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Moon K, Basnet P, Um T, Choi IY. Review of the technology used for structural characterization of the GMO genome using NGS data. Genomics Inform 2024; 22:14. [PMID: 39358775 PMCID: PMC11445869 DOI: 10.1186/s44342-024-00016-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/26/2024] [Indexed: 10/04/2024] Open
Abstract
The molecular characterization of genetically modified organisms (GMOs) is essential for ensuring safety and gaining regulatory approval for commercialization. According to CODEX standards, this characterization involves evaluating the presence of introduced genes, insertion sites, copy number, and nucleotide sequence structure. Advances in technology have led to the increased use of next-generation sequencing (NGS) over traditional methods such as Southern blotting. While both methods provide high reproducibility and accuracy, Southern blotting is labor-intensive and time-consuming due to the need for repetitive probe design and analyses for each target, resulting in low throughput. Conversely, NGS facilitates rapid and comprehensive analysis by mapping whole-genome sequencing (WGS) data to plasmid sequences, accurately identifying T-DNA insertion sites and flanking regions. This advantage allows for efficient detection of T-DNA presence, copy number, and unintended gene insertions without additional probe work. This paper reviews the current status of GMO genome characterization using NGS and proposes more efficient strategies for this purpose.
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Affiliation(s)
- Kahee Moon
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Prakash Basnet
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Taeyoung Um
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea.
- Department of Smart Farm and Agricultural Industry, Kangwon National University, Chuncheon, South Korea.
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Adams PE, Thies JL, Sutton JM, Millwood JD, Caldwell GA, Caldwell KA, Fierst JL. Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing. PeerJ 2024; 12:e18100. [PMID: 39285918 PMCID: PMC11404476 DOI: 10.7717/peerj.18100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024] Open
Abstract
Genetically modified organisms are commonly used in disease research and agriculture but the precise genomic alterations underlying transgenic mutations are often unknown. The position and characteristics of transgenes, including the number of independent insertions, influences the expression of both transgenic and wild-type sequences. We used long-read, Oxford Nanopore Technologies (ONT) to sequence and assemble two transgenic strains of Caenorhabditis elegans commonly used in the research of neurodegenerative diseases: BY250 (pPdat-1::GFP) and UA44 (GFP and human α-synuclein), a model for Parkinson's research. After scaffolding to the reference, the final assembled sequences were ∼102 Mb with N50s of 17.9 Mb and 18.0 Mb, respectively, and L90s of six contiguous sequences, representing chromosome-level assemblies. Each of the assembled sequences contained more than 99.2% of the Nematoda BUSCO genes found in the C. elegans reference and 99.5% of the annotated C. elegans reference protein-coding genes. We identified the locations of the transgene insertions and confirmed that all transgene sequences were inserted in intergenic regions, leaving the organismal gene content intact. The transgenic C. elegans genomes presented here will be a valuable resource for Parkinson's research as well as other neurodegenerative diseases. Our work demonstrates that long-read sequencing is a fast, cost-effective way to assemble genome sequences and characterize mutant lines and strains.
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Affiliation(s)
- Paula E Adams
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
- Department of Biological Sciences, University of Alabama - Tuscaloosa, Tuscaloosa, AL, United States of America
| | - Jennifer L Thies
- Department of Biological Sciences, University of Alabama - Tuscaloosa, Tuscaloosa, AL, United States of America
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - John M Sutton
- Department of Biological Sciences, University of Alabama - Tuscaloosa, Tuscaloosa, AL, United States of America
- Absci, Vancouver, WA, United States of America
| | - Joshua D Millwood
- Department of Biological Sciences, University of Alabama - Tuscaloosa, Tuscaloosa, AL, United States of America
- Department of Biological and Environmental Sciences, University of West Alabama, Livingston, AL, United States of America
| | - Guy A Caldwell
- Department of Biological Sciences, University of Alabama - Tuscaloosa, Tuscaloosa, AL, United States of America
| | - Kim A Caldwell
- Department of Biological Sciences, University of Alabama - Tuscaloosa, Tuscaloosa, AL, United States of America
| | - Janna L Fierst
- Department of Biological Sciences, Florida International University, Miami, FL, United States of America
- Biomolecular Sciences Institute, Florida International University, Miami, FL, United States of America
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César‐Razquin A, Casacuberta J, Dalmay T, Federici S, Jacchia S, Kagkli DM, Moxon S, Papadopoulou N. Technical Note on the quality of DNA sequencing for the molecular characterisation of genetically modified plants. EFSA J 2024; 22:e8744. [PMID: 38634010 PMCID: PMC11022705 DOI: 10.2903/j.efsa.2024.8744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. This Technical Note to the applicants puts together requirements and recommendations for the quality assessment of the methodology, analysis and reporting when DNA sequencing is used for the molecular characterisation of GM plants. In particular, it applies to the use of Sanger sequencing and next-generation sequencing for the characterisation of the inserted genetic material and its flanking regions at each insertion site, the determination of the copy number of all detectable inserts and the analysis of the genetic stability of the inserts. This updated document replaces the EFSA 2018 Technical Note and reflects the current knowledge in scientific-technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. It does not take into consideration the verification and validation of the detection method which remains under the remit of the Joint Research Centre (JRC).
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Siddiqui HA, Asad S, Naqvi RZ, Asif M, Liu C, Liu X, Farooq M, Abro S, Rizwan M, Arshad M, Sarwar M, Amin I, Mukhtar Z, Mansoor S. Development and evaluation of triple gene transgenic cotton lines expressing three genes (Cry1Ac-Cry2Ab-EPSPS) for lepidopteran insect pests and herbicide tolerance. Sci Rep 2022; 12:18422. [PMID: 36319662 PMCID: PMC9626562 DOI: 10.1038/s41598-022-22209-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 10/11/2022] [Indexed: 12/02/2022] Open
Abstract
Cotton is an international agricultural commodity and the main cash crop of Pakistan of which quality and quantity are subject to various whims of nature. Climate change, insect pest complex, and weeds are reducing its productivity. Here, we have developed triple gene cotton containing EPSPS gene along with two Bt toxin genes Cry1Ac and Cry2Ab using a strategy where all three genes are cloned in the same T-DNA, followed by successful cotton transformation via Agrobacterium-mediated transformation. This strategy has been developed to help cotton breeders in developing new cultivars by incorporating these genes into the non-transgenic or single Bt (Cry1Ac) gene cotton background where all three genes will inherit together. The expression of all three proteins was confirmed through immunostrips and was quantified through enzyme-linked immunosorbent assay (ELISA). The spatio-temporal expression of Bt protein in different parts of triple gene NIBGE cotton plants was determined. Maximum expression was found in leaves followed by seeds and boll rinds. Insect bioassays with cotton bollworms (Helicoverpa armigera), armyworms (Spodoptera litura), and pink bollworms (Pectinophora gossypiella) showed more than 90% mortality. The best performing line (NIBGE-E2) on the basis of spatiotemporal expression, glyphosate assays, and insect mortality data, was used for event characterization by using the genome sequencing approach. The event was successfully characterized and named NIBGE 20-01. A diagnostics test based on event-specific PCR was developed and its ability to distinguish NIBGE 20-01 event from other commercial transgenic cotton events was confirmed. To confirm stable expression of all three proteins in the field conditions, homozygous transgenic lines were grown in the field and the expression was confirmed through immunostrip assays. It was found that all three genes are expressed under field conditions. To show that all three genes are inherited together upon crossing with local elite cotton lines, the F1 generation was grown under glasshouse and field conditions. The expression of all three genes was confirmed under field conditions. Our results showed that transgenic cotton with three genes cloned in the same T-DNA can express all genes and can be conveniently transferred into elite cotton lines through a single cross.
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Affiliation(s)
- Hamid Anees Siddiqui
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
- Department of Biotechnology, University of Sialkot, Sialkot, Pakistan
| | - Shaheen Asad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | | | - Xin Liu
- Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Muhammad Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Saifullah Abro
- Plant Breeding and Genetics Division, Nuclear Institute of Agriculture (NIA), Tando Jam, Pakistan
| | - Muhammad Rizwan
- Plant Breeding and Genetics Division, Nuclear Institute of Agriculture (NIA), Tando Jam, Pakistan
| | - Muhammad Arshad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Muhammad Sarwar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan.
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan.
