1
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Najd-Hassan-Bonab L, Hedayati M, Shahzadeh Fazeli SA, Daneshpour MS. An optimized method for PCR-based genotyping to detect human APOE polymorphisms. Heliyon 2023; 9:e21102. [PMID: 37954297 PMCID: PMC10637921 DOI: 10.1016/j.heliyon.2023.e21102] [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: 06/13/2023] [Revised: 09/10/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
Background Apolipoprotein E (APOE) is one of the most polymorphic genes at two single nucleotides (rs429358 and rs7412). The various isoforms of APOE have been associated with a variety of diseases, including neurodegenerative, type 2 diabetes, etc. Hence, predicting the APOE genotyping is critical for disease risk evaluation. The purpose of this study was to optimize the tetra amplification refractory mutation system (Tetra-ARMS) PCR method for the detection of APOE mutations. Material and methods Here, in our optimized Tetra-ARMS PCR method, different factors like cycle conditions, using HiFidelity enzyme instead of Taq polymerase and setting its best concentration, and the lack of using dimethylsulfoxide (DMSO) for amplifying the GC-regions were set up for all primer pairs. The sensitivity and accuracy were tested. For validation of the assay, the results were compared with known genotypes for the APOE gene that were previously obtained by two independent methods, RFLP and Chip-typing. Results Successful Tetra-ARMS PCR and genotyping are influenced by multiple factors. Our developed method enabled us to amplify the DNA fragment by 25 cycles without adding any hazardous reagent, like DMSO. Our findings showed 100 % accuracy and sensitivity of the optimized Tetra-ARMS PCR while both criteria were 95 % for RFLP and 100 % for the chip-typing method. In addition, our results showed 91 % and 100 % consistency with RFLP and chip typing methods, respectively. Conclusions Our current method is a simple and accurate approach for detecting APOE polymorphisms within a large sample size in a short time and can be performed even in low-tech laboratories.
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Affiliation(s)
- Leila Najd-Hassan-Bonab
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Abolhassan Shahzadeh Fazeli
- Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Maryam S. Daneshpour
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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2
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Carvalho J, Yadav S, Garrido-Maestu A, Azinheiro S, Trujillo I, Barros-Velázquez J, Prado M. Evaluation of simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)-based methods in olive varieties from the Northwest of Spain and potential for miniaturization. FOOD CHEMISTRY: MOLECULAR SCIENCES 2021; 3:100038. [PMID: 35415648 PMCID: PMC8991621 DOI: 10.1016/j.fochms.2021.100038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 07/10/2021] [Accepted: 07/31/2021] [Indexed: 11/17/2022]
Abstract
SSR- and SNP-based methods were evaluated for the identification of olive varieties. SNP identification was performed for the first time for two autochthonous varieties. The potential for future miniaturization of the genotyping methods was evaluated. Allele-specific PCR provided the best results for the tested olive varieties.
Miniaturization of DNA-based techniques can bring interesting advantages for food analysis, such as portability of complex analytical procedures. In the olive oil industry, miniaturization can be particularly interesting for authenticity and traceability applications, through in situ control of raw materials before production and/or the final products. However, variety identification is challenging, and implementation on miniaturized settings must be carefully evaluated, starting from the selected analytical approach. In this work, SSR- and SNP-based genotyping strategies were investigated for the identification and differentiation of two olive varieties from the Northwest of Spain. For the selected SNPs two genotyping methods were tested: real-time allele-specific PCR and high resolution melting analysis. These methods were compared and evaluated regarding their potential for integration in a microfluidic device. Both SNP-based methods proved to be successful for identification of the selected varieties, however real-time allele-specific PCR was the one that achieved the best results when analyzing mixtures, allowing the identification of both monovarietal samples and mixtures of the varieties tested with up to 25%.
