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Gan Z, Zhou Q, Zheng C, Wang J. Challenges and applications of volatile organic compounds monitoring technology in plant disease diagnosis. Biosens Bioelectron 2023; 237:115540. [PMID: 37523812 DOI: 10.1016/j.bios.2023.115540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/09/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Biotic and abiotic stresses are well known to increase the emission of volatile organic compounds (VOCs) from plants. The analysis of VOCs emissions from plants enables timely diagnostic of plant diseases, which is critical for prompting sustainable agriculture. Previous studies have predominantly focused on the utilization of commercially available devices, such as electronic noses, for diagnosing plant diseases. However, recent advancements in nanomaterials research have significantly contributed to the development of novel VOCs sensors featuring exceptional sensitivity and selectivity. This comprehensive review presents a systematic analysis of VOCs monitoring technologies for plant diseases diagnosis, providing insights into their distinct advantages and limitations. Special emphasis is placed on custom-made VOCs sensors, with detailed discussions on their design, working principles, and detection performance. It is noteworthy that the application of VOCs monitoring technologies in the diagnostic process of plant diseases is still in its emerging stage, and several critical challenges demand attention and improvement. Specifically, the identification of specific stress factors using a single VOC sensor remains a formidable task, while environmental factors like humidity can potentially interfere with sensor readings, leading to inaccuracies. Future advancements should primarily focus on addressing these challenges to enhance the overall efficacy and reliability of VOCs monitoring technologies in the field of plant disease diagnosis.
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Affiliation(s)
- Ziyu Gan
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Qin'an Zhou
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Chengyu Zheng
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jun Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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Noweiska A, Bobrowska R, Spychała J, Tomkowiak A, Kwiatek MT. Multiplex PCR assay for the simultaneous identification of race specific and non-specific leaf resistance genes in wheat (Triticum aestivum L.). J Appl Genet 2023; 64:55-64. [PMID: 36577933 PMCID: PMC9837178 DOI: 10.1007/s13353-022-00745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/04/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022]
Abstract
Race-nonspecific resistance is a key to sustainable management of pathogens in bread wheat (Triticum aestivum L.) breeding. It is more durable compared to race-specific immunity, conferred by the major genes (R), which are often overcome by pathogens. The accumulation of the genes, which provide the resistance to a specific race of a pathogen, together with the introduction of race-non-specific resistance genes is the most effective strategy aimed at preventing the breakdown of genetically conditioned immunity. PCR markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). Multiplexing assays provide increased throughput, reduced reaction cost, and conservation of limited sample material, which are beneficial for breeding purposes. Here, we described the process of customizing multiplex PCR assay for the simultaneous identification of the major leaf rust resistance genes Lr19, Lr24, Lr26, and Lr38, as well as the slow rusting, race-nonspecific resistance genes: Lr34 and Lr68, in thirteen combinations. The adaptation of PCR markers for multiplex assays relied on: (1) selection of primers with an appropriate length; (2) selection of common annealing/extension temperature for given primers; and (3) PCR mixture modifications consisting of increased concentration of primers for the scanty band signals or decreased concentration of primers for the strong bands. These multiplex PCR protocols can be integrated into a marker-assisted selection of the leaf rust-resistant wheat genotypes.
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Affiliation(s)
- Aleksandra Noweiska
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poland
| | - Roksana Bobrowska
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poland
| | - Julia Spychała
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poland
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poland
| | - Michał T. Kwiatek
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poland
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Qualitative and Quantitative Real-Time PCR Methods for Assessing False-Positive Rates in Genetically Modified Organisms Based on the Microbial-Infection-Linked HPT Gene. Int J Mol Sci 2022; 23:ijms231710000. [PMID: 36077399 PMCID: PMC9456445 DOI: 10.3390/ijms231710000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
The hygromycin phosphotransferase (HPT) gene as a selective marker is normally used in screening tests as a first step in detecting and quantifying genetically modified organisms (GMOs) in seeds, food, and feed materials. Nevertheless, if researchers only focus on the HPT gene, it is difficult to distinguish genetically modified (GM) crops from microbial infection, leading to miscalculation of the rate of GM materials in a given sample set. Here, we cloned the 7259 bp sequence carrying the HPT gene from soybean sprouts using the genome walking strategy. BLAST analysis revealed that this sequence was derived from plasmids naturally occurring in microorganisms, such as Escherichia coli, Klebsiella pneumoniae or Salmonella sp. Using the reconstructed plasmid pFP-hpt, qualitative PCR and quantitative real-time PCR (qPCR) methods were established, and 261 bp and 156 bp products were produced. The specificity of these assays was assessed against related pFP-hpt plasmids, plant species with important agronomic traits, and GM crops containing the HPT gene. No unexpected results were observed between samples using these qualitative PCR and qPCR methods. The sensitivity of this qualitative PCR assay was determined at 20 copies, while the limit of detection (LOD) and limit of quantification (LOQ) of qPCR were both 5 copies per reaction. Our in-house validation indicated that the amplification efficiency, linearity, and repeatability of this qPCR assay were in line with performance requirements. Furthermore, a qualitative and quantitative duplex PCR showed high reliability for the simultaneous detection of the HPT gene in a plant sample and environmental micro-organisms harboring the HPT gene in one PCR reaction. These qualitative PCR and qPCR assays were able to differentiate between plants infected with E. coli harboring the HPT gene from GM plants, indicating that these two methods are broadly applicable for routine GMO testing.
