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Yeasmin S, Takabatake R, Kagiya Y, Okazaki N, Minegishi Y, Kitta K. [Evaluation of a Species-specific, Stable, and Endogenous Sequence of Eggplant (Solanum melongena) using LAMP for the Detection of Genetically Modified Eggplants]. Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 2021; 62:180-186. [PMID: 34955468 DOI: 10.3358/shokueishi.62.180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Species-specific endogenous reference sequences are indispensable in the development of methods to detect genetically modified (GM) crops for food and feed. We analyzed a partial sequence derived from the β-fructosidase gene among several solanaceous species and developed a new eggplant specific detection method using loop-mediated isothermal amplification (LAMP). LAMP is a rapid, specific, and cost-effective technique. The species-specificity and stability of the developed method were evaluated using 18 eggplant cultivars and other crops including solanaceous plants. The limit of detection was also evaluated. The developed method showed high specificity for eggplants and stability among the eggplant cultivars tested. These results suggested that the developed method would be useful as a positive control for the detection of GM eggplants with LAMP.
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Affiliation(s)
| | - Reona Takabatake
- Institute of Food Research, National Agriculture and Food Research Organization
| | | | - Noriko Okazaki
- Institute of Food Research, National Agriculture and Food Research Organization
| | | | - Kazumi Kitta
- Institute of Food Research, National Agriculture and Food Research Organization
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2
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Dalla Costa L, Vinciguerra D, Giacomelli L, Salvagnin U, Piazza S, Spinella K, Malnoy M, Moser C, Marchesi U. Integrated approach for the molecular characterization of edited plants obtained via Agrobacterium tumefaciens-mediated gene transfer. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03881-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
AbstractAgrobacterium tumefaciens-mediated gene transfer—actually the most used method to engineer plants—may lead to integration of multiple copies of T-DNA in the plant genome, as well as to chimeric tissues composed of modified cells and wild type cells. A molecular characterization of the transformed lines is thus a good practice to select the best ones for further investigation. Nowadays, several quantitative and semi-quantitative techniques are available to estimate the copy number (CN) of the T-DNA in genetically modified plants. In this study, we compared three methods based on (1) real-time polymerase chain reaction (qPCR), (2) droplet digital PCR (ddPCR), and (3) next generation sequencing (NGS), to carry out a molecular characterization of grapevine edited lines. These lines contain a knock-out mutation, obtained via CRISPR/Cas9 technology, in genes involved in plant susceptibility to two important mildew diseases of grapevine. According to our results, qPCR and ddPCR outputs are largely in agreement in terms of accuracy, especially for low CN values, while ddPCR resulted more precise than qPCR. With regard to the NGS analysis, the CNs detected with this method were often not consistent with those calculated by qPCR and ddPCR, and NGS was not able to discriminate the integration points in three out of ten lines. Nevertheless, the NGS method can positively identify T-DNA truncations or the presence of tandem/inverted repeats, providing distinct and relevant information about the transgene integration asset. Moreover, the expression analysis of Cas9 and single guide RNA (sgRNA), and the sequencing of the target site added new information to be related to CN data. This work, by reporting a practical case-study on grapevine edited lines, explores pros and cons of the most advanced diagnostic techniques available for the precocious selection of the proper transgenic material. The results may be of interest both to scientists developing new transgenic lines, and to laboratories in charge of GMO control.
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Singh M, Sodhi KK, Paliwal A, Sharma S, Randhawa G. Efficient DNA Extraction Procedures for Processed Food Derivatives—a Critical Step to Ensure Quality for GMO Analysis. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-02051-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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4
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Zhang C, Lei Z, Li Y, Yi L, Shang Y. Identification of Tps2 Used as an Endogenous Reference Gene in Qualitative and Real-time Quantitative PCR Detection of Flammulina velutipes. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-02043-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Shang Y, Xu Y, Huang K, Luo Y, Xu W. Multiplex pyrosequencing quantitative detection combined with universal primer-multiplex-PCR for genetically modified organisms. Food Chem 2020; 320:126634. [PMID: 32208182 DOI: 10.1016/j.foodchem.2020.126634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 10/24/2022]
Abstract
A multiplex pyrosequencing quantitative detection technique combined with universal primer-multiplex-PCR (UP-M-PCR) was established. In this study, a pyrosequencing results analysis software was first self-compiled, which realized the DNA sequences degeneration, and converted the pyrosequencing results and base composition of the target sequences into mathematic relations. Five calculation models were put forward based on the actual situation, which adjusted the values smaller than zero or the detection limit. By applying this method, samples containing five genetically modified (GM) lines mixed in random ratio were quantified, it showed that the quantification was very close to the actual value, and the detection sensitivity was as low as 1.47% of a single component, which satisfied most labeling policies. This novel method is realized without fluorescent group labeling, hence the number of targets is not limited by factors inherent in method or equipment, and is proven to be a reliable tool for the quantitative detection.
