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Hwang EM, Jeong KS, Yoo SY, Kim J, Choe S, Kim JY. Development of a diagnostic variable number tandem repeat marker and dual TaqMan genotyping assay to distinguish Lophophora species. Int J Legal Med 2024:10.1007/s00414-024-03318-9. [PMID: 39190119 DOI: 10.1007/s00414-024-03318-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
The Lophophora genus of the Cactaceae family includes Lophophora diffusa and Lophophora williamsii, which has traditionally been used as a natural analgesic; however, its use is now under strict regulation worldwide as it contains mescaline, a unique psychotropic agent. Recently, non-medical and illegal distribution and abuse of L. williamsii have increased worldwide; thus, effective species identification methods are urgently needed. Here, we identified a new variable number tandem repeat (VNTR) marker in the trnL intron region to identify and characterize species in forensic analyses. The VNTR marker has a unique structure of tandem repeats, each with 13 nucleotides; one repeat unit was found in L. williamsii and two in L. diffusa. Phylogenetic and length polymorphism analyses confirmed that this novel VNTR marker could distinguish between Lophophora species. Furthermore, our newly developed TaqMan genotyping assay utilizes two probes; the color and position of dots on the discrimination plot differ according to the tandem repeat count within the VNTR marker. The limits of detection of the assay were 0.000063 ng (LW-VNTR probe-1) and 0.000066 ng (LW-VNTR probe-2), indicating high sensitivity. Moreover, when crime scene samples of 16 presumed L. williamsii species were analyzed, the results coincided with those of gas chromatography-mass spectrometry, confirming the applicability of our marker for Lophophora species identification. Thus, the tandem repeats within the trnL intron region can be exploited as a VNTR marker to identify L. williamsii and L. diffusa. Our dual TaqMan genotyping assay based on a novel marker demonstrates potential for forensic applications.
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Affiliation(s)
- Eun-Mi Hwang
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Kyu-Sik Jeong
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Seong Yeon Yoo
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Jihyun Kim
- Forensic Toxicology and Chemistry Division, Seoul Institute, National Forensic Service, Seoul, 08036, Republic of Korea
| | - Sanggil Choe
- Forensic Toxicology Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Joo-Young Kim
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea.
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Kaňuková Š, Ondreičková K, Mihálik D, Kraic J. New Set of EST-STR Markers for Discrimination of Related Papaver somniferum L. Varieties. Life (Basel) 2023; 14:72. [PMID: 38255686 PMCID: PMC10820365 DOI: 10.3390/life14010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Papaver somniferum L. is cultivated for its edible seeds and for the production of alkaloids. A serious problem in seed trade and processing is the intentional mixing of excellent food-quality seeds with non-food-grade-quality seeds. Tracking the correct or illegitimate handling of seeds requires an efficient method for discrimination and individualization of poppy varieties. As in human and animal forensics, DNA variable regions containing short tandem repeats (STRs) located either in non-coding DNA or in gene sequences (EST-STRs) are preferred markers for discrimination between genotypes. Primers designed for 10 poppy EST-STR loci not analyzed so far were tested for their discriminatory ability on a set of 23 related P. somniferum L. genotypes. Thirty-three EST-STR alleles were identified together. Their polymorphic information content (PIC) values were in the range of 0.175-0.649. The PI value varied in the range of 0.140-0.669, and the cumulative PI was 1.2 × 10-5. PIsibs values varied between 0.436 and 0.820 and the cumulative value was lower (5.0 × 10-3). All analyzed genotypes were distinguished mutually, each with its own unique EST-STR profile. These newly developed EST-STR markers more effectively discriminated P. somniferum L. genotypes, even those genotypes whose DNA profiles were previously identical.
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Affiliation(s)
- Šarlota Kaňuková
- Department of Applied Biology and Genetics, Research Institute of Plant Production, National Agricultural and Food Centre, Bratislavska cesta 122, 92168 Piestany, Slovakia; (Š.K.); (K.O.); (D.M.)