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Zhang W, Wang Y, Zhang T, Zhang J, Shen L, Zhang B, Ding C, Su X. Transcriptomic Analysis of Mature Transgenic Poplar Expressing the Transcription Factor JERF36 Gene in Two Different Environments. Front Bioeng Biotechnol 2022; 10:929681. [PMID: 35774064 PMCID: PMC9237257 DOI: 10.3389/fbioe.2022.929681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
During the last several decades, a number of transgenic or genetically modified tree varieties with enhanced characteristics and new traits have been produced. These trees have become associated with generally unsubstantiated concerns over health and environmental safety. We conducted transcriptome sequencing of transgenic Populus alba × P. berolinensis expressing the transcription factor JERF36 gene (ABJ01) and the non-transgenic progenitor line (9#) to compare the transcriptional changes in the apical buds. We found that 0.77% and 1.31% of the total expressed genes were significant differentially expressed in ABJ01 at the Daqing and Qiqihar sites, respectively. Among them, 30%–50% of the DEGs contained cis-elements recognized by JERF36. Approximately 5% of the total number of expressed genes showed significant differential expression between Daqing and Qiqihar in both ABJ01 and 9#. 10 DEGs resulting from foreign gene introduction, 394 DEGs that resulted solely from the environmental differences, and 47 DEGs that resulted from the combination of foreign gene introduction and the environment were identified. The number of DEGs resulting from environmental factors was significantly greater than that resulting from foreign gene introduction, and the combined effect of the environmental effects with foreign gene introduction was significantly greater than resulting from the introduction of JERF36 alone. GO and KEGG annotation showed that the DEGs mainly participate in the photosynthesis, oxidative phosphorylation, plant hormone signaling, ribosome, endocytosis, and plant-pathogen interaction pathways, which play important roles in the responses to biotic and abiotic stresses ins plant. To enhance its adaptability to salt-alkali stress, the transgenic poplar line may regulate the expression of genes that participate in the photosynthesis, oxidative phosphorylation, MAPK, and plant hormone signaling pathways. The crosstalk between biotic and abiotic stress responses by plant hormones may improve the ability of both transgenic and non-transgenic poplars to defend against pathogens. The results of our study provide a basis for further studies on the molecular mechanisms behind improved stress resistance and the unexpected effects of transgenic gene expression in poplars, which will be significant for improving the biosafety evaluation of transgenic trees and accelerating the breeding of new varieties of forest trees resistant to environmental stresses.
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Affiliation(s)
- Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Yanbo Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
- Nanchang Institute of Technology, Nanchang, China
| | - Tengqian Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Jing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Le Shen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Bingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
- *Correspondence: Changjun Ding, ; Xiaohua Su,
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Changjun Ding, ; Xiaohua Su,
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Chen L, Zhou J, Li T, Fang Z, Li L, Huang G, Gao L, Zhu X, Zhou X, Xiao H, Zhang J, Xiong Q, Zhang J, Ma A, Zhai W, Zhang W, Peng H. GmoDetector: An accurate and efficient GMO identification approach and its applications. Food Res Int 2021; 149:110662. [PMID: 34600664 DOI: 10.1016/j.foodres.2021.110662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
The rapid increase of genetically modified organisms (GMOs) entering the food and feed markets, and the contamination of donor (micro)organisms of transgenic elements make it more challenging for the existing GMO detection. In this study, we developed a high-throughput and contamination-removal GMO detection approach named as GmoDetector. GmoDetector targeted 64 common transgenic elements and 76 GMO-specific events collected from 251 singular GM events, and combined with next generation sequencing (NGS) and target enrichment technology to detect various GMOs. As a result, GmoDetector was able to exclude the donor (micro)organism contamination, and detect the authorized and unauthorized GMOs (UGMOs) in any forms of food or feed, such as processed or unprocessed. The sensitivity of GmoDetector is as low as 0.1% (GMO content), which has met the GMO labeling threshold for all countries. Therefore, GmoDetector is a robust tool for accurate and efficient detection of the authorized and UGMOs.
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Affiliation(s)
- Lihong Chen
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Tiantian Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Gang Huang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Lifen Gao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Xiaobo Zhu
- Wuhan Qingfahesheng Seed Co., Ltd., Wuhan, Hubei 430056, PR China
| | - Xusheng Zhou
- Wuhan Qingfahesheng Seed Co., Ltd., Wuhan, Hubei 430056, PR China
| | - Huafeng Xiao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Jing Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - QiJie Xiong
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Jianan Zhang
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang 050035, PR China
| | - Aijin Ma
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China.
| | - Weixiong Zhang
- Department of Computer Science and Engineering, Department of Genetics, Washington University in St. Louis, MO 63130, USA.
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, PR China; Mingliao Biotechnology Co., Ltd., Wuhan 430056, PR China; School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
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Skarzyńska A, Pawełkowicz M, Pląder W. Influence of transgenesis on genome variability in cucumber lines with a thaumatin II gene. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:985-996. [PMID: 34092948 PMCID: PMC8139995 DOI: 10.1007/s12298-021-00990-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/25/2021] [Accepted: 04/04/2021] [Indexed: 06/01/2023]
Abstract
UNLABELLED The development of new plant varieties by genetic modification aims at improving their features or introducing new qualities. However, concerns about the unintended effects of transgenes and negative environmental impact of genetically modified plants are an obstacle for the use of these plants in crops. To analyze the impact of transgenesis on plant genomes, we analyze three cucumber transgenic lines with an introduced thaumatin II gene. After genomes sequencing, we analyzed the transgene insertion site and performed variant prediction. As a result, we obtained similar number of variants for all analyzed lines (average of 4307 polymorphisms), with high abundance in one region of chromosome 4. According to SnpEff analysis, the presence of genomic variants generally does not influence the genome functionality, as less than 2% of polymorphisms have high impact. Moreover, analysis indicates that these changes were more likely induced by in vitro culture than by the transgenesis itself. The insertion site analysis shows that the region of transgene integration could cause changes in gene expression, by gene disruption or loss of promoter region continuity. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00990-8.
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Affiliation(s)
- Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
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Zarka KA, Hokanson K, Douches DS. Molecular characterization for food safety assessment of a genetically modified late blight resistant potato: an unusual case. Transgenic Res 2021; 30:169-183. [PMID: 33751337 DOI: 10.1007/s11248-021-00241-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
Standard food safety assessments of genetically modified crops require a thorough molecular characterization of the novel DNA as inserted into the plant that is intended for commercialization, as well as a comparison of agronomic and nutritional characteristics of the genetically modified to the non-modified counterpart. These characterization data are used to identify any unintended changes in the inserted DNA or in the modified plant that would require assessment for safety in addition to the assessment of the intended modification. An unusual case of an unintended effect discovered from the molecular characterization of a genetically modified late blight resistant potato developed for growing in Bangladesh and Indonesia is presented here. Not only was a significant portion of the plasmid vector backbone DNA inserted into the plant along with the intended insertion of an R-gene for late blight resistance, but the inserted DNA was split into two separate fragments and inserted into two separate chromosomes. One fragment carries the R-gene and the other fragment carries the NPTII selectable marker gene and the plasmid backbone DNA. The implications of this for the food safety assessment of this late blight resistant potato are considered.
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Affiliation(s)
- Kelly A Zarka
- Department of Plant, Soil and Microbial Sciences, Molecular Plant Science Bldg, Michigan State University, East Lansing, MI, USA.
| | - Karen Hokanson
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA
| | - David S Douches
- Department of Plant, Soil and Microbial Sciences, Molecular Plant Science Bldg, Michigan State University, East Lansing, MI, USA
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Asif M, Siddiqui HA, Naqvi RZ, Amin I, Asad S, Mukhtar Z, Bashir A, Mansoor S. Development of event-specific detection method for identification of insect resistant NIBGE-1601 cotton harboring double gene Cry1Ac-Cry2Ab construct. Sci Rep 2021; 11:3479. [PMID: 33568702 PMCID: PMC7876094 DOI: 10.1038/s41598-021-82798-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022] Open
Abstract
Bt cotton expressing Cry1Ac is being cultivated in Pakistan. It has been observed that pink bollworm may have developed resistance against single Bt gene (Cry1Ac). For durable resistance, insect resistant NIBGE-1601 cotton harboring double gene Cry1Ac-Cry2Ab construct was developed. There was a need to characterize NIBGE-1601 event for intellectual property rights protection. The Presence of NIBGE Cry1Ac and NIBGE Cry2Ab genes was checked in NIBGE-1601 cotton plants through PCR, while there was no amplification using primers specific for Monsanto events (MON531, MON15985, MON1445). Using genome walking technology, NIBGE-601 event has been characterized. Event-specific primers of NIBGE-1601 were designed and evaluated to differentiate it from other cotton events mentioned above. NIBGE-1601 event detection primers are highly specific, therefore, can detect NIBGE 1601 event at different conditions using single or multiplex PCR. In the qualitative PCR, using NIBGE-1601 event specific primers, 0.05 ng was the limit of detection for NIBGE-1601double gene cotton genomic DNA. Thus event characterization and development of event-specific diagnostics will help in breeding new cotton varieties resistant to cotton bollworms.
