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Singh M, Young RG, Hellberg RS, Hanner RH, Corradini MG, Farber JM. Twenty-three years of PCR-based seafood authentication assay development: What have we learned? Compr Rev Food Sci Food Saf 2024; 23:e13401. [PMID: 39073284 DOI: 10.1111/1541-4337.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/27/2024] [Accepted: 06/14/2024] [Indexed: 07/30/2024]
Abstract
Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA-based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer-probe pairs used for DNA amplification, for specificity, and (5) makes recommendations for ensuring standardized assay-based reporting for future studies. A total of 313 original assays for the detection and authentication of commercial fish species from 191 primary articles published over the last 23 years were examined. The most explored DNA-based method was real-time polymerase chain reaction (qPCR), followed by DNA sequencing. The most targeted gene regions were cytb (cytochrome b) and COI (cytochrome c oxidase 1). Tuna was the most targeted commercial fish species. A case study of published tuna assays (n = 19) targeting the cytb region found that most assays were not species-specific through in silico testing. This was conducted by examining the primer mismatch for each assay using multiple sequence alignment. Therefore, there is need for more standardized DNA-based assay reporting in the literature to ensure specificity, reproducibility, and reliability of results. Factors, such as cost, sensitivity, quality of the DNA, and species, should be considered when designing assays.
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Affiliation(s)
- Maleeka Singh
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert G Young
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rosalee S Hellberg
- Schmid College of Science and Technology, Food Science Program, Chapman University, Orange, California, USA
| | - Robert H Hanner
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Maria G Corradini
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Arrell Food Institute, University of Guelph, Guelph, Ontario, Canada
| | - Jeffrey M Farber
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada
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Wang Y, Zhang T, Chen Q, Wu Y, Cai Q, Zhao Y, Cen J, Wei Y. Effects of immersion freezing with coolant on the quality of grouper (♀ Epinephelus fuscoguttatus ×♂ Epinephelus lanceolatus) during frozen storage. CYTA - JOURNAL OF FOOD 2021. [DOI: 10.1080/19476337.2021.1946159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yueqi Wang
- Key Lab of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, South China Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Tao Zhang
- Key Lab of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, South China Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Qian Chen
- Key Lab of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, South China Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yanyan Wu
- Key Lab of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, South China Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qiuxing Cai
- Guangxi Colleges and Universities Key Laboratory Development and High-value Utilization of Beibu Gulf Seafood Resources, College of Food Engineering, Beibu Gulf University, Qinzhou, China
| | - Yongqiang Zhao
- Key Lab of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, South China Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jianwei Cen
- Key Lab of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, South China Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Ya Wei
- Key Lab of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, South China Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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Hassanien HA, Al-Rashada Y. Assessment of genetic diversity and phylogenetic relationship among grouper species Epinephelus spp. from the Saudi waters of the Arabian Gulf. Saudi J Biol Sci 2021; 28:1779-1786. [PMID: 33732062 PMCID: PMC7938112 DOI: 10.1016/j.sjbs.2020.12.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/01/2022] Open
Abstract
Understanding of fish genetic characterization plays a vital role in the conservation and utilization of fish genetic resources of grouper species. The present study was carried out to assess the genetic diversity and phylogenetic relationships in five grouper species, Epinephelus spp. from eastern Saudi Arabian coast using two molecular marker systems, inter simple sequence repeat (ISSR) and microsatellite (SSR) markers. In total, 219 individuals grouper specimens (Epinephelus tauvina, E. coioides, E. bleekeri, E. malabaricus, and E. areolatus) were genotyped with 10 ISSR and 11 SSR selected primers. The ISSR produced 94 DNA fragments, of which 44 were polymorphic with an average of 2.13 fragment per primer. While SSR primers generated 107 alleles, all of them were polymorphic with an average 9.72 per primer. ISSR and SSR techniques demonstrated a high level of gene diversity and genetic distances illustrated by UPGMA dendrograms among the grouper species. The results proved that the SSR markers were highly informative and efficient in detecting genetic variability and relationships of the Epinephelus spp.