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Namestie J. Herdu 2, 91701 Trnava, Slovakia
| | - Katarína Ondreičková
- Department of Applied Biology and Genetics, Research Institute of Plant Production, National Agricultural and Food Centre, Bratislavska cesta 122, 92168 Piestany, Slovakia; (Š.K.); (K.O.); (D.M.)
| | - Daniel Mihálik
- Department of Applied Biology and Genetics, Research Institute of Plant Production, National Agricultural and Food Centre, Bratislavska cesta 122, 92168 Piestany, Slovakia; (Š.K.); (K.O.); (D.M.)
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Namestie J. Herdu 2, 91701 Trnava, Slovakia
| | - Ján Kraic
- Department of Applied Biology and Genetics, Research Institute of Plant Production, National Agricultural and Food Centre, Bratislavska cesta 122, 92168 Piestany, Slovakia; (Š.K.); (K.O.); (D.M.)
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Namestie J. Herdu 2, 91701 Trnava, Slovakia
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Chang M, Kim JY, Lee H, Lee EJ, Lee WH, Moon S, Choe S, Choung CM. Development of diagnostic SNP markers and a novel SNP genotyping assay for distinguishing opium poppies. Forensic Sci Int 2022; 339:111416. [DOI: 10.1016/j.forsciint.2022.111416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/14/2022] [Accepted: 08/02/2022] [Indexed: 11/04/2022]
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Tittarelli R, Gismondi A, Di Marco G, Mineo F, Vernich F, Russo C, Marsella LT, Canini A. Forensic Application of Genetic and Toxicological Analyses for the Identification and Characterization of the Opium Poppy ( Papaver somniferum L.). BIOLOGY 2022; 11:672. [PMID: 35625400 PMCID: PMC9138826 DOI: 10.3390/biology11050672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND A reliable and science-based taxonomic determination of Papaver somniferum L. (opium poppy), the illegal species of the genus Papaver, may have practical and legal implications for law enforcement. P. somniferum is a controlled plant because of its narcotic substances, such as morphine and codeine. As poppy plants have rather similar morphological features, both chemical and genetic analysis are required in order to achieve an accurate characterization of such species. The chemical structures of alkaloids are extremely variable even within the same species, which is why the genetic approach may lead to a more scientific Papaver sp. differentiation. The aim of our study was the taxonomic identification of poppy capsules seized by the Italian Police Forces being considered as potential P. somniferum derivatives. METHODS The alkaloids detected using gas chromatography/mass-spectrometry (GC/MS) were morphine, codeine, thebaine, noscapine, meconin, hydrocotarnine, and traces of papaverine. Further genetic analysis was carried out simultaneously using three plastid DNA barcoding regions (matK, trnH-psbA, and rbcL) for the samples' identification. RESULTS The Random Amplification of Polymorphic DNA (RAPD) method showed that the analysed samples were genetically identical. CONCLUSIONS The morphological, toxicological, and genetic profile of the samples revealed that they belonged to P. somniferum species. Furthermore, the alkaloid content of dried poppy capsules might be used to investigate and track their origin.
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Affiliation(s)
- Roberta Tittarelli
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Angelo Gismondi
- Laboratory of Botany, Department of Biology, Faculty of Mathematical, Physical and Natural Science, University Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.G.); (G.D.M.); (A.C.)
| | - Gabriele Di Marco
- Laboratory of Botany, Department of Biology, Faculty of Mathematical, Physical and Natural Science, University Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.G.); (G.D.M.); (A.C.)
| | - Federico Mineo
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Francesca Vernich
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Carmelo Russo
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Luigi Tonino Marsella
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Antonella Canini
- Laboratory of Botany, Department of Biology, Faculty of Mathematical, Physical and Natural Science, University Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.G.); (G.D.M.); (A.C.)