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3
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Dimitrakopoulou ME, Vantarakis A. Does Traceability Lead to Food Authentication? A Systematic Review from A European Perspective. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1923028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Apostolos Vantarakis
- Department of Public Health, Medical School, University of Patras, Patras, Greece
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4
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Kafantaris I, Amoutzias GD, Mossialos D. Foodomics in bee product research: a systematic literature review. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03634-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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5
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Batrinou A, Strati IF, Houhoula D, Tsaknis J, Sinanoglou VJ. Authentication of olive oil based on DNA analysis. GRASAS Y ACEITES 2020. [DOI: 10.3989/gya.0682191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Olive oil, which has been produced mainly in the Mediterranean area since the ancient times, has a high nutritional value linked to many health benefits. Extra virgin, which is the purest form of olive oil, has excellent quality and premium prices. Many cases of adulteration and fraud necessitate the development of reliable and accurate methods for olive oil authentication. DNA-based methods analyze the residual DNA extracted from olive oil and use molecular markers for genetic identification of different species, subspecies or cultivars because these markers act as signs which reflect distinct genetic profiles. This study reviews the process by which DNA from olive oil is extracted and analyzed by the most recently used markers in the authentication of olive oil, such as Simple Sequence Repeats (SSR) or microsatellites and the single nucleotide polymorphisms (SNPs). Methods of analysis such as qPCR and digital PCR are also discussed with a special emphasis placed on the method of High-Resolution Melting (HRM), a post-polymerase chain reaction method, which enables rapid, high performing identification of genetic variants in the DNA regions of interest without sequencing, and may differentiate very similar cultivars which differ in only one nucleotide in a specific locus.
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6
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Chedid E, Rizou M, Kalaitzis P. Application of high resolution melting combined with DNA-based markers for quantitative analysis of olive oil authenticity and adulteration. Food Chem X 2020; 6:100082. [PMID: 32154510 PMCID: PMC7058896 DOI: 10.1016/j.fochx.2020.100082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023] Open
Abstract
A plethora of biotechnological methodologies is used to authenticate quality olive oils. Among the DNA-based approaches, SNPs and SSRs combined with high resolution melting (HRM) provide certain advantages such as speed, simplicity and reliability. SNP-HRM and SSR-HRM were used for the authentication of monovarietal olive oils as well as the quantification of varietal composition in olive oil DNA admixtures and olive oil blends of two different cultivars. The SSR-HRM was more efficient in distinguishing monovarietal olive oils while the SNP-HRM assay was more reliable in discriminating olive oil blends. HRM was also used for the detection of adulteration of olive oil with oils of different plant origin by using plastid trnL indels and SNPs. The trnL-indels-HRM showed higher discrimination power than the trnL-SNP-HRM in determining adulteration in olive oil. These results indicate that traceability of adulteration might be more reliable than authentication of the varietal origin in olive oil blends.
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Affiliation(s)
| | | | - Panagiotis Kalaitzis
- Department of Horticultural Genetics & Biotechnology, Mediterranean Agronomic Institute of Chania, Crete, Greece
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7
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Kyriakopoulou CI, Kalogianni DP. Genetic Identification of the Wild Form of Olive ( Olea Europaea var. Sylvestris) Using Allele-Specific Real-Time PCR. Foods 2020; 9:foods9040467. [PMID: 32283713 PMCID: PMC7230518 DOI: 10.3390/foods9040467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 02/05/2023] Open
Abstract
The wild-type of olive tree, Olea europaea var Sylvestris or oleaster, is the ancestor of the cultivated olive tree. Wild-type olive oil is considered to be more nutritious with increased antioxidant activity compared to the common cultivated type (Olea europaea L. var Europaea). This has led to the wild-type of olive oil having a much higher financial value. Thus, wild olive oil is one of the most susceptible agricultural food products to adulteration with other olive oils of lower nutritional and economical value. As cultivated and wild-type olives have similar phenotypes, there is a need to establish analytical methods to distinguish the two plant species. In this work, a new method has been developed which is able to distinguish Olea europaea var Sylvestris (wild-type olive) from Olea europaea L. var Europaea (cultivated olive). The method is based, for the first time, on the genotyping, by allele-specific, real-time PCR, of a single nucleotide polymorphism (SNP) present in the two olives’ chloroplastic genomes. With the proposed method, we were able to detect as little as 1% content of the wild-type olive in binary DNA mixtures of the two olive species.