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Affiliation(s)
- Ying Shang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Faulty of Agriculture and Food, Kunming University of Science and Technology, Kunming, Yunnan 650500, 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
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, 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; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, 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; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China.
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6
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Yang Z, Wang K, Aziz U, Zhao C, Zhang M. Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat ( Avena sativa L.). PLANT METHODS 2020; 16:138. [PMID: 33072174 PMCID: PMC7560290 DOI: 10.1186/s13007-020-00679-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/05/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, no suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented for oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids. RESULTS In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for "all samples", "shoots and roots of seedlings", "developing seeds" and "developing endosperms" were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively. Among these RGs, UBC21 was a four-copy duplicated gene. The reliability was validated by the expression patterns of four various genes normalized to the most and the least stable RGs in different sample sets. CONCLUSIONS Results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.
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Affiliation(s)
- Zheng Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Usman Aziz
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Cuizhu Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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Development of Real-time PCR Assays for the Detection of the pin II Terminator (tpinII) Used in GM Constructs and Its Donor Organism, Potato (Solanum tuberosum). FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1203-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Paternò A, Verginelli D, Bonini P, Misto M, Quarchioni C, Dainese E, Peddis S, Fusco C, Vinciguerra D, Marchesi U. In-House Validation and Comparison of Two Wheat (Triticum aestivum) Taxon-Specific Real-Time PCR Methods for GMO Quantification Supported by Droplet Digital PCR. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-1097-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Yang L, Quan S, Zhang D. Endogenous Reference Genes and Their Quantitative Real-Time PCR Assays for Genetically Modified Bread Wheat (Triticum aestivum L.) Detection. Methods Mol Biol 2017; 1679:259-268. [PMID: 28913806 DOI: 10.1007/978-1-4939-7337-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Endogenous reference genes (ERG) and their derivate analytical methods are standard requirements for analysis of genetically modified organisms (GMOs). Development and validation of suitable ERGs is the primary step for establishing assays that monitoring the genetically modified (GM) contents in food/feed samples. Herein, we give a review of the ERGs currently used for GM wheat analysis, such as ACC1, PKABA1, ALMT1, and Waxy-D1, as well as their performances in GM wheat analysis. Also, we discussed one model for developing and validating one ideal RG for one plant species based on our previous research work.
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Affiliation(s)
- Litao Yang
- National Center for Molecular Characterization of Genetically Modified Organisms, SJTU-Bor Luh Food Safety Center, School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Sheng Quan
- National Center for Molecular Characterization of Genetically Modified Organisms, SJTU-Bor Luh Food Safety Center, School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Dabing Zhang
- National Center for Molecular Characterization of Genetically Modified Organisms, SJTU-Bor Luh Food Safety Center, School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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Gao H, Yu X, Deng T, Sun M, Xiao X, Huang X, Chen Y, Li R. Event-specific detection of transgenic potato AV43-6-G7 using real-time and digital PCR methods. BMC Biotechnol 2016; 16:74. [PMID: 27784303 PMCID: PMC5081928 DOI: 10.1186/s12896-016-0303-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/13/2016] [Indexed: 01/09/2023] Open
Abstract
Background The isolation of unknown DNA sequences flanked by known sequences is an important task in the event-specific detection of GMOs. None of event-specific detection method was developed based on the junction sequence of an exogenous integrant in the transgenic potato AV43-6-G7. Results The flanking sequence between the exogenous fragment and recombinant chromosome of this potato was successfully acquired through exogenous gene 5′-RACE. The event-specific primers and Taqman probe were designed to amplify fragments spanning the exogenous DNA and potato genomic DNA. The specific real-time PCR and digital PCR detection methods for AV43-6-G7 potato were established based on primers designed according to the flanking sequences. The detection limit of the qualitative PCR assay was 0.01 % for AV43-6-G7 potato in 100 ng of potato genomic DNA, corresponding to approximately 11.6 copies of the potato haploid genome. The ddPCR assays for Potato AV43-6-G7 achieved a limit of quantification of approximately 58 target copies, with RSD ≤ 25 %. The aLOQ of this system was approximately 1.2 copies. Conclusions These results indicated that these event-specific methods would be useful for the identification of potato AV43-6-G7. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0303-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongwei Gao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China.