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Development of SSR and SNP markers for identifying opium poppy. Int J Legal Med 2022; 136:1261-1271. [PMID: 35316386 DOI: 10.1007/s00414-022-02810-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/01/2022] [Indexed: 01/23/2023]
Abstract
Papaver somniferum L. (opium poppy) is the original plant of heroin, which is a major narcotic drug, and this plant has brought great harm to human health. However, the ban on opium poppy cultivation and trafficking is facing great challenges because of abnormal profits. Therefore, rapid and accurate identification is important to address the abovementioned problems. In this study, eleven simple sequence repeats (SSR) markers and two single nucleotide polymorphism (SNP) markers were mined to distinguish opium poppy from other six Papaver species. These molecular markers were further verified through a large number of plant materials of these seven Papaver species. An excellent multiplex polymerase chain reaction (PCR) system that simultaneously amplifies the three of eleven SSR markers was developed, which effectively improves the efficiency and speed of identification. The present research is of great implication for identifying and investigating the illegal cultivation and trafficking of opium poppy.
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Chang M, Lee EJ, Kim JY, Lee H, Choe S, Moon S. A new minisatellite VNTR marker, Pscp1, discovered for the identification of opium poppy. Forensic Sci Int Genet 2021; 55:102581. [PMID: 34517229 DOI: 10.1016/j.fsigen.2021.102581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Opium poppy, a member of the Papaveraceae family, is an ancient herbaceous plant and well-known medical resource in the pharmaceutical industry. However, opium poppies are grown worldwide for producing illicit drugs, significantly increasing the incidence of narcotic drug abuse. Since the narcotic poppy has not yet been genetically investigated, we characterized a novel variable number tandem repeat (VNTR) marker of forensically important poppy species based on the genetic analysis of 164 samples collected from two locations spanning the Jeolla province and Jeju island of South Korea. Comparing analysis of the chloroplast (cp) genome sequences for four representative species of Papaver (Papaver somniferum, Papaver somniferum subs. setigerum, Papaver orientale, and Papaver rhoeas) revealed a unique region with 1-3 repeats for 16 nucleotide motifs in the genome inverted repeat A (IRA, positions 128,651 to 128,698) region. For 16 nucleotide motifs, 3 repeats were found in P. somniferum, and 2 repeats were found in P. somniferum subs. setigerum. Therefore, 10 known and the 133 unknown, seized Papaver species were compared to determine whether the species could be identified via variations in the repeat units. The sizes of a novel VNTR ranged from 181 to 252 bp between the species. Phylogenetic analysis confirmed that a novel VNTR, which we named Pscp1, could clearly distinguish between the narcotic and non-narcotic types of Papaver species based on the patterns of sequence variation. Interestingly, we found that Pscp1 could also distinguish between P. somniferum and P. somniferum subs. setigerum. The regions of eight non-narcotic species displayed similar patterns and also differences were found due to the nucleotide substitution and deletion events. The structural differences of Pscp1 were observed within the two narcotic species or between the narcotic and non-narcotic species, suggesting that these variations may act as a genetic marker. We, therefore, developed a new Pscp1 PCR-capillary electrophoresis (CE) method that can reliably identify the narcotic type of Papaver species. Taken together, our findings suggest that the newly developed Pscp1 can be used as an identification marker of opium poppy, and establish that the Pscp1 genotyping method by PCR-CE is an effective primary screening tool that can also contribute to species discrimination in the field of forensic diagnosis and applications.
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Affiliation(s)
- Miwha Chang
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea
| | - Eun-Jung Lee
- Crime-scene DNA Section, Gwangju Institute, National Forensic Service, Gwangju 57231, Republic of Korea
| | - Joo-Young Kim
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea
| | - Haeyong Lee
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea
| | - Sanggil Choe
- Forensic Toxicology and Chemistry Division, Seoul Institute, National Forensic Service, Seoul 08036, Republic of Korea
| | - Seohyun Moon
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea.