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8
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Oliinyk B, Isaieva K, Manilov AI, Nychyporuk T, Geloen A, Joffre F, Skryshevsky VA, Litvinenko SV, Lysenko V. Silicon-Based Optoelectronic Tongue for Label-Free and Nonspecific Recognition of Vegetable Oils. ACS OMEGA 2020; 5:5638-5642. [PMID: 32226839 PMCID: PMC7097904 DOI: 10.1021/acsomega.9b03196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/24/2020] [Indexed: 05/08/2023]
Abstract
A special electronic tongue system based on photoelectric measurements on Si-Si/SiN X sensitive structures is reported. The sensing approach is based on measuring of minority carrier lifetime in silicon-based substrates using microwave-detected photoconductance decay. This inexpensive and environmentally friendly combinatorial electronic sensing platform is able to create characteristic electronic fingerprints of liquids, detect, and recognize them. In particular, an application of the optoelectronic tongue for recognition of vegetable oils and their mixtures is described.
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Affiliation(s)
- Bohdan
V. Oliinyk
- Institute
of Analytical Sciences (ISA), UMR CNRS 5280,
UCBL, University of Lyon, 69100 Villeurbanne, France
- OlisensTech, 5, Place
Maréchal Lyautey, 69006 Lyon, France
| | - Karyna Isaieva
- IADI,
Université de Lorraine, INSERM U1254, Nancy F-54000, France
| | - Anton I. Manilov
- Institute
of High Technologies, Taras Shevchenko National
University of Kyiv, 01033 Kyiv, Ukraine
- Corporation
Science Park Taras Shevchenko University of Kyiv, 01033 Kyiv, Ukraine
| | - Tetyana Nychyporuk
- Nanotechnology
Institute of Lyon (INL), UMR CNRS 5270,
INSA de Lyon, University of Lyon, 69621 Lyon, France
| | - Alain Geloen
- CarMeN
Laboratory, INRA UMR1397, INSERM U1060,
INSA de Lyon, IMBL, University of Lyon, 69621 Lyon, France
| | | | - Valeriy A. Skryshevsky
- Institute
of High Technologies, Taras Shevchenko National
University of Kyiv, 01033 Kyiv, Ukraine
- Corporation
Science Park Taras Shevchenko University of Kyiv, 01033 Kyiv, Ukraine
| | - Sergii V. Litvinenko
- Institute
of High Technologies, Taras Shevchenko National
University of Kyiv, 01033 Kyiv, Ukraine
- Corporation
Science Park Taras Shevchenko University of Kyiv, 01033 Kyiv, Ukraine
| | - Vladimir Lysenko
- Light-Matter
Institute (ILM), UMR CNRS 5306, University
of Lyon (UCBL), 69622 Lyon, France
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9
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Li D, Long C, Pang X, Ning D, Wu T, Dong M, Han X, Guo H. The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions. PeerJ 2020; 8:e8573. [PMID: 32095373 PMCID: PMC7024576 DOI: 10.7717/peerj.8573] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/15/2020] [Indexed: 12/30/2022] Open
Abstract
Background Olive (Olea europaea L.) is an important oil and fruit crop worldwide, owning a rich germplasm with a large number of cultivars. Simple sequence repeats (SSRs) are excellent markers and have been used for the identification of olive cultivars. However, the limited number of SSR markers and the occurrence of confusion on the names of cultivars, as well as the possible appearance of clonal variation make it difficult to identify cultivars and interpret relationships among olive cultivars. Method SSR markers were designed based on trinucleotide repeat sequences by screening the whole genome of olive, and the polymorphic SSR markers were developed that were applied to the identification of 53 olive accessions. The genetic characteristics and relationships of these olive accessions were evaluated based on the developed SSR markers. Results Twenty-one highly polymorphic genomic-SSR markers were developed, covering most chromosomes of olive. These SSR markers could well distinguish all 53 olive accessions, confirming their effectiveness. DNA fingerprints of the 53 olive accessions were constructed based on the 21 SSR markers. The dendrogram clearly divided the tested accessions into two main groups, which was also supported by the results of principal coordinate analysis. A total of 31 private alleles were detected in 15 olive accessions, which reflected the genetic diversity within 53 olive accessions to some extent. Six homonymy cases were also clarified by genetic analysis. These results suggest that the newly developed olive SSR markers are informative for the exploitation, preservation and breeding of olive.