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Affiliation(s)
- Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Hamid Anees Siddiqui
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Shaheen Asad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Aftab Bashir
- Department of Biological Sciences, Forman Christian College, Lahore, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan.
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Giraldo PA, Shinozuka H, Spangenberg GC, Smith KF, Cogan NOI. Rapid and Detailed Characterization of Transgene Insertion Sites in Genetically Modified Plants via Nanopore Sequencing. FRONTIERS IN PLANT SCIENCE 2021; 11:602313. [PMID: 33613582 PMCID: PMC7889508 DOI: 10.3389/fpls.2020.602313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/24/2020] [Indexed: 05/15/2023]
Abstract
Molecular characterization of genetically modified plants can provide crucial information for the development of detection and identification methods, to comply with traceability, and labeling requirements prior to commercialization. Detailed description of the genetic modification was previously a challenging step in the safety assessment, since it required the use of laborious and time-consuming techniques. In this study an accurate, simple, and fast method was developed for molecular characterization of genetically modified (GM) plants, following a user-friendly workflow for researchers with limited bioinformatic capabilities. Three GM events from a diverse array of crop species-perennial ryegrass, white clover, and canola-were used to test the approach that exploits long-read sequencing by the MinION device, from Oxford Nanopore Technologies. The method delivered a higher degree of resolution of the transgenic events within the host genome than has previously been possible with the standard Illumina short-range sequencing strategies. The flanking sequences, copy number, and presence of backbone sequences, and overall transgene insertion structure were determined for each of the plant genomes, with the additional identification of moderate-sized secondary insertions that would have previously been missed. The proposed workflow takes only about 1 week from DNA extraction to analyzed result, and the method will complement the existing approaches for molecular characterization of GM plants, since it makes the process faster, simpler, and more cost-effective.
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Affiliation(s)
- Paula A. Giraldo
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Hiroshi Shinozuka
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- AgriBio, The Centre for AgriBioscience, School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Kevin F. Smith
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
- Agriculture Victoria Research, Hamilton, VIC, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- AgriBio, The Centre for AgriBioscience, School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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11
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Fu W, Zhu P, Qu M, Zhi W, Zhang Y, Li F, Zhu S. Evaluation on reprogramed biological processes in transgenic maize varieties using transcriptomics and metabolomics. Sci Rep 2021; 11:2050. [PMID: 33479482 PMCID: PMC7820507 DOI: 10.1038/s41598-021-81637-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 12/16/2020] [Indexed: 11/12/2022] Open
Abstract
Genetic engineering (GM) has great potential to improve maize productivity, but rises some concerns on unintended effects, and equivalent as their comparators. There are some limitations through targeted analysis to detect the UE in genetically modified organisms in many previous studies. We here reported a case-study on the effects of introducing herbicides and insect resistance (HIR) gene cassette on molecular profiling (transcripts and metabolites) in a popular maize variety Zhengdan958 (ZD958) in China. We found that introducing HIR gene cassette bring a limited numbers of differential abundant genes (DAGs) or differential abundant metabolites (DAMs) between transgenic events and non-transgenic control. In contrast, averaged 10 times more DAGs and DAMs were observed when performed comparison under different growing environments in three different ecological regions of China than the numbers induced by gene effects. Major biological pathways relating to stress response or signaling transduction could explain somehow the effects of growing environments. We further compared two transgenic events mediated ZD958 (GM-ZD958) with either transgenic parent GM-Z58, and other genetic background nonGM-Z58, nonGM-ZD958, and Chang7-2. We found that the numbers of DAGs and DAMs between GM-ZD958 and its one parent maize variety, Z58 or GM-Z58 is equivalent, but not Chang7-2. These findings suggest that greater effects due to different genetic background on altered molecular profiling than gene modification itself. This study provides a case evidence indicating marginal effects of gene pleiotropic effects, and environmental effects should be emphasized.
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Affiliation(s)
- Wei Fu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Pengyu Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Mingnan Qu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 200032, China
| | - Wang Zhi
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Yongjiang Zhang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Feiwu Li
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China.
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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12
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Duan L, Zhang S, Yang Y, Wang Q, Lan Q, Wang Y, Xu W, Jin W, Li L, Chen R. A feasible method for detecting unknown GMOs via a combined strategy of PCR-based suppression subtractive hybridization and next-generation sequencing. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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13
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Kim MS, Jo H, Kim JH, Bae DN, Pack IS, Kim CG, Kwon T, Nam J, Chung YS, Jeong SC. Elucidation of genomic organizations of transgenic soybean plants through de novo genome assembly with short paired-end reads. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:1. [PMID: 37309526 PMCID: PMC10231564 DOI: 10.1007/s11032-020-01191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/26/2020] [Indexed: 06/14/2023]
Abstract
Elucidation of the genomic organizations of transgene insertion sites is essential for the genetic studies of transgenic plants. Herein, we establish an analysis pipeline that identifies the transgene insertion sites as well as the presence of vector backbones, through de novo genome assembly with high-throughput sequencing data in two transgenic soybean lines, AtYUCCA6-#5 and 35S-UGT72E3/2-#7. Sequencing data of approximately 28× and 29× genome coverages for each line generated by high-throughput sequencing were de novo assembled. The databases generated from the de novo assembled sequences were used to search contigs that contained putative insertion sites and their flanking sequences (integration sites) of transgene fragments using transgenic vector sequences as queries. The predicted integration site sequences, which are located at three annotated genes that might regulate plant development or confer disease resistance, were then confirmed by local alignment against the soybean reference genome and PCR amplification. As results, we revealed the precise transgene-flanking sequences and sequence rearrangements at insertion sites in both the transgenic lines, as well as the aberrant insertion of a transgene fragment. Consequently, relative to experimental or enrichment technologies, our approach is straightforward and time-effective, providing an alternative method for the identification of insertion sites in transgenic plants.
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Affiliation(s)
- Myung-Shin Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116 Republic of Korea
| | - Hojin Jo
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116 Republic of Korea
| | - Ji Hong Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116 Republic of Korea
| | - Dong Nyuk Bae
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116 Republic of Korea
| | - In-Soon Pack
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116 Republic of Korea
| | - Chang-Gi Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116 Republic of Korea
| | - Tackmin Kwon
- Department of Molecular Genetics, College of Natural Resources and Life Science, Dong-A University, Busan, 49315 Republic of Korea
| | - Jaesung Nam
- Department of Molecular Genetics, College of Natural Resources and Life Science, Dong-A University, Busan, 49315 Republic of Korea
| | - Young-Soo Chung
- Department of Molecular Genetics, College of Natural Resources and Life Science, Dong-A University, Busan, 49315 Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116 Republic of Korea
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14
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Callahan AM, Zhebentyayeva TN, Humann JL, Saski CA, Galimba KD, Georgi LL, Scorza R, Main D, Dardick CD. Defining the 'HoneySweet' insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica). HORTICULTURE RESEARCH 2021; 8:8. [PMID: 33384410 PMCID: PMC7775438 DOI: 10.1038/s41438-020-00438-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 09/30/2020] [Accepted: 10/08/2020] [Indexed: 05/30/2023]
Abstract
'HoneySweet' plum (Prunus domestica) is resistant to Plum pox potyvirus, through an RNAi-triggered mechanism. Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum. DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well as a multicopy insertion event. To confirm the transgene arrangement of the insertion event, 'HoneySweet' DNA was subjected to whole genome sequencing using Illumina short-read technology. Results indicated two different insertion events, one containing seven partial copies flanked by putative plum DNA sequence and a second with the predicted inverted repeat of the coat protein gene driven by a double 35S promoter on each side, flanked by plum DNA. To determine the locations of the two transgene insertions, a phased plum genome assembly was developed from the commercial plum 'Improved French'. A subset of the scaffolds (2447) that were >10 kb in length and representing, >95% of the genome were annotated and used for alignment against the 'HoneySweet' transgene reads. Four of eight matching scaffolds spanned both insertion sites ranging from 157,704 to 654,883 bp apart, however we were unable to identify which scaffold(s) represented the actual location of the insertion sites due to potential sequence differences between the two plum cultivars. Regardless, there was no evidence of any gene(s) being interrupted as a result of the insertions. Furthermore, RNA-seq data verified that the insertions created no new transcriptional units and no dramatic expression changes of neighboring genes.