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Vašek J, Čílová D, Melounová M, Svoboda P, Zdeňková K, Čermáková E, Ovesná J. OpiumPlex is a novel microsatellite system for profiling opium poppy (Papaver somniferum L.). Sci Rep 2021; 11:12799. [PMID: 34140548 PMCID: PMC8211840 DOI: 10.1038/s41598-021-91962-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Opium poppy (Papaver somniferum L.) is a versatile plant exploited by the pharmaceutical and food industries. Unfortunately, it is also infamously known as a source of highly addictive narcotics, primarily heroin. Drug abuse has devastating consequences for users and also has many direct or indirect negative impacts on human society as a whole. Therefore, developing a molecular genetic tool for the individualization of opium poppy, raw opium or heroin samples could help in the fight against the drug trade by retrieving more information about the source of narcotics and linking isolated criminal cases. Bioinformatic analysis provided insight into the distribution, density and other characteristics of roughly 150 thousand microsatellite loci within the poppy genome and indicated underrepresentation of microsatellites with the desired attributes. Despite this fact, 27 polymorphic STR markers, divided into three multiplexed assays, were developed in this work. Internal validation confirmed species-specific amplification, showed that the optimal amount of DNA is within the range of 0.625-1.25 ng per reaction, and indicate relatively well balanced assays according to the metrics used. Moreover, the stutter ratio (mean + 3 SD 2.28-15.59%) and allele-specific stutters were described. The analysis of 187 individual samples led to the identification of 158 alleles in total, with a mean of 5.85 alleles and a range of 3-14 alleles per locus. Most of the alleles (151) were sequenced by the Sanger method, which enabled us to propose standardized nomenclature and create three allelic ladders. The OpiumPlex system discriminates most of the varieties from each other and pharmaceutical varieties from the others (culinary, dual and ornamental).
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Affiliation(s)
- Jakub Vašek
- grid.15866.3c0000 0001 2238 631XDepartment of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Daniela Čílová
- grid.15866.3c0000 0001 2238 631XDepartment of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Martina Melounová
- grid.15866.3c0000 0001 2238 631XDepartment of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Svoboda
- grid.417626.00000 0001 2187 627XDivision of Crop Genetics and Breeding, Crop Research Institute, Prague, Czech Republic
| | - Kamila Zdeňková
- grid.448072.d0000 0004 0635 6059Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Eliška Čermáková
- grid.448072.d0000 0004 0635 6059Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Jaroslava Ovesná
- grid.417626.00000 0001 2187 627XDivision of Crop Genetics and Breeding, Crop Research Institute, Prague, Czech Republic
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Kaňuková Š, Mrkvová M, Mihálik D, Kraic J. Procedures for DNA Extraction from Opium Poppy ( Papaver somniferum L.) and Poppy Seed-Containing Products. Foods 2020; 9:foods9101429. [PMID: 33050241 PMCID: PMC7601356 DOI: 10.3390/foods9101429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/19/2022] Open
Abstract
Several commonly used extraction procedures and commercial kits were compared for extraction of DNA from opium poppy (Papaver somniferum L.) seeds, ground seeds, pollen grains, poppy seed filling from a bakery product, and poppy oil. The newly developed extraction protocol was much simpler, reduced the cost and time required for DNA extraction from the native and ground seeds, and pollen grains. The quality of extracted DNA by newly developed protocol was better or comparable to the most efficient ones. After being extended by a simple purification step on a silica membrane column, the newly developed protocol was also very effective in extracting of poppy DNA from poppy seed filling. DNA extracted from this poppy matrix was amplifiable by PCR analysis. DNA extracted from cold-pressed poppy oil and suitable for amplifications was obtained only by methods developed previously for olive oil. Extracted poppy DNA from all tested matrices was analysed by PCR using primers flanking a microsatellite locus (156 bp) and two different fragments of the reference tubulin gene (553 bp and 96 bp). The long fragment of the reference gene was amplified in DNA extracted from native seeds, ground seeds, and pollen grains. Poppy DNA extracted from the filling of bakery product was confirmed only by amplification of short fragments (96 bp and 156 bp). DNA extracted from cold-pressed poppy oil was determined also only by amplification of these two short fragments.