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Affiliation(s)
- Hesham Abdallah Hassanien
- Aquaculture and Animal Production Department, Agricultural & Food Sciences College, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
- Animal Production Department, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Yousof Al-Rashada
- Aquaculture and Animal Production Department, Agricultural & Food Sciences College, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
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Kotsanopoulos KV, Exadactylos A, Gkafas GA, Martsikalis PV, Parlapani FF, Boziaris IS, Arvanitoyannis IS. The use of molecular markers in the verification of fish and seafood authenticity and the detection of adulteration. Compr Rev Food Sci Food Saf 2021; 20:1584-1654. [PMID: 33586855 DOI: 10.1111/1541-4337.12719] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/17/2020] [Accepted: 01/10/2021] [Indexed: 12/11/2022]
Abstract
The verification of authenticity and detection of food mislabeling are elements that have been of high importance for centuries. During the last few decades there has been an increasing consumer demand for the verification of food identity and the implementation of stricter controls around these matters. Fish and seafood are among the most easily adulterated foodstuffs mainly due to the significant alterations of the species' morphological characteristics that occur during the different types of processing, which render the visual identification of the animals impossible. Even simple processes, such as filleting remove very important morphological elements and suffice to prevent the visual identification of species in marketed products. Novel techniques have therefore been developed that allow identification of species, the differentiation between species and also the differentiation of individuals that belong to the same species but grow in different populations and regions. Molecular markers have been used during the last few decades to fulfill this purpose and several improvements have been implemented rendering their use applicable to a commercial scale. The reliability, accuracy, reproducibility, and time-and cost-effectiveness of these techniques allowed them to be established as routine methods in the industry and research institutes. This review article aims at presenting the most important molecular markers used for the authentication of fish and seafood. The most important techniques are described, and the results of numerous studies are outlined and discussed, allowing interested parties to easily access and compare information about several techniques and fish/seafood species.
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Affiliation(s)
- Konstantinos V Kotsanopoulos
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Athanasios Exadactylos
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - George A Gkafas
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Petros V Martsikalis
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Foteini F Parlapani
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Ioannis S Boziaris
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Ioannis S Arvanitoyannis
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
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DNA-based techniques for seafood species authentication. ADVANCES IN FOOD AND NUTRITION RESEARCH 2020; 95:207-255. [PMID: 33745513 DOI: 10.1016/bs.afnr.2020.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Global trade of seafood has increased in the last decade, leading to significant concerns associated with seafood fraud. Seafood fraud involves the intentional misrepresentation of fish or shellfish for the purpose of economic gain and includes acts such as species substitution, illegal transshipment, overtreatment/short weighting, and mislabeling country of origin or production method. These fraudulent acts have had economic, environmental, and public health consequences on a global level. DNA-based techniques for seafood authentication are utilized by regulatory agencies and can be employed as part of a food fraud risk mitigation plan. This chapter will focus specifically on the use of DNA-based methods for the detection of seafood species substitution. Various methods have been developed for DNA-based species identification of seafood, including polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), species-specific PCR, real-time PCR, Sanger sequencing, microarrays, and high-resolution melting (HRM). Emerging techniques for seafood authentication include droplet digital PCR, isothermal amplification, PCR-enzyme-linked immunosorbent assay (ELISA), and high-throughput or next-generation sequencing. Some of these DNA-based methods target specific species, such as real-time PCR and droplet digital PCR, while other methods allow for simultaneous differentiation of a wide range of fish species, including Sanger sequencing and high-throughput sequencing. This chapter will begin with an introduction on seafood fraud and species substitution, followed by an analysis of the main DNA-based authentication methods and emerging techniques for species identification.
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Wang Q, Wang X, Xie Z, Li Y, Xiao L, Peng C, Zhang H, Li S, Zhang Y, Lin H. Microsatellite analysis of the genetic relationships between wild and cultivated giant grouper in the South China Sea. J Genet 2016; 95:369-76. [PMID: 27350681 DOI: 10.1007/s12041-016-0647-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The giant grouper (Epinephelus lanceolatus) is a coral fish with high commercial value in Southeast Asia. In the present study, we isolated 11 microsatellite DNA markers, and analysed the genetic diversity and differentiation between cultured stocks and wild populations of the giant grouper originating from the South China Sea. A total of 390 alleles at 11 microsatellite loci were detected in 130 individuals from five different populations. The expected heterozygosity varied from 0.131 to 0.855 with a mean value of 0.623 and the observed heterozygosity varied from 0.145 to 0.869 with a mean value of 0.379. The allelic richness and heterozygosity studies revealed that the genetic diversity of the cultured population was significantly reduced when compared with that of the wild population. The Fis, pairwise Fst values, analysis of molecular variance (AMOVA), threedimensional factorial correspondence analysis and structure analysis revealed significant population differentiation between the cultured stocks and the wild populations, among the three cultured populations and between the two wild populations. These differences may be caused by random genetic drift, the effects of artificial selection and founder effects. Our results will be useful in the management of cultured stocks and conservation of wild populations of the giant grouper.
