Evaluation of 19 short tandem repeat markers for individualization of Papaver somniferum

Young, Blake; Roman, Madeline G.; LaRue, Bobby; Gangitano, David; Houston, Rachel

doi:10.1016/j.scijus.2019.12.002

Cited by 7 publications

(8 citation statements)

References 33 publications

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“…According to the results, the optimal amount of DNA is within the range of 0.625–1.25 ng per reaction, which is equivalent to the nuclear content of 107–213 diploid cells based on poppy genome size estimation 14 . Our data are in accordance with an earlier study of opium poppy using different multiplexed STR assays 20 and correspond to commonly reported sensitivities in other nonhuman organisms if genome size is taken into account 37 , 58 . Samples with less than 0.625 ng DNA suffered from an elevated error rate, and we can expect a low amount of extracted DNA from complex matrices such as heroin.…”

Section: Discussionsupporting

confidence: 93%

“…The Hb method provides information about the directionality of preferential amplification, but is less robust against influential points, unlike the Hb′ method, which is also easier to interpret 41 . Our data showed that the typical threshold for heterozygote balance, set to 0.6 39 , 57 or even 0.7 by some authors 20 , 37 , was exceeded for all loci on average. The newly developed markers seem to be more stable than the markers tested in the study of Young et al 20 , who reported a common drop in the Hb′ ratio below the 0.7 threshold, but the presence of several outliers reminds us of the potential occurrence of suboptimal heterozygote balance in multiplexed assays.…”

Section: Discussionmentioning

confidence: 55%

“…Our data showed that the typical threshold for heterozygote balance, set to 0.6 39 , 57 or even 0.7 by some authors 20 , 37 , was exceeded for all loci on average. The newly developed markers seem to be more stable than the markers tested in the study of Young et al 20 , who reported a common drop in the Hb′ ratio below the 0.7 threshold, but the presence of several outliers reminds us of the potential occurrence of suboptimal heterozygote balance in multiplexed assays. Only 4 out of 27 markers slightly favoured the amplification of high molecular weight (HMW) alleles over low molecular weight (LMW) alleles.…”

Section: Discussionmentioning

confidence: 55%

“…Therefore, most of the STR markers were developed by the data mining of sequences from transcriptomic studies 15 – 18 or by screening sequences of unplaced genomic fragments retrieved via next-generation sequencing (NGS) 19 . Unfortunately, many of these markers suffer from one or more weaknesses, such as low polymorphism 20 , short lengths of repeated motifs or unknown localization on a chromosome. Therefore, the purpose of this study is to develop a new set of genomic STR markers with potential for application in the field of plant forensics.…”

Section: Introductionmentioning

confidence: 99%

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OpiumPlex is a novel microsatellite system for profiling opium poppy (Papaver somniferum L.)

Vašek

Čílová

Melounová

et al. 2021

Sci Rep

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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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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 55%

Section: Discussionmentioning

confidence: 55%

Section: Introductionmentioning

confidence: 99%

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OpiumPlex is a novel microsatellite system for profiling opium poppy (Papaver somniferum L.)

Vašek

Čílová

Melounová

et al. 2021

Sci Rep

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“…The number of relevant scientific reports in poppy is very limited and DNA extraction procedures have been published only from defatted seeds [ 21 ] and heroin samples [ 22 ]. Three commercial kits were tested for DNA extraction from seeds [ 23 ]. Very useful would be efficient, simple, and universal protocol for extraction of DNA from poppy seeds, grains, and products containing or made from poppy seeds.…”

Section: Introductionmentioning

confidence: 99%

Procedures for DNA Extraction from Opium Poppy (Papaver somniferum L.) and Poppy Seed-Containing Products

Kaňuková

Mrkvová

Mihálik

et al. 2020

Foods

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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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DNA-Based Analysis of Plant Material in Forensic Investigations

Robertson¹,

Damaso²,

Meiklejohn³

2021

Handbook of DNA Profiling

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Evaluation of 19 short tandem repeat markers for individualization of Papaver somniferum

Cited by 7 publications

References 33 publications

OpiumPlex is a novel microsatellite system for profiling opium poppy (Papaver somniferum L.)

OpiumPlex is a novel microsatellite system for profiling opium poppy (Papaver somniferum L.)

Procedures for DNA Extraction from Opium Poppy (Papaver somniferum L.) and Poppy Seed-Containing Products

DNA-Based Analysis of Plant Material in Forensic Investigations

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