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Affiliation(s)
- Šarlota Kaňuková
- Department of Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Námestie J. Herdu 2, SK-917 01 Trnava, Slovakia; (Š.K.); (M.M.); (D.M.)
| | - Michaela Mrkvová
- Department of Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Námestie J. Herdu 2, SK-917 01 Trnava, Slovakia; (Š.K.); (M.M.); (D.M.)
| | - Daniel Mihálik
- Department of Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Námestie J. Herdu 2, SK-917 01 Trnava, Slovakia; (Š.K.); (M.M.); (D.M.)
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, SK-921 68 Piešťany, Slovakia
| | - Ján Kraic
- Department of Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Námestie J. Herdu 2, SK-917 01 Trnava, Slovakia; (Š.K.); (M.M.); (D.M.)
- Research Institute of Plant Production, National Agricultural and Food Center, Bratislavská cesta 122, SK-921 68 Piešťany, Slovakia
- Correspondence: ; Tel.: +421-337-947-168; Fax: +421-337-726-306
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Jones NS, Comparin JH. Interpol review of controlled substances 2016-2019. Forensic Sci Int Synerg 2020; 2:608-669. [PMID: 33385148 PMCID: PMC7770462 DOI: 10.1016/j.fsisyn.2020.01.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/23/2020] [Indexed: 12/14/2022]
Abstract
This review paper covers the forensic-relevant literature in controlled substances from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium. The review papers are also available at the Interpol website at: https://www.interpol.int/content/download/14458/file/Interpol%20Review%20Papers%202019.pdf.
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Affiliation(s)
- Nicole S. Jones
- RTI International, Applied Justice Research Division, Center for Forensic Sciences, 3040 E. Cornwallis Road, Research Triangle Park, NC, 22709-2194, USA
| | - Jeffrey H. Comparin
- United States Drug Enforcement Administration, Special Testing and Research Laboratory, USA
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Young B, Roman MG, LaRue B, Gangitano D, Houston R. Evaluation of 19 short tandem repeat markers for individualization of Papaver somniferum. Sci Justice 2020; 60:253-262. [PMID: 32381242 DOI: 10.1016/j.scijus.2019.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/07/2019] [Accepted: 12/08/2019] [Indexed: 11/28/2022]
Abstract
Papaver somniferum, commonly known as opium poppy, is the source of natural opiates, which are used as analgesics or as precursors in the creation of semi-synthetic opioids such as heroin. An increase in opioid addiction in the United States has resulted in high rates of illicit opioid use and overdoses. It has recently been shown that P. somniferum DNA suitable for genetic analysis can be recovered from heroin samples. The development of a comprehensive genetic individualization tool for opium poppy could serve to link cases and strengthen programs such as the Drug Enforcement Administration's (DEA) Heroin Signature Program, which seeks to combat rising opioid use. The purpose of this study was to develop a quantitative real-time PCR (qPCR) method for the quantification of opium poppy DNA, compare three commercial DNA extraction kits for their ability to isolate DNA from poppy seeds, and evaluate nineteen opium poppy short tandem repeat (STR) markers for their use in a forensic identification panel. Such a panel could be used for individualizing samples and determining the geographic origin in heroin or poppy seed tea cases. The qPCR method was proven to be reproducible and reliable, specific for P. somniferum, and sensitive enough for forensic case-type samples. Of the three kits tested, the nexttec™ one-step DNA Isolation Kit for Plants was the optimal method and facilitated rapid extraction of DNA from poppy seeds. The majority of evaluated STR primer sets were unreliable or had low discriminatory power, limiting their use for individualization of poppy samples. A six-locus STR multiplex was developed and evaluated according to Scientific Working Group on DNA Analysis Methods (SWGDAM) and International Society of Forensic Genetics (ISFG) guidelines, including the use of a sequenced allelic ladder. The multiplex was found to have low discriminatory power, with greater than two-thirds of samples analyzed having just two different genotypes. The multiplex was determined to be unsuitable for individualization; however, a genotype map was developed as a proof of concept that these markers may be useful for determining the biogeographical origin of samples. Searching the poppy genome for new STR markers and developing new primer sets may be necessary for the creation of a powerful genetic tool for the individualization of P. somniferum.
