Alvaro del Portillo 21Rome00128Italy
| | - Francesco Loreto
- Department of Biology, Agriculture, and Food SciencesNational Research Council of Italy (CNR‐DISBA)Piazzale Aldo Moro 7Rome00185Italy
- Department of BiologyUniversity Federico IIvia CinthiaNaples80126Italy
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Dunn SE, Karberg KA, Vicini J, Swarthout J. Comment on "how many premature deaths from pesticide suicide have occurred since the agricultural green revolution". Clin Toxicol (Phila) 2019; 58:858. [PMID: 31809206 DOI: 10.1080/15563650.2019.1696465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Torkamaneh D, Boyle B, Belzile F. Efficient genome-wide genotyping strategies and data integration in crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:499-511. [PMID: 29352324 DOI: 10.1007/s00122-018-3056-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/12/2018] [Indexed: 05/21/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genotyping methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration. Next-generation sequencing technologies provide powerful and flexible genotyping methods to plant breeders and researchers. These methods offer a wide range of applications from genome-wide analysis to routine screening with a high level of accuracy and reproducibility. Furthermore, they provide a straightforward workflow to identify, validate, and screen genetic variants in a short time with a low cost. NGS-based genotyping methods include whole-genome re-sequencing, SNP arrays, and reduced representation sequencing, which are widely applied in crops. The main challenges facing breeders and geneticists today is how to choose an appropriate genotyping method and how to integrate genotyping data sets obtained from various sources. Here, we review and discuss the advantages and challenges of several NGS methods for genome-wide genetic marker development and genotyping in crop plants. We also discuss how imputation methods can be used to both fill in missing data in genotypic data sets and to integrate data sets obtained using different genotyping tools. It is our hope that this synthetic view of genotyping methods will help geneticists and breeders to integrate these NGS-based methods in crop plant breeding and research.
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Affiliation(s)
- Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada.
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Cameron JN, Han Y, Wang L, Beavis WD. Systematic design for trait introgression projects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1993-2004. [PMID: 28647895 PMCID: PMC5606951 DOI: 10.1007/s00122-017-2938-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/15/2017] [Indexed: 05/18/2023]
Abstract
Using an Operations Research approach, we demonstrate design of optimal trait introgression projects with respect to competing objectives. We demonstrate an innovative approach for designing Trait Introgression (TI) projects based on optimization principles from Operations Research. If the designs of TI projects are based on clear and measurable objectives, they can be translated into mathematical models with decision variables and constraints that can be translated into Pareto optimality plots associated with any arbitrary selection strategy. The Pareto plots can be used to make rational decisions concerning the trade-offs between maximizing the probability of success while minimizing costs and time. The systematic rigor associated with a cost, time and probability of success (CTP) framework is well suited to designing TI projects that require dynamic decision making. The CTP framework also revealed that previously identified 'best' strategies can be improved to be at least twice as effective without increasing time or expenses.
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Affiliation(s)
- John N. Cameron
- Department of Agronomy, Iowa State University, Ames, IA 50010 USA
| | - Ye Han
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, IA 50010 USA
| | - Lizhi Wang
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, IA 50010 USA
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Chvátalová K, Frébort I. Guest Editorial. Biotechnol Adv 2014; 32:1. [DOI: 10.1016/j.biotechadv.2013.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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The economics of creative research. Research can drive economic development, but only if it is shielded from political whims and capitalist ideas. EMBO Rep 2012; 14:222-5. [PMID: 23392222 DOI: 10.1038/embor.2013.11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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11
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Josse EM, Gan Y, Bou-Torrent J, Stewart KL, Gilday AD, Jeffree CE, Vaistij FE, Martínez-García JF, Nagy F, Graham IA, Halliday KJ. A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling. THE PLANT CELL 2011; 23:1337-51. [PMID: 21478445 PMCID: PMC3101537 DOI: 10.1105/tpc.110.082594] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/03/2011] [Accepted: 03/16/2011] [Indexed: 05/19/2023]
Abstract
The period following seedling emergence is a particularly vulnerable stage in the plant life cycle. In Arabidopsis thaliana, the phytochrome-interacting factor (PIF) subgroup of basic-helix-loop-helix transcription factors has a pivotal role in regulating growth during this early phase, integrating environmental and hormonal signals. We previously showed that SPATULA (SPT), a PIF homolog, regulates seed dormancy. In this article, we establish that unlike PIFs, which mainly promote hypocotyl elongation, SPT is a potent regulator of cotyledon expansion. Here, SPT acts in an analogous manner to the gibberellin-dependent DELLAs, REPRESSOR OF GA1-3 and GIBBERELLIC ACID INSENSITIVE, which restrain cotyledon expansion alongside SPT. However, although DELLAs are not required for SPT action, we demonstrate that SPT is subject to negative regulation by DELLAs. Cross-regulation of SPT by DELLAs ensures that SPT protein levels are limited when DELLAs are abundant but rise following DELLA depletion. This regulation provides a means to prevent excessive growth suppression that would result from the dual activity of SPT and DELLAs, yet maintain growth restraint under DELLA-depleted conditions. We present evidence that SPT and DELLAs regulate common gene targets and illustrate that the balance of SPT and DELLA action depends on light quality signals in the natural environment.
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Affiliation(s)
- Eve-Marie Josse
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Yinbo Gan
- Department of Biology, Centre for Novel Agricultural Products, University of York, York YO10 5YW, United Kingdom
| | - Jordi Bou-Torrent
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Cientificas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona, 08034 Barcelona, Spain
| | - Kelly L. Stewart
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Alison D. Gilday
- Department of Biology, Centre for Novel Agricultural Products, University of York, York YO10 5YW, United Kingdom
| | - Christopher E. Jeffree
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Fabián E. Vaistij
- Department of Biology, Centre for Novel Agricultural Products, University of York, York YO10 5YW, United Kingdom
| | - Jaime F. Martínez-García
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Cientificas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona, 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Ferenc Nagy
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- Plant Biology Institute, Biological Research Center, H-6726 Szeged, Hungary
| | - Ian A. Graham
- Department of Biology, Centre for Novel Agricultural Products, University of York, York YO10 5YW, United Kingdom
| | - Karen J. Halliday
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- Address correspondence to
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