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Affiliation(s)
- Danyang Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Cui Long
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Delu Ning
- Yunnan Academy of Forestry and Grassland, Kunming, Yunnan, China
| | - Tao Wu
- Yunnan Academy of Forestry and Grassland, Kunming, Yunnan, China
| | - Mingliang Dong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaoning Han
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Huihong Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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10
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Espunyes J, Espunya C, Chaves S, Calleja JA, Bartolomé J, Serrano E. Comparing the accuracy of PCR-capillary electrophoresis and cuticle microhistological analysis for assessing diet composition in ungulates: A case study with Pyrenean chamois. PLoS One 2019; 14:e0216345. [PMID: 31116750 PMCID: PMC6530829 DOI: 10.1371/journal.pone.0216345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/18/2019] [Indexed: 11/18/2022] Open
Abstract
The study of diet composition is required to understand the interactions between animal and plant ecosystems. Different non-invasive techniques applied on faecal samples have commonly been used for such purposes, with cuticle microhistological analysis (CMA) and emerging DNA-based methods being the most relevant. In this work, we refined and optimized a qualitative DNA-based approach combining PCR amplification of long trnL(UAA) and ITS2 fragments and capillary electrophoresis (PCR-CE), instead of short trnL(UAA) fragments and massive sequencing technologies commonly reported. To do so, we developed a controlled diet assay using a stabled Pyrenean chamois specimen (Rupicapra pyrenaica pyrenaica), which included representative herbaceous and shrubby plant species. We also assessed the impact of sample freshness on the diet determination of this mountain caprinae by exposing faecal samples to the outdoor environment for three weeks. Faecal samples from both experiments were analysed by qualitative PCR-CE and semi-quantitative CMA in order to compare the pros and cons of both approaches. Our results show that all of the offered plant species were detected by both methodologies although CMA over-detected shrubs compared to herbaceous species. At the same time, sample degradation due to sustained climate exposure is a limiting factor for molecular analysis, but not for CMA. Taken all together, our results suggest that the qualitative information obtained by CMA and PCR-CE can be interchangeable when faecal samples are fresh (less than one week after deposition) but, afterwards, molecular analysis underestimates diet composition probably due to DNA degradation. CMA, however, can accurately be used at least three weeks after defecation. Moreover, by combining the results of simultaneous PCR amplification of two complementary genes, this optimized PCR-CE methodology provides a reliable, feasible and more affordable alternative for multiple and routine analyses of complex samples. Neither CMA nor PCR-CE seems to solve comprehensively the quatification of herbivore diets and thus further research needs to be done.
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Affiliation(s)
- Johan Espunyes
- Wildlife Ecology & Health Group (WE&H) and Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i de Cirurgia Animals, Universitat Autònoma de Barcelona UAB, Bellaterra, Spain
| | - Carme Espunya
- Departament de Bioquímica i de Biologia Molecular, UAB, Bellaterra, Spain
| | - Sara Chaves
- Wildlife Ecology & Health Group (WE&H) and Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i de Cirurgia Animals, Universitat Autònoma de Barcelona UAB, Bellaterra, Spain
| | - Juan Antonio Calleja
- Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), Cerdanyola del Vallès, Spain
| | - Jordi Bartolomé
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, UAB, Bellaterra, Spain
| | - Emmanuel Serrano
- Wildlife Ecology & Health Group (WE&H) and Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i de Cirurgia Animals, Universitat Autònoma de Barcelona UAB, Bellaterra, Spain
- Dipartimento di Scienze Veterinarie, Universitá di Torino, Grugliasco, Torino, Italy
- * E-mail:
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11
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Agrimonti C, Marmiroli N. Food Genomics for the Characterization of PDO and PGI Virgin Olive Oils. EUR J LIPID SCI TECH 2018. [DOI: 10.1002/ejlt.201800132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Caterina Agrimonti
- Department of Chemistry, Life Sciences and Environmental Sustainability. University of Parmav.le Parco Area delle Scienze 11/A43124 ParmaItaly
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability. University of Parmav.le Parco Area delle Scienze 11/A43124 ParmaItaly
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12
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Jung MJ, Kim MS, Yun JH, Lee JY, Kim PS, Lee HW, Ha JH, Roh SW, Bae JW. Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community. Food Microbiol 2018; 76:319-327. [DOI: 10.1016/j.fm.2018.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022]
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13