| | - Xiaofan Yu
- Qingdao University Medical College, Qingdao, China
| | - Tingting Deng
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Min Sun
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xizhi Xiao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xin Huang
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ronggui Li
- Qingdao University Medical College, Qingdao, China
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Liu YK, Li HP, Huang T, Cheng W, Gao CS, Zuo DY, Zhao ZX, Liao YC. Wheat-specific gene, ribosomal protein l21, used as the endogenous reference gene for qualitative and real-time quantitative polymerase chain reaction detection of transgenes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:10405-10413. [PMID: 25325387 DOI: 10.1021/jf503559b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Wheat-specific ribosomal protein L21 (RPL21) is an endogenous reference gene suitable for genetically modified (GM) wheat identification. This taxon-specific RPL21 sequence displayed high homogeneity in different wheat varieties. Southern blots revealed 1 or 3 copies, and sequence analyses showed one amplicon in common wheat. Combined analyses with sequences from common wheat (AABBDD) and three diploid ancestral species, Triticum urartu (AA), Aegilops speltoides (BB), and Aegilops tauschii (DD), demonstrated the presence of this amplicon in the AA genome. Using conventional qualitative polymerase chain reaction (PCR), the limit of detection was 2 copies of wheat haploid genome per reaction. In the quantitative real-time PCR assay, limits of detection and quantification were about 2 and 8 haploid genome copies, respectively, the latter of which is 2.5-4-fold lower than other reported wheat endogenous reference genes. Construct-specific PCR assays were developed using RPL21 as an endogenous reference gene, and as little as 0.5% of GM wheat contents containing Arabidopsis NPR1 were properly quantified.
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Affiliation(s)
- Yi-Ke Liu
- Molecular Biotechnology Laboratory of Triticeae Crops, ‡College of Life Science and Technology, §College of Plant Science and Technology, and ∥National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University , Wuhan, Hubei 430070, People's Republic of China
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Randhawa GJ, Singh M, Sood P, Bhoge RK. Multitarget real-time PCR-based system: monitoring for unauthorized genetically modified events in India. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:7118-7130. [PMID: 24971889 DOI: 10.1021/jf502190e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A multitarget TaqMan real-time PCR (RTi-PCR) based system was developed to monitor unauthorized genetically modified (GM) events in India. Most of the GM events included in this study are either authorized for commercial cultivation or field trials, which were indigenously developed or imported for research purposes. The developed system consists of a 96-well prespotted plate with lyophilized primers and probes, for simultaneous detection of 47 targets in duplicate, including 21 event-specific sequences, 5 construct regions, 15 for transgenic elements, and 6 taxon-specific targets for cotton, eggplant, maize, potato, rice, and soybean. Limit of detection (LOD) of assays ranged from 0.1 to 0.01% GM content for different targets. Applicability, robustness, and practical utility of the developed system were verified with stacked GM cotton event, powdered samples of proficiency testing and two unknown test samples. This user-friendly multitarget approach can be efficiently utilized for monitoring the unauthorized GM events in an Indian context.