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Detection and identification of authorized and unauthorized GMOs using high-throughput sequencing with the support of a sequence-based GMO database. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 4:100096. [PMID: 35415691 PMCID: PMC8991651 DOI: 10.1016/j.fochms.2022.100096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/23/2022]
Abstract
Sequence-based database Nexplorer describing EU-authorized GMOs was developed. Sequences were annotated and presented in structured and extractable formats. Workflow for an efficient analysis of NGS data using Nexplorer database was designed. Method was successfully tested for various scenarios for routine GMO analysis. This paves the way for the use of NGS for routine GMO detection and identification.
The increasing number and diversity of genetically modified organisms (GMOs) for the food and feed market calls for the development of advanced methods for their detection and identification. This issue can be addressed by next generation sequencing (NGS). However, the efficiency of NGS-based strategies depends on the availability of bioinformatic methods to find sequences of the transgenic insert and junction regions, which is a challenging topic. To facilitate this task, we have developed Nexplorer, a sequence-based database in which annotated sequences of GM events are stored in a structured, searchable and extractable format. As a proof of concept, we have developed a methodology for the analysis of sequencing data of DNA walking libraries of samples containing GMOs using the database. The efficiency of the method has been tested on datasets representing various scenarios that can be encountered in routine GMO analysis. Database-guided analysis allowed obtaining detailed and reliable information with limited hands-on time. As the database allows for efficient analysis of NGS data, it paves the way for the use of NGS sequencing technology to aid routine detection and identification of GMO.
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Cao G, Dong J, Chen X, Lu P, Xiong Y, Peng L, Li J, Huo D, Hou C. Simultaneous detection of CaMV35S and T-nos utilizing CRISPR/Cas12a and Cas13a with multiplex-PCR (MPT-Cas12a/13a). Chem Commun (Camb) 2022; 58:6328-6331. [PMID: 35527517 DOI: 10.1039/d2cc01300b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here, we established a strategy (MPT-Cas12a/13a) that combined CRISPR/Cas12a and Cas13a for simultaneously detecting CaMV35S and T-nos based on multiplex PCR (M-PCR) and transcription. It realized a simultaneous detection mode with different signals in the same space. The MPT-Cas12a/13a had excellent sensitivity with the limit of detection as low as 11 copies of T-nos and 13 copies of CaMV35S and it had outstanding specificity and anti-interference ability in actual sample analysis. Therefore, it is a potential candidate in the detection of GM crops.