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Nenadis N, Mastralexi A, Tsimidou MZ. Physicochemical Characteristics and Antioxidant Potential of the Greek PDO and PGI Virgin Olive Oils (VOOs). EUR J LIPID SCI TECH 2018. [DOI: 10.1002/ejlt.201800172] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Nikolaos Nenadis
- Laboratory of Food Chemistry and Technology; School of Chemistry; Aristotle University of Thessaloniki (AUTH); 541 24 Thessaloniki Greece
| | - Aspasia Mastralexi
- Laboratory of Food Chemistry and Technology; School of Chemistry; Aristotle University of Thessaloniki (AUTH); 541 24 Thessaloniki Greece
| | - Maria Z. Tsimidou
- Laboratory of Food Chemistry and Technology; School of Chemistry; Aristotle University of Thessaloniki (AUTH); 541 24 Thessaloniki Greece
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14
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Uncu AO, Torlak E, Uncu AT. A Cost-Efficient and Simple Plant Oil DNA Extraction Protocol Optimized for DNA-Based Assessment of Product Authenticity. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-1070-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Lian DS, Zeng HS. Capillary Electrophoresis Based on Nucleic Acid Detection as Used in Food Analysis. Compr Rev Food Sci Food Saf 2017; 16:1281-1295. [DOI: 10.1111/1541-4337.12297] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Dong-Sheng Lian
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
| | - Hua-Song Zeng
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
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16
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Sebastiani L, Busconi M. Recent developments in olive (Olea europaea L.) genetics and genomics: applications in taxonomy, varietal identification, traceability and breeding. PLANT CELL REPORTS 2017; 36:1345-1360. [PMID: 28434019 DOI: 10.1007/s00299-017-2145-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/17/2017] [Indexed: 05/20/2023]
Abstract
The latest results in DNA markers application and genomic studies in olive. Olive (Olea europaea L.) is among the most ancient tree crops worldwide and the source of oil beneficial for human health. Despite this, few data on olive genetics are available in comparison with other cultivated plant species. Molecular information is mainly linked to molecular markers and their application to the study of DNA variation in the Olea europaea complex. In terms of genomic research, efforts have been made in sequencing, heralding the era of olive genomic. The present paper represents an update of a previous review work published in this journal in 2011. The review is again mainly focused on DNA markers, whose application still constitutes a relevant percentage of the most recently published researches. Since the olive genomic era has recently started, the latest results in this field are also being discussed.
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Affiliation(s)
- L Sebastiani
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33, 56127, Pisa, Italy.
| | - M Busconi
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
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17
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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. PLoS Genet 2017; 13:e1006960. [PMID: 28934201 PMCID: PMC5608170 DOI: 10.1371/journal.pgen.1006960] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipe Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Veronica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Angel Carracedo
- Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
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18
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Kalaitzis P, El-Zein Z. Olive oil authentication, traceability and adulteration detection using DNA-based approaches. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/lite.201600048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Panagiotis Kalaitzis
- Department of Horticultural Genetics & Biotechnology; Mediterranean Agronomic Institute of Chania; Chania Crete Greece
| | - Zeina El-Zein
- Department of Horticultural Genetics & Biotechnology; Mediterranean Agronomic Institute of Chania; Chania Crete Greece
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19
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Fang W, Meinhardt LW, Tan H, Zhou L, Mischke S, Wang X, Zhang D. Identification of the varietal origin of processed loose-leaf tea based on analysis of a single leaf by SNP nanofluidic array. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Pasqualone A, Montemurro C, di Rienzo V, Summo C, Paradiso VM, Caponio F. Evolution and perspectives of cultivar identification and traceability from tree to oil and table olives by means of DNA markers. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:3642-3657. [PMID: 26991131 DOI: 10.1002/jsfa.7711] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/21/2016] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
Abstract