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Affiliation(s)
- Gurinder Jit Randhawa
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi 110 012, India
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13
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Xue B, Guo J, Que Y, Fu Z, Wu L, Xu L. Selection of suitable endogenous reference genes for relative copy number detection in sugarcane. Int J Mol Sci 2014; 15:8846-62. [PMID: 24857916 PMCID: PMC4057763 DOI: 10.3390/ijms15058846] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/20/2014] [Accepted: 05/07/2014] [Indexed: 11/17/2022] Open
Abstract
Transgene copy number has a great impact on the expression level and stability of exogenous gene in transgenic plants. Proper selection of endogenous reference genes is necessary for detection of genetic components in genetically modification (GM) crops by quantitative real-time PCR (qPCR) or by qualitative PCR approach, especially in sugarcane with polyploid and aneuploid genomic structure. qPCR technique has been widely accepted as an accurate, time-saving method on determination of copy numbers in transgenic plants and on detection of genetically modified plants to meet the regulatory and legislative requirement. In this study, to find a suitable endogenous reference gene and its real-time PCR assay for sugarcane (Saccharum spp. hybrids) DNA content quantification, we evaluated a set of potential "single copy" genes including P4H, APRT, ENOL, CYC, TST and PRR, through qualitative PCR and absolute quantitative PCR. Based on copy number comparisons among different sugarcane genotypes, including five S. officinarum, one S. spontaneum and two S. spp. hybrids, these endogenous genes fell into three groups: ENOL-3--high copy number group, TST-1 and PRR-1--medium copy number group, P4H-1, APRT-2 and CYC-2--low copy number group. Among these tested genes, P4H, APRT and CYC were the most stable, while ENOL and TST were the least stable across different sugarcane genotypes. Therefore, three primer pairs of P4H-3, APRT-2 and CYC-2 were then selected as the suitable reference gene primer pairs for sugarcane. The test of multi-target reference genes revealed that the APRT gene was a specific amplicon, suggesting this gene is the most suitable to be used as an endogenous reference target for sugarcane DNA content quantification. These results should be helpful for establishing accurate and reliable qualitative and quantitative PCR analysis of GM sugarcane.
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Affiliation(s)
- Bantong Xue
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China.
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China.
| | - Zhiwei Fu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China.
| | - Luguang Wu
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China.
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Ražná K, Bežo M, Nikolaieva N, Garkava K, Brindza J, Ziarovská J. Variability of Corylus avellana, L. CorA and profilin pollen allergens expression. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2014; 49:639-645. [PMID: 25035912 DOI: 10.1080/03601234.2014.922403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Corylus avellana is the source of inhalant allergies induced by hazel pollen as well as food allergies induced after ingestion of hazelnuts. In this study, real-time PCR approach was used to analyse expression of hazel pollen allergens on the molecular level. Relative quantity of hazelnut allergens Corylus avellana, L. CorA and Corylus avellana, L. pollen profiling in samples from different Ukraine areas were determining and comparing. Differences among the levels of both analysed allergen transcripts were found for hazel CorA and profillin. In both cases, the expression within the urbanized growth conditions was higher when compared to the sample from village area. The average expression for CorA was 0.84 times higher than for profilin and the results are very variable depending on the place of growth. Expression levels here were within the range of 2.957 up to the 52.936. Profilin expression was the highest in the sample from the polluted place of growth-cement plant area with the value of 52 times higher when compared to the sample from the village area. In this study, comparison of expression levels of hazel CorA and profiling pollen allergens was performed for the first time. Real-time PCR assay developed in this study proved the sensitivity for detection of the changes of the hazel pollen allergens expression levels and could benefit labs by fast and reproducible detection method of these allergens.
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Affiliation(s)
- Katarína Ražná
- a Department of Genetics and Plant Breeding , Slovak University of Agriculture in Nitra , Slovak Republic
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15
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Scali M, Elisa P, Jacopo B, Mauro C, Vignani R. Vineyards genetic monitoring and Vernaccia di San Gimignano wine molecular fingerprinting. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/abb.2014.52018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Cottenet G, Blancpain C, Sonnard V, Chuah PF. Development and validation of a multiplex real-time PCR method to simultaneously detect 47 targets for the identification of genetically modified organisms. Anal Bioanal Chem 2013; 405:6831-44. [DOI: 10.1007/s00216-013-7125-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/29/2013] [Accepted: 06/05/2013] [Indexed: 11/28/2022]
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17
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Relative quantification in seed GMO analysis: state of art and bottlenecks. Transgenic Res 2013; 22:461-76. [PMID: 23400878 DOI: 10.1007/s11248-012-9684-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 12/28/2012] [Indexed: 10/27/2022]
Abstract
Reliable quantitative methods are needed to comply with current EU regulations on the mandatory labeling of genetically modified organisms (GMOs) and GMO-derived food and feed products with a minimum GMO content of 0.9 %. The implementation of EU Commission Recommendation 2004/787/EC on technical guidance for sampling and detection which meant as a helpful tool for the practical implementation of EC Regulation 1830/2003, which states that "the results of quantitative analysis should be expressed as the number of target DNA sequences per target taxon specific sequences calculated in terms of haploid genomes". This has led to an intense debate on the type of calibrator best suitable for GMO quantification. The main question addressed in this review is whether reference materials and calibrators should be matrix based or whether pure DNA analytes should be used for relative quantification in GMO analysis. The state of the art, including the advantages and drawbacks, of using DNA plasmid (compared to genomic DNA reference materials) as calibrators, is widely described. In addition, the influence of the genetic structure of seeds on real-time PCR quantitative results obtained for seed lots is discussed. The specific composition of a seed kernel, the mode of inheritance, and the ploidy level ensure that there is discordance between a GMO % expressed as a haploid genome equivalent and a GMO % based on numbers of seeds. This means that a threshold fixed as a percentage of seeds cannot be used as such for RT-PCR. All critical points that affect the expression of the GMO content in seeds are discussed in this paper.