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Affiliation(s)
- Blake Young
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - Madeline G Roman
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States.
| | - Bobby LaRue
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States.
| | - David Gangitano
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States.
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Vašek J, Čílová D, Melounová M, Svoboda P, Vejl P, Štikarová R, Vostrý L, Kuchtová P, Ovesná J. New EST-SSR Markers for Individual Genotyping of Opium Poppy Cultivars ( Papaver somniferum L.). PLANTS 2019; 9:plants9010010. [PMID: 31861643 PMCID: PMC7020189 DOI: 10.3390/plants9010010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 12/25/2022]
Abstract
High-quality simple sequence repeat (SSR) markers are invaluable tools for revealing genetic variability which could be utilized for many purposes, such as breeding new varieties or the identifying current ones, among other applications. Based on the analysis of 3.7 million EST sequences and 15 genomic sequences from bacterial artificial chromosome (BAC) libraries, 200 trinucleotide genic (EST)-SSR and three genomic (gSSR) markers were tested, where 17 of them fulfilled all criteria for quality markers. Moreover, the reproducibility of these new markers was verified by two genetics laboratories, with a mean error rate per allele and per locus equal to 0.17%. These markers were tested on 38 accessions of Papaver somniferum and nine accessions of another five species of the Papaver and Argemone genera. In total, 118 alleles were detected for all accessions (median = 7; three to ten alleles per locus) and 88 alleles (median = 5; three to nine alleles per locus) within P. somniferum alone. Multivariate methods and identity analysis revealed high resolution capabilities of the new markers, where all but three pair accessions (41 out of 47) had a unique profile and opium poppy was distinguished from other species.
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Affiliation(s)
- Jakub Vašek
- Czech University of Life Sciences Prague, FAFNR, Department of Genetics and Breeding, Kamýcká 129, 6 Suchdol, 16500 Prague, Czech Republic; (D.Č.); (M.M.); (P.V.); (R.Š.); (L.V.)
- Correspondence: ; Tel.: +420-22438-2562
| | - Daniela Čílová
- Czech University of Life Sciences Prague, FAFNR, Department of Genetics and Breeding, Kamýcká 129, 6 Suchdol, 16500 Prague, Czech Republic; (D.Č.); (M.M.); (P.V.); (R.Š.); (L.V.)
| | - Martina Melounová
- Czech University of Life Sciences Prague, FAFNR, Department of Genetics and Breeding, Kamýcká 129, 6 Suchdol, 16500 Prague, Czech Republic; (D.Č.); (M.M.); (P.V.); (R.Š.); (L.V.)
| | - Pavel Svoboda
- Crop Research Institute, Division of Crop Genetics and Breeding, Drnovská 507/73, 6 Ruzyně, 16106 Prague, Czech Republic; (P.S.); (J.O.)
| | - Pavel Vejl
- Czech University of Life Sciences Prague, FAFNR, Department of Genetics and Breeding, Kamýcká 129, 6 Suchdol, 16500 Prague, Czech Republic; (D.Č.); (M.M.); (P.V.); (R.Š.); (L.V.)
| | - Radka Štikarová
- Czech University of Life Sciences Prague, FAFNR, Department of Genetics and Breeding, Kamýcká 129, 6 Suchdol, 16500 Prague, Czech Republic; (D.Č.); (M.M.); (P.V.); (R.Š.); (L.V.)
| | - Luboš Vostrý
- Czech University of Life Sciences Prague, FAFNR, Department of Genetics and Breeding, Kamýcká 129, 6 Suchdol, 16500 Prague, Czech Republic; (D.Č.); (M.M.); (P.V.); (R.Š.); (L.V.)
| | - Perla Kuchtová
- Czech University of Life Sciences, FAFNR, Department of Agroecology and Crop Production, Kamýcká 129, 6 Suchdol, 16500 Prague, Czech Republic;
| | - Jaroslava Ovesná
- Crop Research Institute, Division of Crop Genetics and Breeding, Drnovská 507/73, 6 Ruzyně, 16106 Prague, Czech Republic; (P.S.); (J.O.)
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