In recent years, an increasing number of typicality marks has been awarded to high-quality olive oils produced from local cultivars. In this case, quality control requires effective varietal checks of the starting materials. Moreover, accurate cultivar identification is essential in vegetative-propagated plants distributed by nurseries and is a pre-requisite to register new cultivars. Food genomics provides many tools for cultivar identification and traceability from tree to oil and table olives. The results of the application of different classes of DNA markers to olive with the purpose of checking cultivar identity and variability of plant material are extensively discussed in this review, with special regard to repeatability issues and polymorphism degree. The characterization of olive germplasm from all countries of the Mediterranean basin and from less studied geographical areas is described and innovative high-throughput molecular tools to manage reference collections are reviewed. Then the transferability of DNA markers to processed products - virgin olive oils and table olives - is overviewed to point out strengths and weaknesses, with special regard to (i) the influence of processing steps and storage time on the quantity and quality of residual DNA, (ii) recent advances to overcome the bottleneck of DNA extraction from processed products, (iii) factors affecting whole comparability of DNA profiles between fresh plant materials and end-products, (iv) drawbacks in the analysis of multi-cultivar versus single-cultivar end-products and (v) the potential of quantitative polymerase chain reaction (PCR)-based techniques. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Antonella Pasqualone
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Valentina di Rienzo
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Carmine Summo
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Vito Michele Paradiso
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Francesco Caponio
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
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21
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Vidal C, Li J, Fulton R, Fernando S. A polymorphism within the psoriasis susceptibility 1 candidate 1 (PSORS1C1) gene is not linked to HLA-B*58:01 in an Australian cohort. Drug Metab Pharmacokinet 2016; 31:252-5. [DOI: 10.1016/j.dmpk.2015.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/21/2015] [Accepted: 08/23/2015] [Indexed: 02/02/2023]
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22
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Bazakos C, Khanfir E, Aoun M, Spano T, Zein ZE, Chalak L, Riachy ME, Abou-Sleymane G, Ali SB, Grati Kammoun N, Kalaitzis P. The potential of SNP-based PCR-RFLP capillary electrophoresis analysis to authenticate and detect admixtures of Mediterranean olive oils. Electrophoresis 2016; 37:1881-90. [DOI: 10.1002/elps.201500537] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 01/12/2016] [Accepted: 01/27/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Christos Bazakos
- Department of Horticultural Genetics & Biotechnology; Mediterranean Agronomic Institute of Chania; Chania Crete Greece
| | - Emna Khanfir
- Department of Horticultural Genetics & Biotechnology; Mediterranean Agronomic Institute of Chania; Chania Crete Greece
| | - Mariem Aoun
- Department of Horticultural Genetics & Biotechnology; Mediterranean Agronomic Institute of Chania; Chania Crete Greece
| | - Thodhoraq Spano
- Department of Horticultural Genetics & Biotechnology; Mediterranean Agronomic Institute of Chania; Chania Crete Greece
| | - Zeina El Zein
- Department of Horticultural Genetics & Biotechnology; Mediterranean Agronomic Institute of Chania; Chania Crete Greece
| | - Lamis Chalak
- Faculty of Agronomy; Lebanese University; Dekwaneh Beirut Lebanon
| | - Milad El Riachy
- Department of Olive and Olive Oil; Lebanese Agricultural Research Institute; Tal Amara Zahle
| | - Gretta Abou-Sleymane
- Department of Laboratory Science and Technology; American University of Science and Technology; Ashrafieh Lebanon
| | | | | | - Panagiotis Kalaitzis
- Department of Horticultural Genetics & Biotechnology; Mediterranean Agronomic Institute of Chania; Chania Crete Greece
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23
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Sensory intensity assessment of olive oils using an electronic tongue. Talanta 2016; 146:585-93. [DOI: 10.1016/j.talanta.2015.08.071] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/28/2015] [Accepted: 08/30/2015] [Indexed: 11/22/2022]
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24
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Arhondakis S, Bita CE, Perrakis A, Manioudaki ME, Krokida A, Kaloudas D, Kalaitzis P. In silico Transcriptional Regulatory Networks Involved in Tomato Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2016; 7:1234. [PMID: 27625653 PMCID: PMC5003879 DOI: 10.3389/fpls.2016.01234] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 08/03/2016] [Indexed: 05/18/2023]
Abstract
Tomato fruit ripening is a complex developmental programme partly mediated by transcriptional regulatory networks. Several transcription factors (TFs) which are members of gene families such as MADS-box and ERF were shown to play a significant role in ripening through interconnections into an intricate network. The accumulation of large datasets of expression profiles corresponding to different stages of tomato fruit ripening and the availability of bioinformatics tools for their analysis provide an opportunity to identify TFs which might regulate gene clusters with similar co-expression patterns. We identified two TFs, a SlWRKY22-like and a SlER24 transcriptional activator which were shown to regulate modules by using the LeMoNe algorithm for the analysis of our microarray datasets representing four stages of fruit ripening, breaker, turning, pink and red