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Chaouachi M, Alaya A, Ali IBH, Hafsa AB, Nabi N, Bérard A, Romaniuk M, Skhiri F, Saïd K. Development of real-time PCR method for the detection and the quantification of a new endogenous reference gene in sugar beet "Beta vulgaris L.": GMO application. PLANT CELL REPORTS 2013; 32:117-128. [PMID: 23052591 DOI: 10.1007/s00299-012-1346-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/08/2012] [Accepted: 09/11/2012] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE : Here, we describe a new developed quantitative real-time PCR method for the detection and quantification of a new specific endogenous reference gene used in GMO analysis. The key requirement of this study was the identification of a new reference gene used for the differentiation of the four genomic sections of the sugar beet (Beta vulgaris L.) (Beta, Corrollinae, Nanae and Procumbentes) suitable for quantification of genetically modified sugar beet. A specific qualitative polymerase chain reaction (PCR) assay was designed to detect the sugar beet amplifying a region of the adenylate transporter (ant) gene only from the species of the genomic section I of the genus Beta (cultivated and wild relatives) and showing negative PCR results for 7 species of the 3 other sections, 8 related species and 20 non-sugar beet plants. The sensitivity of the assay was 15 haploid genome copies (HGC). A quantitative real-time polymerase chain reaction (QRT-PCR) assay was also performed, having high linearity (R (2) > 0.994) over sugar beet standard concentrations ranging from 20,000 to 10 HGC of the sugar beet DNA per PCR. The QRT-PCR assay described in this study was specific and more sensitive for sugar beet quantification compared to the validated test previously reported in the European Reference Laboratory. This assay is suitable for GMO quantification in routine analysis from a wide variety of matrices.
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Affiliation(s)
- Maher Chaouachi
- Laboratoire de Génétique, Biodiversité et Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir (ISBM), Université de Monastir, Avenue Tahar Haddad 5000, BP74, Monastir, Tunisia.
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Žiarovská J, Labajová M, Ražná K, Bežo M, Štefúnová V, Shevtsova T, Garkava K, Brindza J. Changes in expression of BetV1 allergen of silver birch pollen in urbanized area of Ukraine. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2013; 48:1479-1484. [PMID: 23802156 DOI: 10.1080/10934529.2013.796788] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The aim of the study was to determinate the level of expression of silver birch allergen Betv1 in pollen samples from different Ukraine areas by RT-qPCR SYBR Green assay. Protocol for quantifying the expression of Betv1 allergen was developed when testing of three housekeeping genes-cyclophylin, alpha-tubulin and transcription factor CBF1. Samples from urbanized area was analysed by real-time PCR when a sample from forest growth conditions was used as a calibrator. Real-time PCR based quantifying of Betv1 provides a useful method for rapid and sensitive analyses of this silver birch allergen. Our results show higher expression levels in samples from central parts of urbanized area as housing estates when compared to the samples from borders of the urbanized area.
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Affiliation(s)
- Jana Žiarovská
- Department of Genetics and Plant Breeding, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic.