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Affiliation(s)
- Ann M Callahan
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA.
| | - Tetyana N Zhebentyayeva
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jodi L Humann
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Christopher A Saski
- Plant and Environmental Sciences Department, Clemson University, Clemson, SC, 29634, USA
| | - Kelsey D Galimba
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
| | - Laura L Georgi
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Ralph Scorza
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
| | - Dorrie Main
- Plant and Environmental Sciences Department, Clemson University, Clemson, SC, 29634, USA
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15
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Takabatake R, Kaneko M, Yanagida M, Kitta K. Detection of 30 bp DNA fragments with a sensitive modified Southern blot analysis. Biosci Biotechnol Biochem 2020; 84:2405-2414. [PMID: 32856548 DOI: 10.1080/09168451.2020.1809988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
To evaluate crops generated by new breeding techniques, it is important to confirm the removal of recombinant DNAs (rDNAs) derived from foreign genes including unintentionally introduced short rDNA(s). We attempted to develop a sensitive detection method for such short rDNAs using Southern blot analysis and performed a model study targeting single-copy endogenous genes in plants. To increase the detection sensitivity, the general protocol for Southern blot analysis was modified. In the model study, we used endogenous-gene-targeting probes in which complementary sequences were serially replaced by dummy sequences, and detected complementary sequences as well as 30 bp. We further evaluated the sensitivity using short rDNAs derived from GM sequences as pseudoinsertions, and the results demonstrated that rDNA-insertions as small as 30 bp could be detected. The results suggested that unintentionally introduced rDNA-insertions were 30 bp or more in length could be detected by the Southern blot analysis.
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Affiliation(s)
- Reona Takabatake
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization , Tsukuba, Japan
| | - Machiko Kaneko
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization , Tsukuba, Japan
| | - Makiko Yanagida
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization , Tsukuba, Japan
| | - Kazumi Kitta
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization , Tsukuba, Japan
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16
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Kersten B, Leite Montalvão AP, Hoenicka H, Vettori C, Paffetti D, Fladung M. Sequencing of two transgenic early-flowering poplar lines confirmed vector-free single-locus T-DNA integration. Transgenic Res 2020; 29:321-337. [PMID: 32356192 PMCID: PMC7283205 DOI: 10.1007/s11248-020-00203-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/18/2020] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing (NGS) approaches are attractive alternatives to the PCR-based characterisation of genetically modified plants for safety assessment and labelling since NGS is highly sensitive to the detection of T-DNA inserts as well as vector backbone sequences in transgenic plants. In this study, two independent transgenic male Populus tremula lines, T193-2 and T195-1, both carrying the FLOWERING LOCUS T gene from Arabidopsis thaliana under control of a heat-inducible promoter (pHSP::AtFT) and the non-transgenic control clone W52, were further characterised by NGS and third-generation sequencing. The results support previous findings that the T-DNA was hemizygously inserted in one genomic locus of each line. However, the T-DNA insertions consist of conglomerations of one or two T-DNA copies together with a small T-DNA fragment without AtFT parts. Based on NGS data, no additional T-DNA splinters or vector backbone sequences could be identified in the genome of the two transgenic lines. Seedlings derived from crosses between the pHSP::AtFT transgenic male parents and female wild type plants are therefore expected to be T-DNA splinter or vector backbone free. Thus, PCR analyses amplifying a partial T-DNA fragment with AtFT-specific primers are sufficient to determine whether the seedlings are transgenic or not. An analysis of 72 second generation-seedlings clearly showed that about 50% of them still reveal the presence of the T-DNA, confirming data already published. To prove if unanticipated genomic changes were induced by T-DNA integration, extended future studies using long-range sequencing technologies are required once a suitable chromosome-level P. tremula reference genome sequence is available.
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Affiliation(s)
- Birgit Kersten
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany.
| | | | - Hans Hoenicka
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany
| | - Cristina Vettori
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry, Agricultural Genetics Section, University of Florence, P. le delle Cascine 18, 50144, Florence, Italy
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany.
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17
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Fu W, Wang C, Zhu P, Xu W, Li X, Zhu S. A universal analytical approach for screening and monitoring of authorized and unauthorized GMOs. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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18
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Zeng T, Zhang D, Li Y, Li C, Liu X, Shi Y, Song Y, Li Y, Wang T. Identification of genomic insertion and flanking sequences of the transgenic drought-tolerant maize line "SbSNAC1-382" using the single-molecule real-time (SMRT) sequencing method. PLoS One 2020; 15:e0226455. [PMID: 32275664 PMCID: PMC7147794 DOI: 10.1371/journal.pone.0226455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/22/2020] [Indexed: 11/22/2022] Open
Abstract
Safety assessment of genetically modified (GM) crops is crucial at the product-development phase before GM crops are placed on the market. Determining characteristics of sequences flanking exogenous insertion sequences is essential for the safety assessment and marketing of transgenic crops. In this study, we used genome walking and whole-genome sequencing (WGS) to identify the flanking sequence characteristics of the SbSNAC1 transgenic drought-tolerant maize line "SbSNAC1-382", but both of the two methods failed. Then, we constructed a genomic fosmid library of the transgenic maize line, which contained 4.18×105 clones with an average insertion fragment of 35 kb, covering 5.85 times the maize genome. Subsequently, three positive clones were screened by pairs of specific primers, and one of the three positive clones was sequenced by using single-molecule real-time (SMRT) sequencing technology. More than 1.95 Gb sequence data (~105× coverage) for the sequenced clone were generated. The junction reads mapped to the boundaries of T-DNA, and the flanking sequences in the transgenic line were identified by comparing all sequencing reads with the maize reference genome and the sequence of the transgenic vector. Furthermore, the putative insertion loci and flanking sequences were confirmed by PCR amplification and Sanger sequencing. The results indicated that two copies of the exogenous T-DNA fragments were inserted at the same genomic site, and the exogenous T-DNA fragments were integrated at the position of Chromosome 5 from 177155650 to 177155696 in the transgenic line 382. In this study, we demonstrated the successful application of the SMRT technology for the characterization of genomic insertion and flanking sequences.
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Affiliation(s)
- Tingru Zeng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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19
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Itoh T, Onuki R, Tsuda M, Oshima M, Endo M, Sakai H, Tanaka T, Ohsawa R, Tabei Y. Foreign DNA detection by high-throughput sequencing to regulate genome-edited agricultural products. Sci Rep 2020; 10:4914. [PMID: 32188926 PMCID: PMC7080720 DOI: 10.1038/s41598-020-61949-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/05/2020] [Indexed: 12/11/2022] Open
Abstract
Although the advent of several new breeding techniques (NBTs) is revolutionizing agricultural production processes, technical information necessary for their regulation is yet to be provided. Here, we show that high-throughput DNA sequencing is effective for the detection of unintended remaining foreign DNA segments in genome-edited rice. A simple k-mer detection method is presented and validated through a series of computer simulations and real data analyses. The data show that a short foreign DNA segment of 20 nucleotides can be detected and the probability that the segment is overlooked is 10-3 or less if the average sequencing depth is 30 or more, while the number of false hits is less than 1 on average. This method was applied to real sequencing data, and the presence and absence of an external DNA segment were successfully proven. Additionally, our in-depth analyses also identified some weaknesses in current DNA sequencing technologies. Hence, for a rigorous safety assessment, the combination of k-mer detection and another method, such as Southern blot assay, is recommended. The results presented in this study will lay the foundation for the regulation of NBT products, where foreign DNA is utilized during their generation.
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Affiliation(s)
- Takeshi Itoh
- Bioinformatics Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan.