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Affiliation(s)
- Qing Wang
- 1State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China.
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Delamare-Deboutteville J, Bowater R, Condon K, Reynolds A, Fisk A, Aviles F, Barnes AC. Infection and pathology in Queensland grouper, Epinephelus lanceolatus, (Bloch), caused by exposure to Streptococcus agalactiae via different routes. JOURNAL OF FISH DISEASES 2015; 38:1021-1035. [PMID: 25117665 DOI: 10.1111/jfd.12273] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 06/03/2014] [Accepted: 06/25/2014] [Indexed: 06/03/2023]
Abstract
Since 2007, 96 wild Queensland groupers, Epinephelus lanceolatus, (Bloch), have been found dead in NE Australia. In some cases, Streptococcus agalactiae (Group B Streptococcus, GBS) was isolated. At present, a GBS isolate from a wild grouper case was employed in experimental challenge trials in hatchery-reared Queensland grouper by different routes of exposure. Injection resulted in rapid development of clinical signs including bilateral exophthalmia, hyperaemic skin or fins and abnormal swimming. Death occurred in, and GBS was re-isolated from, 98% fish injected and was detected by PCR in brain, head kidney and spleen from all fish, regardless of challenge dose. Challenge by immersion resulted in lower morbidity with a clear dose response. Whilst infection was established via oral challenge by admixture with feed, no mortality occurred. Histology showed pathology consistent with GBS infection in organs examined from all injected fish, from fish challenged with medium and high doses by immersion, and from high-dose oral challenge. These experimental challenges demonstrated that GBS isolated from wild Queensland grouper reproduced disease in experimentally challenged fish and resulted in pathology that was consistent with that seen in wild Queensland grouper infected with S. agalactiae.
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Affiliation(s)
- J Delamare-Deboutteville
- School of Biological Sciences and Centre for Marine Science, The University of Queensland, Brisbane, Qld, Australia
| | - R Bowater
- Biosecurity Queensland, Department of Agriculture Fisheries & Forestry, Townsville, Qld, Australia
| | - K Condon
- Biosecurity Queensland, Department of Agriculture Fisheries & Forestry, Townsville, Qld, Australia
| | - A Reynolds
- Northern Fisheries Centre (NFC), Department of Agriculture Fisheries & Forestry, Cairns, Qld, Australia
| | - A Fisk
- Biosecurity Queensland, Department of Agriculture Fisheries & Forestry, Townsville, Qld, Australia
| | - F Aviles
- School of Biological Sciences and Centre for Marine Science, The University of Queensland, Brisbane, Qld, Australia
| | - A C Barnes
- School of Biological Sciences and Centre for Marine Science, The University of Queensland, Brisbane, Qld, Australia
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Xu K, Feng J, Ma X, Wang X, Zhou D, Dai Z. Identification of tuna species (Thunnini tribe) by PCR-RFLP analysis of mitochondrial DNA fragments. FOOD AGR IMMUNOL 2015. [DOI: 10.1080/09540105.2015.1086978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Genetic diversity of ivory shell (Babylonia areolata) in Taiwan and identification of species using DNA-based assays. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.05.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Galal-Khallaf A, Ardura A, Mohammed-Geba K, Borrell YJ, Garcia-Vazquez E. DNA barcoding reveals a high level of mislabeling in Egyptian fish fillets. Food Control 2014. [DOI: 10.1016/j.foodcont.2014.06.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Veneza I, Felipe B, Oliveira J, Silva R, Sampaio I, Schneider H, Gomes G. A barcode for the authentication of the snappers (Lutjanidae) of the western Atlantic: rDNA 5S or mitochondrial COI? Food Control 2014. [DOI: 10.1016/j.foodcont.2013.10.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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