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Dinon AZ, Brod FCA, Mello CS, Oliveira EMM, Faria JC, Arisi ACM. Primers and probes development for specific PCR detection of genetically modified common bean (Phaseolus vulgaris) Embrapa 5.1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:4672-4677. [PMID: 22506690 DOI: 10.1021/jf3011257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The genetically modified common bean Embrapa 5.1, developed by Brazilian Agricultural Research Corporation (Embrapa), is the first commercial GM plant produced in Latin America. It presents high resistance to the Bean golden mosaic virus. In this work, primers and probes targeting a taxon-specific reference DNA sequence for the common bean (Phaseolus vulgaris L.) and a construct-specific DNA sequence of Embrapa 5.1 GM common bean were successfully developed. The primers and probes showed high specificity for the target detection. Both methods showed suitable efficiency and performance to be used as an endogenous target for detection of common bean DNA and for construct-specific detection of GM common bean Embrapa 5.1, respectively. Both real-time PCR assays proved to be valuable for future assessment of interlaboratory studies.
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Affiliation(s)
- Andréia Z Dinon
- Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346, 88034-001, Florianópolis, Santa Catarina, Brazil
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Pafundo S, Gullì M, Marmiroli N. Comparison of DNA extraction methods and development of duplex PCR and real-time PCR to detect tomato, carrot, and celery in food. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:10414-10424. [PMID: 21894887 DOI: 10.1021/jf202382s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Traceability is of particular importance for those persons who suffer allergy or intolerance to some food component(s) and need a strict avoidance of the allergenic food. In this paper, methodologies are described to fingerprint the presence of allergenic species such as carrot, tomato, and celery by DNA detection. Three DNA extraction methods were applied on vegetables and foods containing or not containing the allergens, and the results were compared and discussed. Fast SYBR Green DNA melting curve temperature analyses and duplex PCR assays with internal control have been developed for detection of these allergenic vegetables and have been tested on commercial foods. Spiking food experiments were also performed, assessing that limits of detection (LOD) of 1 mg/kg for carrot and tomato DNA and 10 mg/kg for celery DNA have been reached.
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Affiliation(s)
- Simona Pafundo
- Division of Genetics and Environmental Biotechnology, Department of Environmental Sciences, University of Parma , Viale G. P. Usberti 11/A, 43100 Parma, Italy
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Randhawa GJ, Singh M, Chhabra R, Sharma R. Qualitative and Quantitative Molecular Testing Methodologies and Traceability Systems for Commercialised Bt Cotton Events and Other Bt Crops Under Field Trials in India. FOOD ANAL METHOD 2010. [DOI: 10.1007/s12161-010-9126-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Longhi S, Cristofori A, Gatto P, Cristofolini F, Grando MS, Gottardini E. Biomolecular identification of allergenic pollen: a new perspective for aerobiological monitoring? Ann Allergy Asthma Immunol 2010; 103:508-14. [PMID: 20084845 DOI: 10.1016/s1081-1206(10)60268-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Accurate and updated information on airborne pollen in specific areas can help allergic patients. Current monitoring systems are based on a morphologic identification approach, a time-consuming method that may represent a limiting factor for sampling network enhancement. OBJECTIVE To verify the feasibility of developing a real-time polymerase chain reaction (PCR) approach, an alternative to optical analysis, as a rapid, accurate, and automated tool for the detection and quantification of airborne allergenic pollen taxa. METHODS The traditional cetyl trimethyl ammonium bromide-based method was modified for DNA isolation from pollen. Taxon-specific DNA sequences were identified via bioinformatics or literature searches and were PCR amplified from the matching allergenic taxa; based on the sequences of PCR products, complementary or degenerate TaqMan probes were developed. The accuracy of the quantitative real-time PCR assay was tested on 3 plant species. RESULTS The setup of a modified DNA extraction protocol allowed us to achieve good-quality pollen DNA. Taxon-specific nuclear gene fragments were identified and sequenced. Designed primer pairs and probes identified selected pollen taxa, mostly at the required classification level. Pollen was properly identified even when collected on routine aerobiological tape. Preliminary quantification assays on pollen grains were successfully performed on test species and in mixes. CONCLUSIONS The real-time PCR approach revealed promising results in pollen identification and quantification, even when analyzing pollen mixes. Future perspectives could concern the development of multiplex real-time PCR for the simultaneous detection of different taxa in the same reaction tube and the application of high-throughput molecular methods.