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Ritsuko Onuki
- Bioinformatics Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
- Research Institute, National Cancer Center Japan, Chuo-ku, Tokyo, 104-0045, Japan
| | - Mai Tsuda
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Masao Oshima
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Masaki Endo
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8634, Japan
| | - Hiroaki Sakai
- Bioinformatics Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Tsuyoshi Tanaka
- Bioinformatics Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518, Japan
| | - Ryo Ohsawa
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yutaka Tabei
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8634, Japan
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20
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Identification of T-DNA Insertion Site and Flanking Sequence of a Genetically Modified Maize Event IE09S034 Using Next-Generation Sequencing Technology. Mol Biotechnol 2020; 61:694-702. [PMID: 31256331 DOI: 10.1007/s12033-019-00196-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Molecular characteristics including information of insertion site, flanking sequence, and copy numbers are the base for the safety assessment and subsequent monitoring of genetically modified organisms (GMOs), which has to be revealed thoroughly in a case-by-case manner. Although both polymerase chain reaction (PCR)-based and next-generation sequencing (NGS)-based approaches are proven to be effective in the molecular characterization of most of GM events, they often fail to work with GM maize events, mainly due to the genome complexity. In this study, by using NGS, we successfully identified the 3' end T-DNA insertion site and flanking sequence of a GM maize event IE09S034, which were confirmed by PCR amplification and Sanger sequencing. Notably, insertions of unintended exogenous elements were revealed in this event although the single copy of target exogenous genes was also confirmed by digital PCR. The output of this study provides novel and important genetic evidence for the safety assessment and monitoring of GM maize event IE09S034.
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21
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Giraldo PA, Shinozuka H, Spangenberg GC, Cogan NO, Smith KF. Safety Assessment of Genetically Modified Feed: Is There Any Difference From Food? FRONTIERS IN PLANT SCIENCE 2019; 10:1592. [PMID: 31921242 PMCID: PMC6918800 DOI: 10.3389/fpls.2019.01592] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Food security is one of major concerns for the growing global population. Modern agricultural biotechnologies, such as genetic modification, are a possible solution through enabling an increase of production, more efficient use of natural resources, and reduced environmental impacts. However, new crop varieties with altered genetic materials may be subjected to safety assessments to fulfil the regulatory requirements, prior to marketing. The aim of the assessment is to evaluate the impact of products from the new crop variety on human, animal, and the environmental health. Although, many studies on the risk assessment of genetically modified (GM) food have been published, little consideration to GM feedstuff has been given, despite that between 70 to 90% of all GM crops and their biomass are used as animal feed. In addition, in some GM plants such as forages that are only used for animal feeds, the assessment of the genetic modification may be of relevance only to livestock feeding. In this article, the regulatory framework of GM crops intended for animal feed is reviewed using the available information on GM food as the baseline. Although, the majority of techniques used for the safety assessment of GM food can be used in GM feed, many plant parts used for livestock feeding are inedible to humans. Therefore, the concentration of novel proteins in different plant tissues and level of exposure to GM feedstuff in the diet of target animals should be considered. A further development of specific methodologies for the assessment of GM crops intended for animal consumption is required, in order to provide a more accurate and standardized assessment to the GM feed safety.
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Affiliation(s)
- Paula A. Giraldo
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Hiroshi Shinozuka
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Noel O.I. Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Kevin F. Smith
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Agriculture Victoria Research, Hamilton, VIC, Australia
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22
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Zhu P, Fu W, Wei S, Liu X, Wang C, Lu Y, Shang Y, Wu X, Wu Y, Zhu S. A high-throughput and ultrasensitive identification methodology for unauthorized GMP component based on suspension array and logical calculator. Sci Rep 2019; 9:7311. [PMID: 31086245 PMCID: PMC6513989 DOI: 10.1038/s41598-019-43863-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/24/2019] [Indexed: 01/08/2023] Open
Abstract
To solve the problem of the unauthorized GMP components within import and export goods, the LI-US (Logic Identification of unauthorized GMP content by Universal-primer Suspension-array) system, which takes advantage of suspension array and logic calculator, was developed in the present study. Seventeen signal input channels have been optimized and validated in our research to ensure the multiplex practicality of the LI-US system. Three LI-US logic gates, including a YES gate, an OR gate and an AND gate, were designed as different detection strategies for GMP identification. The feasibility and specificity of the LI-US system were validated in the present study. Combining the optimization and evaluation of the signal input procedure, the sensitivity of this LI-US system reached 0.05% of the GMP mass concentration. The practicability evaluation of LI-US demonstrated its application within different substrates and varieties. In conclusion, the LI-US system was developed with extremely high specificity, sensitivity and practicability among different substrates and varieties, which could meet the demands of unauthorized GMP contents for both import and export goods.
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Affiliation(s)
- Pengyu Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Wei Fu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Shuang Wei
- Guangdong Entry-Exit Inspection and Quarantine Bureau, Guangdong, 510000, China
| | - Xiao Liu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Chenguang Wang
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Yun Lu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Ying Shang
- Yunnan Insititute of Food Safety, Kunmming University of Science and technology, Yunnan, 650500, China
| | - Xiyang Wu
- Department of Food Science and Engineering, Jinan University, Guangzhou, 510000, China
| | - Yuping Wu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China.
| | - Shuifang Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China.
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23
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Fu W, Wang C, Xu W, Zhu P, Lu Y, Wei S, Wu X, Wu Y, Zhao Y, Zhu S. Unintended effects of transgenic rice revealed by transcriptome and metabolism. GM CROPS & FOOD 2019; 10:20-34. [PMID: 30955410 DOI: 10.1080/21645698.2019.1598215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Genetically modified (GM) organisms have been developed for decades. However, unintended effects are the main concerns of safety assessment that needs to be carefully investigated. Here, eight varieties of GM rice that were developed in China were selected to assess the unintended effects through transcriptome and metabolism. There are 2892-8758 differentially expressed genes (DEGs) and 7-50 metabolites at significant level between GM varieties and their isogenic counterparts, which were far fewer than that between traditional rice varieties. The function enrichment analysis showed altered transcription in stress-related pathway and starch and sucrose metabolism. DEGs shared among eight GM samples constitute less than 1% of the genes in the genome, and none of them is reported more than four times. The insertion effect on the nearby gene expression and the associated metabolism is only restricted to 50 genes. All the results provide a comprehensive analysis of unintended effects and indication of difference in Chinese transgenic rice based on their backgrounds, transformation, and insertion elements.
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Affiliation(s)
- Wei Fu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Chenguang Wang
- a Chinese Academy of Inspection and Quarantine , Beijing , China.,b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences , China Agricultural University , Beijing , China.,c College of Plant Protection , China Agricultural University , Beijing , China
| | - Wenjie Xu
- a Chinese Academy of Inspection and Quarantine , Beijing , China.,b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences , China Agricultural University , Beijing , China.,c College of Plant Protection , China Agricultural University , Beijing , China
| | - Pengyu Zhu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Yun Lu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Shuang Wei
- d Guangdong Entry-Exit Inspection and Quarantine Bureau , Guangzhou , China
| | - Xiyang Wu
- e Department of Food Science and Engineering , Jinan University , Guangzhou , China
| | - Yuping Wu
- a Chinese Academy of Inspection and Quarantine , Beijing , China
| | - Yiqiang Zhao
- b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences , China Agricultural University , Beijing , China
| | - Shuifang Zhu
- a Chinese Academy of Inspection and Quarantine , Beijing , China.,c College of Plant Protection , China Agricultural University , Beijing , China
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Grohmann L, Keilwagen J, Duensing N, Dagand E, Hartung F, Wilhelm R, Bendiek J, Sprink T. Detection and Identification of Genome Editing in Plants: Challenges and Opportunities. FRONTIERS IN PLANT SCIENCE 2019; 10:236. [PMID: 30930911 PMCID: PMC6423494 DOI: 10.3389/fpls.2019.00236] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/12/2019] [Indexed: 05/21/2023]
Abstract
Conventional genetic engineering techniques generate modifications in the genome via stable integration of DNA elements which do not occur naturally in this combination. Therefore, the resulting organisms and (most) products thereof can unambiguously be identified with event-specific PCR-based methods targeting the insertion site. New breeding techniques such as genome editing diversify the toolbox to generate genetic variability in plants. Several of these techniques can introduce single nucleotide changes without integrating foreign DNA and thereby generate organisms with intended phenotypes. Consequently, such organisms and products thereof might be indistinguishable from naturally occurring or conventionally bred counterparts with established analytical tools. The modifications can entirely resemble random mutations regardless of being spontaneous or induced chemically or via irradiation. Therefore, if an identification of these organisms or products thereof is demanded, a new challenge will arise for (official) seed, food, and feed testing laboratories and enforcement institutions. For detailed consideration, we distinguish between the detection of sequence alterations - regardless of their origin - the identification of the process that generated a specific modification and the identification of a genotype, i.e., an organism produced by genome editing carrying a specific genetic alteration in a known background. This article briefly reviews the existing and upcoming detection and identification strategies (including the use of bioinformatics and statistical approaches) in particular for plants developed with genome editing techniques.
