1
|
Zhu L, Lin Y, Yang W, Pan Z, Chen W, Yao J, Sheng O, Zhou L, Jiang D. The Identification of the Banana Endogenous Reference Gene MaSPS1 and the Construction of Qualitative and Quantitative PCR Detection Methods. Genes (Basel) 2023; 14:2116. [PMID: 38136937 PMCID: PMC10742897 DOI: 10.3390/genes14122116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Endogenous reference genes play a crucial role in the qualitative and quantitative PCR detection of genetically modified crops. Currently, there are no systematic studies on the banana endogenous reference gene. In this study, the MaSPS1 gene was identified as a candidate gene through bioinformatics analysis. The conservation of this gene in different genotypes of banana was tested using PCR, and its specificity in various crops and fruits was also examined. Southern blot analysis showed that there is only one copy of MaSPS1 in banana. The limit of detection (LOD) test showed that the LOD of the conventional PCR method is approximately 20 copies. The real-time fluorescence quantitative PCR (qPCR) method also exhibited high specificity, with a LOD of approximately 10 copies. The standard curve of the qPCR method met the quantitative requirements, with a limit of quantification (LOQ) of 1.14 × 10-2 ng-about 20 copies. Also, the qPCR method demonstrated good repeatability and stability. Hence, the above results indicate that the detection method established in this study has strong specificity, a low detection limit, and good stability. It provides a reliable qualitative and quantitative detection system for banana.
Collapse
Affiliation(s)
- Lili Zhu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (L.Z.); (Y.L.); (W.Y.); (Z.P.); (W.C.); (J.Y.)
| | - Ying Lin
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (L.Z.); (Y.L.); (W.Y.); (Z.P.); (W.C.); (J.Y.)
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Wenli Yang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (L.Z.); (Y.L.); (W.Y.); (Z.P.); (W.C.); (J.Y.)
| | - Zhiwen Pan
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (L.Z.); (Y.L.); (W.Y.); (Z.P.); (W.C.); (J.Y.)
| | - Weiting Chen
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (L.Z.); (Y.L.); (W.Y.); (Z.P.); (W.C.); (J.Y.)
| | - Juan Yao
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (L.Z.); (Y.L.); (W.Y.); (Z.P.); (W.C.); (J.Y.)
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Lingyan Zhou
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Dagang Jiang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (L.Z.); (Y.L.); (W.Y.); (Z.P.); (W.C.); (J.Y.)
| |
Collapse
|
2
|
Hou Y, Chen S, Zheng Y, Zheng X, Lin JM. Droplet-based digital PCR (ddPCR) and its applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
3
|
Long L, Xing Z, He Y, Yan W, Li C, Xia W, Dong L, Zhao N, Ma Y, Xie Y, Liu N, Li F. Establishment and Validation of Reference Genes of Brassica napus L. for Digital PCR Detection of Genetically Modified Canola. Foods 2022; 11:foods11162535. [PMID: 36010535 PMCID: PMC9407334 DOI: 10.3390/foods11162535] [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: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
As an effective tool for genetically modified organism (GMO) quantification in complex matrices, digital PCR (dPCR) has been widely used for the quantification of genetically modified (GM) canola events; however, little is known about the quantification of GM canola events using endogenous reference gene (ERG) characteristics by dPCR. To calculate and quantify the content of GM canola using endogenous reference gene (ERG) characteristics, the suitability of several ERGs of canola, such as cruciferin A (CruA), acetyl-CoA carboxylase (BnAcc), phosphoenolpyruvate carboxylase (PEP), cruciferin storage (BnC1), oleoyl hydrolase (Fat(A)), and high-mobility-group protein I/Y (HMG-I/Y), was investigated by droplet dPCR. BnAcc and BnC1 were more specific and stable in copy number in the genome of Brassica napus L. than the other genes. By performing intra-laboratory validation of the suitability of ERG characteristics for the quantification of GM canola events, the ddPCR methods for BnAcc and BnC1 were comprehensively demonstrated in dPCR assays. The methods could provide technical support for GM labeling regulations.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Feiwu Li
- Correspondence: ; Tel.: +86-431-8507-1386
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Yu N, Ren J, Huang W, Xing R, Deng T, Chen Y. An effective analytical droplet digital PCR approach for identification and quantification of fur-bearing animal meat in raw and processed food. Food Chem 2021; 355:129525. [PMID: 33799266 DOI: 10.1016/j.foodchem.2021.129525] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022]
Abstract
Available nuclear gene sequences for meat detection are still rare and little applicability in the investigation of new types of meat adulteration such as fox, mink and raccoon dog was performed. In the present work, we developed a reliable qualitative and quantitative detection method for fur-bearing animal meat based on droplet digital PCR (ddPCR). Three sets of primers and probes targeted nuclear genes for fox, mink and raccoon dog were designed for ddPCR system; In addition, turkey was selected as internal reference to transform the copy numbers to the fraction of target species. Results indicated that the dynamic ranges of three fur-bearing animals were all from 1% to 90%; the limit of detection (LOD) and limit of quantification (LOQ) for three fur-bearing animals were same, with LOD 0.1% (w/w) and LOQ 1% (w/w). Moreover, we confirmed that different additives had no effect on quantification accuracy in the ddPCR assay.