ripe. The WRKY22-like module comprised a subgroup of six various calcium sensing transcripts with similar to the TF expression patterns according to real time PCR validation. A promoter motif search identified a cis acting element, the W-box, recognized by WRKY TFs that was present in the promoter region of all six calcium sensing genes. Moreover, publicly available microarray datasets of similar ripening stages were also analyzed with LeMoNe resulting in TFs such as SlERF.E1, SlERF.C1, SlERF.B2, SLERF.A2, SlWRKY24, SLWRKY37, and MADS-box/TM29 which might also play an important role in regulation of ripening. These results suggest that the SlWRKY22-like might be involved in the coordinated regulation of expression of the six calcium sensing genes. Conclusively the LeMoNe tool might lead to the identification of putative TF targets for further physiological analysis as regulators of tomato fruit ripening.
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25
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Monovarietal extra-virgin olive oil classification: a fusion of human sensory attributes and an electronic tongue. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2537-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Kalogianni DP, Bazakos C, Boutsika LM, Targem MB, Christopoulos TK, Kalaitzis P, Ioannou PC. Olive oil DNA fingerprinting by multiplex SNP genotyping on fluorescent microspheres. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3121-8. [PMID: 25754746 DOI: 10.1021/jf5054657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Olive oil cultivar verification is of primary importance for the competitiveness of the product and the protection of consumers and producers from fraudulence. Single-nucleotide polymorphisms (SNPs) have emerged as excellent DNA markers for authenticity testing. This paper reports the first multiplex SNP genotyping assay for olive oil cultivar identification that is performed on a suspension of fluorescence-encoded microspheres. Up to 100 sets of microspheres, with unique "fluorescence signatures", are available. Allele discrimination was accomplished by primer extension reaction. The reaction products were captured via hybridization on the microspheres and analyzed, within seconds, by a flow cytometer. The "fluorescence signature" of each microsphere is assigned to a specific allele, whereas the signal from a reporter fluorophore denotes the presence of the allele. As a model, a panel of three SNPs was chosen that enabled identification of five common Greek olive cultivars (Adramytini, Chondrolia Chalkidikis, Kalamon, Koroneiki, and Valanolia).
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Affiliation(s)
| | - Christos Bazakos
- §Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute, Chania (MAICh), Chania, Crete, Greece 73100
| | | | - Mehdi Ben Targem
- §Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute, Chania (MAICh), Chania, Crete, Greece 73100
| | | | - Panagiotis Kalaitzis
- §Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute, Chania (MAICh), Chania, Crete, Greece 73100
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27
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Jaczó Z, Pál E, Dénes R, Somogyi A, Sasvári-Székely M, Guttman A, Rónai Z. Rapid analysis of colipase gene variants by multicapillary electrophoresis. Electrophoresis 2015; 36:1237-43. [DOI: 10.1002/elps.201400551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Zsuzsanna Jaczó
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
| | - Eszter Pál
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
| | - Réka Dénes
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
| | - Anikó Somogyi
- 2 Department of Internal Medicine; Semmelweis University; Budapest Hungary
| | - Mária Sasvári-Székely
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
| | - András Guttman
- Horváth Laboratory of Bioseparation Sciences; University of Debrecen; Debrecen Hungary
- MTA-PE Translational Glycomics Group; University of Pannonia; Veszprém Hungary
| | - Zsolt Rónai
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
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28
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Uncu AT, Frary A, Doganlar S. Cultivar origin and admixture detection in Turkish olive oils by SNP-based CAPS assays. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:2284-95. [PMID: 25673069 DOI: 10.1021/acs.jafc.5b00090] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The aim of this study was to establish a DNA-based identification key to ascertain the cultivar origin of Turkish monovarietal olive oils. To reach this aim, we sequenced short fragments from five olive genes for SNP (single nucleotide polymorphism) identification and developed CAPS (cleaved amplified polymorphic DNA) assays for SNPs that alter restriction enzyme recognition motifs. When applied on the oils of 17 olive cultivars, a maximum of five CAPS assays were necessary to discriminate the varietal origin of the samples. We also tested the efficiency and limit of our approach for detecting olive oil admixtures. As a result of the analysis, we were able to detect admixing down to a limit of 20%. The SNP-based CAPS assays developed in this work can be used for testing and verification of the authenticity of Turkish monovarietal olive oils, for olive tree certification, and in germplasm characterization and preservation studies.