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Affiliation(s)
- Lutz Grohmann
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
- *Correspondence: Lutz Grohmann,
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Nina Duensing
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Emilie Dagand
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Frank Hartung
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Ralf Wilhelm
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Joachim Bendiek
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Thorben Sprink
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
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25
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Casacuberta J, Nogué F, Naegeli H, Birch AN, De Schrijver A, Gralak MA, Guerche P, Manachini B, Messéan A, Nielsen EE, Robaglia C, Rostoks N, Sweet J, Tebbe C, Visioli F, Wal JM, Moxon S, Schneeberger K, Federici S, Ramon M, Papadopoulou N, Jones H. Technical Note on the quality of DNA sequencing for the molecular characterisation of genetically modified plants. EFSA J 2018; 16:e05345. [PMID: 32625981 PMCID: PMC7009663 DOI: 10.2903/j.efsa.2018.5345] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel, 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. The European Commission has mandated EFSA to develop a technical note to the applicants on, and checking of, the quality of the methodology, analysis and reporting covering complete sequencing of the insert and flanking regions, insertion site analysis of the GM event, and generational stability and integrity. This Technical Note puts together requirements and recommendations for when DNA sequencing is part of the molecular characterisation of GM plants, in particular for the characterisation of the inserted genetic material at each insertion site and flanking regions, the determination of the copy number of all detectable inserts, and the analysis of the genetic stability of the inserts, when addressed by Sanger sequencing or NGS. This document reflects the current knowledge in scientific-technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. From 1 October 2018, this Technical Note will replace the JRC guideline of 2016 (updated April 2017) related to the verification and quality assessment of the sequencing of the insert(s) and flanking regions. It does not take into consideration the verification and validation of the detection method which remains under the remit of the JRC.
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Michno JM, Stupar RM. The importance of genotype identity, genetic heterogeneity, and bioinformatic handling for properly assessing genomic variation in transgenic plants. BMC Biotechnol 2018; 18:38. [PMID: 29859067 PMCID: PMC5984819 DOI: 10.1186/s12896-018-0447-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/18/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The advent of -omics technologies has enabled the resolution of fine molecular differences among individuals within a species. DNA sequence variations, such as single nucleotide polymorphisms or small deletions, can be tabulated for many kinds of genotype comparisons. However, experimental designs and analytical approaches are replete with ways to overestimate the level of variation present within a given sample. Analytical pipelines that do not apply proper thresholds nor assess reproducibility among samples are susceptible to calling false-positive variants. Furthermore, issues with sample genotype identity or failing to account for heterogeneity in reference genotypes may lead to misinterpretations of standing variants as polymorphisms derived de novo. RESULTS A recent publication that featured the analysis of RNA-sequencing data in three transgenic soybean event series appeared to overestimate the number of sequence variants identified in plants that were exposed to a tissue culture based transformation process. We reanalyzed these data with a stringent set of criteria and demonstrate three different factors that lead to variant overestimation, including issues related to the genetic identity of the background genotype, unaccounted genetic heterogeneity in the reference genome, and insufficient bioinformatics filtering. CONCLUSIONS This study serves as a cautionary tale to users of genomic and transcriptomic data that wish to assess the molecular variation attributable to tissue culture and transformation processes. Moreover, accounting for the factors that lead to sequence variant overestimation is equally applicable to samples derived from other germplasm sources, including chemical or irradiation mutagenesis and genome engineering (e.g., CRISPR) processes.
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Affiliation(s)
- Jean-Michel Michno
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN USA
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Robert M. Stupar
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN USA
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
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27
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Niu C, Xu Y, Zhang C, Zhu P, Huang K, Luo Y, Xu W. Ultrasensitive Single Fluorescence-Labeled Probe-Mediated Single Universal Primer-Multiplex-Droplet Digital Polymerase Chain Reaction for High-Throughput Genetically Modified Organism Screening. Anal Chem 2018; 90:5586-5593. [PMID: 29652133 DOI: 10.1021/acs.analchem.7b03974] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As genetically modified (GM) technology develops and genetically modified organisms (GMOs) become more available, GMOs face increasing regulations and pressure to adhere to strict labeling guidelines. A singleplex detection method cannot perform the high-throughput analysis necessary for optimal GMO detection. Combining the advantages of multiplex detection and droplet digital polymerase chain reaction (ddPCR), a single universal primer-multiplex-ddPCR (SUP-M-ddPCR) strategy was proposed for accurate broad-spectrum screening and quantification. The SUP increases efficiency of the primers in PCR and plays an important role in establishing a high-throughput, multiplex detection method. Emerging ddPCR technology has been used for accurate quantification of nucleic acid molecules without a standard curve. Using maize as a reference point, four heterologous sequences ( 35S, NOS, NPTII, and PAT) were selected to evaluate the feasibility and applicability of this strategy. Surprisingly, these four genes cover more than 93% of the transgenic maize lines and serve as preliminary screening sequences. All screening probes were labeled with FAM fluorescence, which allows the signals from the samples with GMO content and those without to be easily differentiated. This fiveplex screening method is a new development in GMO screening. Utilizing an optimal amplification assay, the specificity, limit of detection (LOD), and limit of quantitation (LOQ) were validated. The LOD and LOQ of this GMO screening method were 0.1% and 0.01%, respectively, with a relative standard deviation (RSD) < 25%. This method could serve as an important tool for the detection of GM maize from different processed, commercially available products. Further, this screening method could be applied to other fields that require reliable and sensitive detection of DNA targets.
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Affiliation(s)
- Chenqi Niu
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing 100083 , China
| | - Yuancong Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , China.,Laboratory of Food Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing 100083 , China
| | - Chao Zhang
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing 100083 , China
| | - Pengyu Zhu
- The Institute of Plant Quarantine , Chinese Academy of Inspection and Quarantine , Beijing 100029 , China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , China.,Laboratory of Food Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing 100083 , China.,Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) , Ministry of Agriculture , Beijing 100083 , China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , China.,Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) , Ministry of Agriculture , Beijing 100083 , China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , China.,Laboratory of Food Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing 100083 , China.,Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) , Ministry of Agriculture , Beijing 100083 , China
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A nanobiosensor composed of Exfoliated Graphene Oxide and Gold Nano-Urchins, for detection of GMO products. Biosens Bioelectron 2017; 95:72-80. [DOI: 10.1016/j.bios.2017.02.054] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/25/2017] [Accepted: 02/28/2017] [Indexed: 01/14/2023]
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29
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Park D, Park SH, Ban YW, Kim YS, Park KC, Kim NS, Kim JK, Choi IY. A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data. BMC Biotechnol 2017; 17:67. [PMID: 28810845 PMCID: PMC5558722 DOI: 10.1186/s12896-017-0386-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/01/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Genetically modified crops (GM crops) have been developed to improve the agricultural traits of modern crop cultivars. Safety assessments of GM crops are of paramount importance in research at developmental stages and before releasing transgenic plants into the marketplace. Sequencing technology is developing rapidly, with higher output and labor efficiencies, and will eventually replace existing methods for the molecular characterization of genetically modified organisms. METHODS To detect the transgenic insertion locations in the three GM rice gnomes, Illumina sequencing reads are mapped and classified to the rice genome and plasmid sequence. The both mapped reads are classified to characterize the junction site between plant and transgene sequence by sequence alignment. RESULTS Herein, we present a next generation sequencing (NGS)-based molecular characterization method, using transgenic rice plants SNU-Bt9-5, SNU-Bt9-30, and SNU-Bt9-109. Specifically, using bioinformatics tools, we detected the precise insertion locations and copy numbers of transfer DNA, genetic rearrangements, and the absence of backbone sequences, which were equivalent to results obtained from Southern blot analyses. CONCLUSION NGS methods have been suggested as an effective means of characterizing and detecting transgenic insertion locations in genomes. Our results demonstrate the use of a combination of NGS technology and bioinformatics approaches that offers cost- and time-effective methods for assessing the safety of transgenic plants.