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Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Jiangbo Dong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Xiaolong Chen
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Peng Lu
- Chongqing University Three Gorges Hospital, Chongqing, 404000, P. R. China
| | - Yifan Xiong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Lan Peng
- Chongqing Medical and Pharmaceutical College Basic Department, Chongqing, 401331, P. R. China
| | - Jiawei Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China. .,Chongqing University Three Gorges Hospital, Chongqing, 404000, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China. .,Chongqing Key laboratory of Bio-perception & intelligent information Processing, School of microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
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Wang C, Huang C, Zhu P, Du Z, Wei S, Fu W. Applicability of a General Analytical Approach for Detection of Genetically Modified Organisms: Collaborative Trial. J AOAC Int 2021; 105:476-482. [PMID: 34927696 DOI: 10.1093/jaoacint/qsab154] [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: 08/03/2021] [Revised: 11/21/2021] [Accepted: 11/27/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND With the commercialization of genetically modified organisms (GMOs) in the market, laboratories have undergone a significantly increased workload. A universal analytical approach was designed to achieve cost-efficient and high-throughput GMOs screening with high specificity and accuracy. The approach provides accurate qualification of authorized and unauthorized GMOs. OBJECTIVE This paper describes the assessment of this analytical approach developed to detect majority of commercialized GMOs over the world. METHODS Seven elements and three events were detected by qPCR in a single laboratory to detect 59 commercialized GMOs. Certificated reference materials and food/feed samples from Chinese market were also evaluated for the specificity, conformity and robustness of this approach and were challenged in the inter-laboratory study. RESULTS The results showed that elements and events selected can best detect GMO presence with good specificity and sensitivity. The results showed a concordance between 97.5% and 99.56% and the variance between 0.65% and 12.88%, which is in line with the minimum requirement of analytical methods of GMO testing. CONCLUSION The approach validated here can be used to manipulate GMO presence in food and feed and showed the capacity to manipulate GMOs trace in the trade and domestic agriculture grocery in China. HIGHLIGHTS A universal analytical approach used to track GMO presence was evaluated for its specificity, sensitivity and robustness.
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Affiliation(s)
- Chenguang Wang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176 China
| | - Chunmeng Huang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176 China.,College of Plant Protection, China Agricultural University, Beijing, 100083 China
| | - Pengyu Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176 China
| | - Zhixin Du
- Technical Center of Nanning Customs District, Nanning, Guangxi, 530021 China
| | - Shuang Wei
- Inspection and Quarantine Technology Centre of China Customs, Guangzhou, Guangdong, 510623 China
| | - Wei Fu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176 China.,College of Plant Protection, China Agricultural University, Beijing, 100083 China
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Long L, Yan W, Li C, Dong L, Liu N, Xing Z, Li F. Event-specific quantitative polymerase chain reaction methods for detection of double-herbicide-resistant genetically modified corn MON 87419 based on the 3'-junction of the insertion site. Biosci Biotechnol Biochem 2021; 85:1468-1475. [PMID: 33720312 DOI: 10.1093/bbb/zbab040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/03/2021] [Indexed: 11/13/2022]
Abstract
MON 87419 was one of the new transgenic corn events developed in US with the trait of herbicide resistance to both dicamba and glyphosate. To monitor unintended release of genetically modified organism in the future, as well as to meet GM-labeling requirements, it is requisite to develop a reliable method for the detection and quantification of MON 87419, an event-specific primer pair was designed to amplify the 3'-junction site between the endogenous genome sequence and the transferred DNA of GM event MON 87419, amplicons of desired size were produced by qualitative polymerase chain reaction (PCR) assay. For the validation of this quantitative method, the mixed samples containing 10%, 1%, and 0.1% MON 87419 ingredient were quantified. The precisions were expressed as relative standard deviations, deviated by 7.87%, 12.94%, and 19.98%, respectively. These results clearly demonstrate that the PCR methods we developed herein can be used for event-specific quantitative testing of the double-herbicide-resistant corn MON 87419.
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Affiliation(s)
- Likun Long
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wei Yan
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Congcong Li
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Liming Dong
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Na Liu
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Zhenjuan Xing
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Feiwu Li
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
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Shi H, Cui J, Sulemana H, Wang W, Gao L. Protein detection based on rolling circle amplification sensors. LUMINESCENCE 2021; 36:842-848. [PMID: 33502072 DOI: 10.1002/bio.4017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/07/2021] [Accepted: 01/17/2021] [Indexed: 12/22/2022]
Abstract
Rolling circle amplification (RCA) is an isothermal process under the action of DNA polymerases. Large-scale DNA templates have been generated using RCA for target detection. Some signal amplification strategies including optical sensors and electrochemical sensors based on RCA have been applied to achieve sensitive detection. Sensors based on RCA have attracted increasing interest. Advances in RCA-based sensors for protein detection are reviewed in this paper. The advantages and detection mechanisms of sensors based on RCA are revealed and discussed. Finally, possible challenges and future perspectives are also outlined.
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Affiliation(s)
- Haixia Shi
- P. E. Department of Jiangsu University, Zhenjiang, China
| | - Jingjie Cui
- School of Automation, Hangzhou Dianzi University, Hangzhou, China
| | | | - Wunian Wang
- P. E. Department of Jiangsu University, Zhenjiang, China
| | - Li Gao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
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Bak A, Emerson JB. Cauliflower mosaic virus (CaMV) Biology, Management, and Relevance to GM Plant Detection for Sustainable Organic Agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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