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Affiliation(s)
- Ali Tevfik Uncu
- Department of Molecular Biology & Genetics, Izmir Institute of Technology , Urla, Izmir 35430, Turkey
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29
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Single-cultivar extra virgin olive oil classification using a potentiometric electronic tongue. Food Chem 2014; 160:321-9. [DOI: 10.1016/j.foodchem.2014.03.072] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/04/2014] [Accepted: 03/12/2014] [Indexed: 11/30/2022]
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30
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Development of a method to recovery and amplification DNA by real-time PCR from commercial vegetable oils. Food Chem 2014; 158:374-83. [PMID: 24731357 DOI: 10.1016/j.foodchem.2014.02.142] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 02/07/2014] [Accepted: 02/18/2014] [Indexed: 11/22/2022]
Abstract
This study describes the design of a suitable DNA isolation method from commercial vegetable oils for the application of DNA markers for food safety and traceability. Firstly, a comparative study was made of eight methods for the recovery of high quality DNA from olive, sunflower and palm oils, and a CTAB-based method was selected. In order to optimize this method, the effect of the organic compounds and several components in the lysis buffer and the lysis and precipitation time were evaluated. For the purpose of overcoming the limitations detected in spectrophotometric and PCR DNA yield evaluations, the performance of the extraction protocols during the optimization processes was evaluated using qPCR. The suggested DNA extraction optimized is less time consuming than other conventional DNA extraction methods, uses a reduced oil volume and is cheaper than available commercial kits. Additionally, the applicability of this method has been successfully assayed in ten commercial vegetable oils and derivatives.
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31
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Kim JY, Lee SM, Chang MI, Cho YJ, Chae YS. Discrimination of vegetable oils by stable carbon isotope ratio and fatty acid composition. ANALYTICAL SCIENCE AND TECHNOLOGY 2014. [DOI: 10.5806/ast.2014.27.1.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Riahi L, Ayari B, Zoghlami N, Dereeper A, Laucou V, Mliki A, This P. High efficiency and informativeness of a set of SNP molecular markers in Tunisian local grapevines discrimination. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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33
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Monasterio RP, Fernández MDLÁ, Silva MF. Olive oil by capillary electrophoresis: characterization and genuineness. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:4477-4496. [PMID: 23594110 DOI: 10.1021/jf400864q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Olive oil, obtained from Olea europaea L. (Oleaceae) fruits, is an important ingredient in the Mediterranean diet. The purpose of this paper is to review and evaluate olive oil analysis using capillary electrophoresis (CE). This review covers a selection of the literature published on this topic over the past decade. The current state of the art of the topic is evaluated, with special emphasis on separation conditions, analysis purpose, and analytes investigated. CE has been used to characterize or to carry out authenticity studies. Particular attention has been focused on the botanical origin because high-quality monovarietal olive oils have been recently introduced on the markets and their quality control requires the development of new and powerful analytical tools as well as new regulations to avoid fraud. CE represents a good compromise between sample throughput, sample volume, satisfactory characterization, and sustainability for the analysis of target compounds present in olive oils.
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Affiliation(s)
- Romina P Monasterio
- Instituto de Biologı́a Agrícola de Mendoza (IBAM-CONICET), Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Mendoza, Argentina
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