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Affiliation(s)
- Doori Park
- Department of Agriculture and Life Industry, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon 24341 Republic of Korea
- Department of Molecular Bioscience, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon 24341 Republic of Korea
| | - Su-Hyun Park
- Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, 1447, Pyeongchang, Gangwon, 25354 Republic of Korea
- Present address: Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065 USA
| | - Yong Wook Ban
- Department of Agriculture and Life Industry, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon 24341 Republic of Korea
- Department of Forest Resources, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon 24341 Republic of Korea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, 1447, Pyeongchang, Gangwon, 25354 Republic of Korea
| | - Kyoung-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon 24341 Republic of Korea
- Bioherb Research Institute, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon 24341 Republic of Korea
| | - Nam-Soo Kim
- Department of Molecular Bioscience, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon 24341 Republic of Korea
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, 1447, Pyeongchang, Gangwon, 25354 Republic of Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon 24341 Republic of Korea
- Bioherb Research Institute, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon 24341 Republic of Korea
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30
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Fraiture MA, Herman P, De Loose M, Debode F, Roosens NH. How Can We Better Detect Unauthorized GMOs in Food and Feed Chains? Trends Biotechnol 2017; 35:508-517. [DOI: 10.1016/j.tibtech.2017.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/17/2017] [Accepted: 03/02/2017] [Indexed: 12/21/2022]
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31
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Moreira F, Carneiro J, Pereira F. A proposal for standardization of transgenic reference sequences used in food forensics. Forensic Sci Int Genet 2017; 29:e26-e28. [PMID: 28506735 DOI: 10.1016/j.fsigen.2017.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/30/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - João Carneiro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - Filipe Pereira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
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32
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Wolt JD. Safety, Security, and Policy Considerations for Plant Genome Editing. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:215-241. [PMID: 28712498 DOI: 10.1016/bs.pmbts.2017.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome editing with engineered nucleases (GEEN) is increasingly used as a tool for gene discovery and trait development in crops through generation of targeted changes in endogenous genes. The development of the CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein), in particular, has enabled widespread use of genome editing. Research to date has not comprehensively addressed genome-editing specificity and off-target mismatches that may result in unintended changes within plant genomes or the potential for gene drive initiation. Governance and regulatory considerations for bioengineered crops derived from using GEEN will require greater clarity as to target specificity, the potential for mismatched edits, unanticipated downstream effects of off-target mutations, and assurance that genome reagents do not occur in finished products. Since governance and regulatory decision making involves robust standards of evidence extending from the laboratory to the postcommercial marketplace, developers of genome-edited crops must anticipate significant engagement and investment to address questions of regulators and civil society.
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Affiliation(s)
- Jeffrey D Wolt
- Biosafety Institute for Genetically Modified Agricultural Products, Iowa State University, Ames, IA, United States; Crop Bioengineering Consortium, Iowa State University, Ames, IA, United States.
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33
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Paracchini V, Petrillo M, Reiting R, Angers-Loustau A, Wahler D, Stolz A, Schönig B, Matthies A, Bendiek J, Meinel DM, Pecoraro S, Busch U, Patak A, Kreysa J, Grohmann L. Molecular characterization of an unauthorized genetically modified Bacillus subtilis production strain identified in a vitamin B 2 feed additive. Food Chem 2017; 230:681-689. [PMID: 28407967 PMCID: PMC5399532 DOI: 10.1016/j.foodchem.2017.03.042] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/08/2017] [Accepted: 03/08/2017] [Indexed: 12/17/2022]
Abstract
Genetically modified Bacillus subtilis identified in a vitamin B2 product. Whole genome sequencing runs are performed for characterization of the isolated strain. Complex modifications of the genome are identified. Four putative recombinant plasmids are characterized. Real-time PCR methods are developed and available for testing vitamin B2 products.
Many food and feed additives result from fermentation of genetically modified (GM) microorganisms. For vitamin B2 (riboflavin), GM Bacillus subtilis production strains have been developed and are often used. The presence of neither the GM strain nor its recombinant DNA is allowed for fermentation products placed on the EU market as food or feed additive. A vitamin B2 product (80% feed grade) imported from China was analysed. Viable B. subtilis cells were identified and DNAs of two bacterial isolates (LHL and LGL) were subjected to three whole genome sequencing (WGS) runs with different devices (MiSeq, 454 or HiSeq system). WGS data revealed the integration of a chloramphenicol resistance gene, the deletion of the endogenous riboflavin (rib) operon and presence of four putative plasmids harbouring rib operons. Event- and construct-specific real-time PCR methods for detection of the GM strain and its putative plasmids in food and feed products have been developed.
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Affiliation(s)
| | - Mauro Petrillo
- European Commission, Joint Research Centre, Ispra, Italy
| | - Ralf Reiting
- Hessian State Laboratory Kassel (LHL), Kassel, Germany
| | | | - Daniela Wahler
- Federal Office of Consumer Protection and Food Safety (BVL), Genetic Engineering Department, Berlin, Germany
| | - Andrea Stolz
- Federal Office of Consumer Protection and Food Safety (BVL), Genetic Engineering Department, Berlin, Germany
| | - Birgit Schönig
- Federal Office of Consumer Protection and Food Safety (BVL), Genetic Engineering Department, Berlin, Germany
| | - Anastasia Matthies
- Federal Office of Consumer Protection and Food Safety (BVL), Genetic Engineering Department, Berlin, Germany
| | - Joachim Bendiek
- Federal Office of Consumer Protection and Food Safety (BVL), Genetic Engineering Department, Berlin, Germany
| | - Dominik M Meinel
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Sven Pecoraro
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Alex Patak
- European Commission, Joint Research Centre, Ispra, Italy
| | - Joachim Kreysa
- European Commission, Joint Research Centre, Ispra, Italy
| | - Lutz Grohmann
- Federal Office of Consumer Protection and Food Safety (BVL), Genetic Engineering Department, Berlin, Germany.
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Schouten HJ, Vande Geest H, Papadimitriou S, Bemer M, Schaart JG, Smulders MJM, Perez GS, Schijlen E. Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere. PLANT CELL REPORTS 2017; 36:493-504. [PMID: 28155116 PMCID: PMC5316556 DOI: 10.1007/s00299-017-2098-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/02/2017] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE Transformation resulted in deletions and translocations at T-DNA inserts, but not in genome-wide small mutations. A tiny T-DNA splinter was detected that probably would remain undetected by conventional techniques. We investigated to which extent Agrobacterium tumefaciens-mediated transformation is mutagenic, on top of inserting T-DNA. To prevent mutations due to in vitro propagation, we applied floral dip transformation of Arabidopsis thaliana. We re-sequenced the genomes of five primary transformants, and compared these to genomic sequences derived from a pool of four wild-type plants. By genome-wide comparisons, we identified ten small mutations in the genomes of the five transgenic plants, not correlated to the positions or number of T-DNA inserts. This mutation frequency is within the range of spontaneous mutations occurring during seed propagation in A. thaliana, as determined earlier. In addition, we detected small as well as large deletions specifically at the T-DNA insert sites. Furthermore, we detected partial T-DNA inserts, one of these a tiny 50-bp fragment originating from a central part of the T-DNA construct used, inserted into the plant genome without flanking other T-DNA. Because of its small size, we named this fragment a T-DNA splinter. As far as we know this is the first report of such a small T-DNA fragment insert in absence of any T-DNA border sequence. Finally, we found evidence for translocations from other chromosomes, flanking T-DNA inserts. In this study, we showed that next-generation sequencing (NGS) is a highly sensitive approach to detect T-DNA inserts in transgenic plants.
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Affiliation(s)
- Henk J Schouten
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Henri Vande Geest
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sofia Papadimitriou
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Marian Bemer
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan G Schaart
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Elio Schijlen
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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35
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Wolt JD, Wang K, Sashital D, Lawrence-Dill CJ. Achieving Plant CRISPR Targeting that Limits Off-Target Effects. THE PLANT GENOME 2016; 9. [PMID: 27902801 DOI: 10.3835/plantgenome2016.05.0047] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein) has been used to generate targeted changes for direct modification of endogenous genes in an increasing number of plant species; but development of plant genome editing has not yet fully considered potential off-target mismatches that may lead to unintended changes within the genome. Assessing the specificity of CRISPR-Cas9 for increasing editing efficiency as well as the potential for unanticipated downstream effects from off-target mutations is an important regulatory consideration for agricultural applications. Increasing genome-editing specificity entails developing improved design methods that better predict the prevalence of off-target mutations as a function of genome composition and design of the engineered ribonucleoprotein (RNP). Early results from CRISPR-Cas9 genome editing in plant systems indicate that the incidence of off-target mutation frequencies is quite low; however, by analyzing CRISPR-edited plant lines and improving both computational tools and reagent design, it may be possible to further decrease unanticipated effects at potential mismatch sites within the genome. This will provide assurance that CRISPR-Cas9 reagents can be designed and targeted with a high degree of specificity. Improved and experimentally validated design tools for discriminating target and potential off-target positions that incorporate consideration of the designed nuclease fidelity and selectivity will help to increase confidence for regulatory decision making for genome-edited plants.