Collapse
Affiliation(s)
- Ning Yu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176
| | - Junan Ren
- Chinese Academy of Inspection and Quarantine, Beijing, 100176; Beijing Food & Wine Inspection and Testing 1st Station, Beijing, 101111
| | - Wensheng Huang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176
| | - Ranran Xing
- Chinese Academy of Inspection and Quarantine, Beijing, 100176
| | - Tingting Deng
- Chinese Academy of Inspection and Quarantine, Beijing, 100176
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine, Beijing, 100176.
| |
Collapse
|
7
|
Digital PCR: What Relevance to Plant Studies? BIOLOGY 2020; 9:biology9120433. [PMID: 33266157 PMCID: PMC7760125 DOI: 10.3390/biology9120433] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 01/01/2023]
Abstract
Simple Summary Digital PCR is a third-generation technology based on the subdivision of the analytical sample into numerous partitions that are amplified individually. This review presents the major applications of digital PCR (dPCR) technology developed so far in the field of plant science. In greater detail, dPCR assays have been developed to trace genetically modified plant components, pathogenic and non-pathogenic microorganisms, and plant species. Other applications have concerned the study of the aspects of structural and functional genetics. Abstract Digital PCR (dPCR) is a breakthrough technology that able to provide sensitive and absolute nucleic acid quantification. It is a third-generation technology in the field of nucleic acid amplification. A unique feature of the technique is that of dividing the sample into numerous separate compartments, in each of which an independent amplification reaction takes place. Several instrumental platforms have been developed for this purpose, and different statistical approaches are available for reading the digital output data. The dPCR assays developed so far in the plant science sector were identified in the literature, and the major applications, advantages, disadvantages, and applicative perspectives of the technique are presented and discussed in this review.
Collapse
|
8
|
Narushima J, Kimata S, Soga K, Sugano Y, Kishine M, Takabatake R, Mano J, Kitta K, Kanamaru S, Shirakawa N, Kondo K, Nakamura K. Rapid DNA template preparation directly from a rice sample without purification for loop-mediated isothermal amplification (LAMP) of rice genes. Biosci Biotechnol Biochem 2020; 84:670-677. [DOI: 10.1080/09168451.2019.1701406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
ABSTRACT
Rapid DNA template preparation directly from a single rice (Oryza sativa) grain or rice flour of its equivalent weight was developed for loop-mediated isothermal amplification (LAMP). LAMP efficiency using DNA extract obtained from consecutive addition of alkaline lysis reagent (25 mM NaOH, 0.2 mM EDTA) and neutralizing reagent (40 mM Tris–HCl [pH 5]) was comparable to that using an equivalent amount of purified DNA as template. The stability of the prepared DNA extract was confirmed for up to six-day storage at room temperature. Without using any special laboratory devices, the developed method enabled a rapid, simple, and low-cost DNA template preparation method for reliable LAMP testing to detect rice genes.
Collapse
Affiliation(s)
- Jumpei Narushima
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki-ku, Kawasaki, Japan
| | - Shinya Kimata
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki-ku, Kawasaki, Japan
| | - Keisuke Soga
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki-ku, Kawasaki, Japan
| | - Yohei Sugano
- Department of Food Hygiene, Hokkaido Institute of Public Health, Kita-ku, Sapporo, Japan
| | - Masahiro Kishine
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Reona Takabatake
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Junichi Mano
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kazumi Kitta
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Shunsuke Kanamaru
- Food Hygiene Analysis Center, Nippon Kaiji Kentei Kyokai, Kanazawa-ku, Yokohama, Japan
| | - Nanami Shirakawa
- Food Hygiene Analysis Center, Nippon Kaiji Kentei Kyokai, Kanazawa-ku, Yokohama, Japan
| | - Kazunari Kondo
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki-ku, Kawasaki, Japan
| | - Kosuke Nakamura
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki-ku, Kawasaki, Japan
| |
Collapse
|