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Affiliation(s)
- Sara Longhi
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
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Kothari S, Joshi A, Kachhwaha S, Ochoa-Alejo N. Chilli peppers — A review on tissue culture and transgenesis. Biotechnol Adv 2010; 28:35-48. [DOI: 10.1016/j.biotechadv.2009.08.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 08/15/2009] [Accepted: 08/24/2009] [Indexed: 10/20/2022]
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Palmieri L, Bozza E, Giongo L. Soft fruit traceability in food matrices using real-time PCR. Nutrients 2009; 1:316-28. [PMID: 22253987 PMCID: PMC3257598 DOI: 10.3390/nu1020316] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 12/15/2009] [Indexed: 11/16/2022] Open
Abstract
Food product authentication provides a means of monitoring and identifying products for consumer protection and regulatory compliance. There is a scarcity of analytical methods for confirming the identity of fruit pulp in products containing Soft Fruit. In the present work we have developed a very sensible qualitative and quantitative method to determine the presence of berry DNAs in different food matrices. To our knowledge, this is the first study that shows the applicability, to Soft Fruit traceability, of melting curve analysis and multiplexed fluorescent probes, in a Real-Time PCR platform. This methodology aims to protect the consumer from label misrepresentation.
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Affiliation(s)
- Luisa Palmieri
- Fondazione Edmund Mach, IASMA Research and Innovation Centre, Genomics and Crop Biology Area, Via E. Mach 1, 38010, San Michele all'Adige, TN, Italy.
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Lee SH, Kim SJ, Yi BY. Simplex and duplex event-specific analytical methods for functional biotech maize. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:7178-7185. [PMID: 19650633 DOI: 10.1021/jf901078d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Analytical methods are very important in the control of genetically modified organism (GMO) labeling systems or living modified organism (LMO) management for biotech crops. Event-specific primers and probes were developed for qualitative and quantitative analysis for biotech maize event 3272 and LY 038 on the basis of the 3' flanking regions, respectively. The qualitative primers confirmed the specificity by a single PCR product and sensitivity to 0.05% as a limit of detection (LOD). Simplex and duplex quantitative methods were also developed using TaqMan real-time PCR. One synthetic plasmid was constructed from two taxon-specific DNA sequences of maize and two event-specific 3' flanking DNA sequences of event 3272 and LY 038 as reference molecules. In-house validation of the quantitative methods was performed using six levels of mixing samples, from 0.1 to 10.0%. As a result, the biases from the true value and the relative deviations were all within the range of +/-30%. Limits of quantitation (LOQs) of the quantitative methods were all 0.1% for simplex real-time PCRs of event 3272 and LY 038 and 0.5% for duplex real-time PCR of LY 038. This study reports that event-specific analytical methods were applicable for qualitative and quantitative analysis for biotech maize event 3272 and LY 038.
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Affiliation(s)
- Seong-Hun Lee
- GMO Testing Laboratory, Experiment Research Institute of National Agricultural Products Quality Management Service, Seoul, South Korea.
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Ramos-Gómez S, López-Enríquez L, Caminero C, Hernández M. Pea detection in food and feed samples by a real-time PCR method based on a specific legumin gene that allows diversity analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:11098-104. [PMID: 18986147 DOI: 10.1021/jf8023968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Real-time polymerase chain reaction is currently being used for the identification and quantification of plant and animal species as well as microorganisms in food or feed samples based on the amplification of specific sequences of low copy genes. We report here the development of a new real-time PCR method for the detection and quantification of the pea (Pisum sativum) based on the amplification of a specific region of the legS gene. The specificity was evaluated in a wide range of plant species (51 varieties of Pisum sp., and 32 other plant species and varieties taxonomically related or nonrelated). The method allows the detection and quantification of as low as 21.6 pg of DNA, which corresponds to 5 haploid genome copies. The system has been shown to be sensitive, reproducible and 100% specific for the rapid detection and quantification of pea DNA in processed food and feed samples, being therefore suitable for high-throughput analysis.
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Affiliation(s)
- Sonia Ramos-Gómez
- Department of Plant Production and Agronomy, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
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Current awareness in phytochemical analysis. PHYTOCHEMICAL ANALYSIS : PCA 2008; 19:471-478. [PMID: 18773504 DOI: 10.1002/pca.1040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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New trends in bioanalytical tools for the detection of genetically modified organisms: an update. Anal Bioanal Chem 2008; 392:355-67. [DOI: 10.1007/s00216-008-2193-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 05/15/2008] [Accepted: 05/16/2008] [Indexed: 10/22/2022]
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