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Guo B, Guo Y, Hong H, Qiu LJ. Identification of Genomic Insertion and Flanking Sequence of G2-EPSPS and GAT Transgenes in Soybean Using Whole Genome Sequencing Method. FRONTIERS IN PLANT SCIENCE 2016; 7:1009. [PMID: 27462336 PMCID: PMC4940375 DOI: 10.3389/fpls.2016.01009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 06/27/2016] [Indexed: 05/30/2023]
Abstract
Molecular characterization of sequence flanking exogenous fragment insertion is essential for safety assessment and labeling of genetically modified organism (GMO). In this study, the T-DNA insertion sites and flanking sequences were identified in two newly developed transgenic glyphosate-tolerant soybeans GE-J16 and ZH10-6 based on whole genome sequencing (WGS) method. More than 22.4 Gb sequence data (∼21 × coverage) for each line was generated on Illumina HiSeq 2500 platform. The junction reads mapped to boundaries of T-DNA and flanking sequences in these two events were identified by comparing all sequencing reads with soybean reference genome and sequence of transgenic vector. The putative insertion loci and flanking sequences were further confirmed by PCR amplification, Sanger sequencing, and co-segregation analysis. All these analyses supported that exogenous T-DNA fragments were integrated in positions of Chr19: 50543767-50543792 and Chr17: 7980527-7980541 in these two transgenic lines. Identification of genomic insertion sites of G2-EPSPS and GAT transgenes will facilitate the utilization of their glyphosate-tolerant traits in soybean breeding program. These results also demonstrated that WGS was a cost-effective and rapid method for identifying sites of T-DNA insertions and flanking sequences in soybean.
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Affiliation(s)
- Bingfu Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Huilong Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- College of Agriculture, Northeast Agricultural UniversityHarbin, China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
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Braguy J, Zurbriggen MD. Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:118-38. [PMID: 27227549 DOI: 10.1111/tpj.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 05/15/2023]
Abstract
Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.
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Affiliation(s)
- Justine Braguy
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
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Holst-Jensen A, Spilsberg B, Arulandhu AJ, Kok E, Shi J, Zel J. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products. Anal Bioanal Chem 2016; 408:4595-614. [PMID: 27100228 PMCID: PMC4909802 DOI: 10.1007/s00216-016-9549-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 12/13/2022]
Abstract
The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.
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Affiliation(s)
- Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106, Oslo, Norway.
| | - Bjørn Spilsberg
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106, Oslo, Norway
| | - Alfred J Arulandhu
- RIKILT, Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Esther Kok
- RIKILT, Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Jana Zel
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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39
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Ishii T, Araki M. Consumer acceptance of food crops developed by genome editing. PLANT CELL REPORTS 2016; 35:1507-18. [PMID: 27038939 DOI: 10.1007/s00299-016-1974-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/21/2016] [Indexed: 05/22/2023]
Abstract
One of the major problems regarding consumer acceptance of genetically modified organisms (GMOs) is the possibility that their transgenes could have adverse effects on the environment and/or human health. Genome editing, represented by the CRISPR/Cas9 system, can efficiently achieve transgene-free gene modifications and is anticipated to generate a wide spectrum of plants. However, the public attitude against GMOs suggests that people will initially be unlikely to accept these plants. We herein explored the bottlenecks of consumer acceptance of transgene-free food crops developed by genome editing and made some recommendations. People should not pursue a zero-risk bias regarding such crops. Developers are encouraged to produce cultivars with a trait that would satisfy consumer needs. Moreover, they should carefully investigate off-target mutations in resultant plants and initially refrain from agricultural use of multiplex genome editing for better risk-benefit communication. The government must consider their regulatory status and establish appropriate regulations if necessary. The government also should foster communication between the public and developers. If people are informed of the benefits of genome editing-mediated plant breeding and trust in the relevant regulations, and if careful risk-benefit communication and sincere considerations for the right to know approach are guaranteed, then such transgene-free crops could gradually be integrated into society.
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Affiliation(s)
- Tetsuya Ishii
- Office of Health and Safety, Hokkaido University, Sapporo, 060-0808, Hokkaido, Japan.
| | - Motoko Araki
- Office of Health and Safety, Hokkaido University, Sapporo, 060-0808, Hokkaido, Japan
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Devos Y, Naegeli H, Perry JN, Waigmann E. 90-day rodent feeding studies on whole GM food/feed: Is the mandatory EU requirement for 90-day rodent feeding studies on whole GM food/feed fit for purpose and consistent with animal welfare ethics? EMBO Rep 2016; 17:942-5. [PMID: 27283938 DOI: 10.15252/embr.201642739] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Yann Devos
- Genetically Modified Organisms (GMO) Unit, European Food Safety Authority (EFSA), Parma, Italy
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Joe N Perry
- Oaklands Barn, Lug's Lane, Broome, Norfolk, UK
| | - Elisabeth Waigmann
- Genetically Modified Organisms (GMO) Unit, European Food Safety Authority (EFSA), Parma, Italy
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Singh AK, Dubey SK. Current trends in Bt crops and their fate on associated microbial community dynamics: a review. PROTOPLASMA 2016; 253:663-681. [PMID: 26560114 DOI: 10.1007/s00709-015-0903-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/19/2015] [Accepted: 10/21/2015] [Indexed: 06/05/2023]
Abstract
Cry protein expressing insect-resistant trait is mostly deployed to control major devastating pests and minimize reliance on the conventional pesticides. However, the ethical and environmental issues are the major constraints in their acceptance, and consequently, the cultivation of genetically modified (GM) crops has invited intense debate. Since root exudates of Bacillus thuringiensis (Bt) crops harbor the insecticidal protein, there is a growing concern about the release and accumulation of soil-adsorbed Cry proteins and their impact on non-target microorganisms and soil microbial processes. This review pertains to reports from the laboratory studies and field trials to assess the Bt toxin proteins in soil microbes and the processes determining the soil quality in conjunction with the existing hypothesis and molecular approaches to elucidate the risk posed by the GM crops. Ecological perturbations hinder the risk aspect of soil microbiota in response to GM crops. Therefore, extensive research based on in vivo and interpretation of results using high-throughput techniques such as NGS on risk assessment are imperative to evaluate the impact of Bt crops to resolve the controversy related to their commercialization. But more studies are needed on the risk associated with stacked traits. Such studies would strengthen our knowledge about the plant-microbe interactions.
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Affiliation(s)
| | - Suresh Kumar Dubey
- Department of Botany, Banaras Hindu University, Varanasi, 221005, India.
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Guttikonda SK, Marri P, Mammadov J, Ye L, Soe K, Richey K, Cruse J, Zhuang M, Gao Z, Evans C, Rounsley S, Kumpatla SP. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach. PLoS One 2016; 11:e0149515. [PMID: 26908260 PMCID: PMC4764375 DOI: 10.1371/journal.pone.0149515] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/01/2016] [Indexed: 11/18/2022] Open
Abstract
Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.
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Affiliation(s)
- Satish K. Guttikonda
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Pradeep Marri
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Jafar Mammadov
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Liang Ye
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Khaing Soe
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Kimberly Richey
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - James Cruse
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Meibao Zhuang
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Zhifang Gao
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Clive Evans
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Steve Rounsley
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Siva P. Kumpatla
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
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Park D, Kim D, Jang G, Lim J, Shin YJ, Kim J, Seo MS, Park SH, Kim JK, Kwon TH, Choi IY. Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing. Genomics Inform 2015; 13:81-5. [PMID: 26523132 PMCID: PMC4623445 DOI: 10.5808/gi.2015.13.3.81] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 11/30/2022] Open
Abstract
Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (~72× coverage) was sequenced with a 2 × 150 bp paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.
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Affiliation(s)
- Doori Park
- Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Dongin Kim
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Green Jang
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jongsung Lim
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Yun-Ji Shin
- Natural Bio-Materials Inc., Wanju 55322, Korea
| | - Jina Kim
- Natural Bio-Materials Inc., Wanju 55322, Korea
| | | | - Su-Hyun Park
- Crop Biotech Institute, Green-Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Ju-Kon Kim
- Crop Biotech Institute, Green-Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Tae-Ho Kwon
- Natural Bio-Materials Inc., Wanju 55322, Korea
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