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Forensic application of EST-derived STR markers in opium poppy

  • Veronika Mičianová , Katarína Ondreičková , Darina Muchová , Lenka Klčová , Martina Hudcovicová , Michaela Havrlentová , Daniel Mihálik and Ján Kraic EMAIL logo
Published/Copyright: June 30, 2017
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Abstract

Discrimination study in opium poppy (Papaver somniferum L.) genotypes has been performed by short tandem repeat (STR) markers derived from expressed sequence tags (ESTs) retrieved from the opium poppy DNA. Some of STRs originate from the gene sequences involved in the biosynthesis of morphine. Eight of twelve tested EST-derived STR markers generated polymorphism, 2-4 alleles were identified per locus, and the mean polymorphic information content value was 0.338. Seven cultivars developed in Slovakia, registered and released at present time for commercial cultivation were discriminated mutually. All the Slovak and Czech cultivars were also different from each other. EST-derived STR markers have shown a potential for discrimination of opium poppy genotypes cultivated for commercial production of either edible seeds or pharmacologically active alkaloids and could be applicable for the PCR-based forensic analyses.


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Acknowledgements

This work was supported by projects ITMS 26210120039 “Systems biology for protection, reproduction and use of plant resources of Slovakia” supported from the Operational Programme Research and Development co-financed from the European Regional Development Fund and APVV-16-0026 “Metagenomic approach for the identification and characterization of viral diseases in selected medicinal plant species” financed from the Slovak Research and Development Agency.

References

Acharya H. & Sharma V. 2009. Molecular characterization of opium poppy (Papaver somniferum) germplasm. Am. J. Infect. Dis. 5: 148–153.10.3844/ajidsp.2009.148.153Search in Google Scholar

Arbeiter A.B., Hladnik M., Jakşe J. & Bandelj D. 2017. Identification and validation of novel EST-SSR markers in olives. Sci. Agric. 74: 215–225.10.1590/1678-992x-2016-0111Search in Google Scholar

Bassam B.J. & Caetano-Anollés G. 1993. Silver staining of DNA in polyacrylamide gels. Appl. Biochem. Biotechnol. 42: 181–188.10.1007/BF02788051Search in Google Scholar

Bassam B.J. & Gresshoff P.M. 2007. Silver staining of DNA in polyacrylamide gels. Nat. Protoc. 11: 2649–2654.10.1038/nprot.2007.330Search in Google Scholar PubMed

Benson D.A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J. & Sayers E.W. 2013. GenBank. Nucleic Acids Res. 41: D36–D42.10.1093/nar/gks1195Search in Google Scholar PubMed PubMed Central

Celik I., Camci H., Kose A., Celikoglu Kosar F., Doganlar S. & Frary A. 2016. Molecular genetic diversity and association mapping of morphine content and agronomic traits in Turkish opium poppy (Papaver somniferum) germplasm. Mol. Breed. 36: 46.10.1007/s11032-016-0469-8Search in Google Scholar

Celik I., Gultekin V., Allmer J., Doganlar S. & Frafy A. 2014. Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing. Mol. Breed. 34: 323–334.10.1007/s11032-014-0036-0Search in Google Scholar

Choe S., Lee E., Jin G., Lee Y.H., Kim S.Y., Choi H., Chung H., Hwang B.Y. & Kim S. 2012. Genetic and chemical components analysis of Papaver setigerum naturalized in Korea. Forensic Sci. Int. 222: 387–393.10.1016/j.forsciint.2012.08.002Search in Google Scholar PubMed

Da Maia L.C., Palmieri D.A., De Souza V.Q., Kopp M.M., De Carvalho F.I.F. & De Oliveira A.C. 2008. SSR Locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int. J. Plant Genomics 2008: 412–696.10.1155/2008/412696Search in Google Scholar PubMed PubMed Central

Dittbrenner A., Lohwasser U., Mock H.P. & Börner A. 2008. Molecular and phytochemical studies of Papaver somniferum in the context of intraspecific classification. Acta Hortic. 799: 81–88.10.17660/ActaHortic.2008.799.9Search in Google Scholar

Dufresnes C., Jan C., Bienert F., Goudet J. & Fumagalli L. 2017. Broad-scale genetic diversity of Cannabis for forensic applications. PLoS One 12: e0170522.10.1371/journal.pone.0170522Search in Google Scholar PubMed PubMed Central

Evanno G., Regnaut S. & Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611–2620.10.1111/j.1365-294X.2005.02553.xSearch in Google Scholar PubMed

Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.Search in Google Scholar

Hu J., Wang L. & Li J. 2011. Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber. Biol. Plant. 55: 577–580.10.1007/s10535-011-0129-0Search in Google Scholar

Kraic J. 2005. Relevancy of genomic and gene-based variation in distinguishing of elite barleys. Biologia 60: 675–680.Search in Google Scholar

Lee E.J., Hwang I.K., Kim N.Y., Lee K.L., Han M.S., Lee Y.H., Kim M.Y. & Yang M.S. 2010. An assessment of the utility of universal and specific genetic markers for opium poppy identification. J. Forensic Sci. 55: 1202–1208.10.1111/j.1556-4029.2010.01423.xSearch in Google Scholar PubMed

Lee E.J., Jin G.N., Lee K.L., Han M.S., Lee Y.H. & Yang M.S. 2011. Exploiting expressed sequence tag database for the development and characterization of gene-derived simple sequence repeat markers in the opium poppy (Papaver somniferum L.) for forensic applications. J. Forensic Sci. 56: 1131–1135.10.1111/j.1556-4029.2011.01810.xSearch in Google Scholar PubMed

Lijavetzky D., Cabezas J.A., Ibáńez A., Rodríguez V. & Martínez-Zapater J.M. 2007. High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a resequencing approach and SNPlex technology. BMC Genomics 8: 424.10.1186/1471-2164-8-424Search in Google Scholar PubMed PubMed Central

Liu K. & Muse S.V. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129.10.1093/bioinformatics/bti282Search in Google Scholar PubMed

Masárová V., Mihálik D. & Kraic J. 2016. In silico retrieving of opium poppy (Papaver somniferum L.) microsatellites. Agriculture 61: 149–156.10.1515/agri-2015-0020Search in Google Scholar

Parmaksiz I. & Özcan S. 2011. Morphological, chemical, and molecular analyses of Turkish Papaver accessions (Sect. Oxytona). Turk. J. Bot. 35: 1–16.10.3906/bot-1003-39Search in Google Scholar

Peakall R. & Smouse P.E. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28: 2537–2539.10.1093/bioinformatics/bts460Search in Google Scholar PubMed PubMed Central

Perrier X. & Jacquemound-Collet J.P. 2006. DARwin software (release 6.0). http://darwin.cirad.fr (accessed 2.5.2017).Search in Google Scholar

Pritchard J.K., Stephens M. & Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.10.1093/genetics/155.2.945Search in Google Scholar PubMed PubMed Central

Saitou N. & Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.Search in Google Scholar

Saunders J.A., Pedroni M.J., Penrose L.D.J. & Fist A.J. 2001. AFLP Analysis of opium poppy. Crop Sci. 41: 1596–1601.10.2135/cropsci2001.4151596xSearch in Google Scholar

Schulz H., Baranska M., Quilitzsch R. & Schütze W. 2004. Determination of alkaloids in capsules, milk and ethanolic extracts of poppy (Papaver somniferum L.) by ATR-FT-IR and FT-Raman spectroscopy. Analyst 129: 917–920.10.1039/B408930HSearch in Google Scholar PubMed

Şelale H., Çelik I., Gültekin V., Allmer J., Doğanlar S. & Frafy A. 2013. Development of EST-SSR markers for diversity and breeding studies in opium poppy. Plant Breed. 132: 344–351.10.1111/pbr.12059Search in Google Scholar

Thiel T., Michalek W., Varshney R.K. & Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106: 411–422.10.1007/s00122-002-1031-0Search in Google Scholar PubMed

Vischi M., Chiaba C., Raranciuc S., Poggetti L., Messina R., Ermacora P., Cipriani G., Paffetti D., Vettori C. & Testolin R. 2017. Genetic diversity of walnut (Juglans Regia L.) in the Eastern Italian Alps. Forests 8: 81.10.3390/f8030081Search in Google Scholar

You F.M., Huo N., Gu Y.Q., Luo M., Ma Y., Hane D., Lazo G.R., Dvorak J. & Anderson O.D. 2007. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9: 253.10.1186/1471-2105-9-253Search in Google Scholar PubMed PubMed Central

Abbreviations

AFLP

amplified fragment length polymorphism

DI

diversity index

EST

expressed sequence tag

HE

expected heterozygosity

HO

observed heterozygosity

PCA

principal component analysis

PI

probability of identity

PIC

polymorphic information content

SSR

simple sequence repeat

STR

short tandem repeat

Received: 2017-5-26
Accepted: 2017-6-12
Published Online: 2017-6-30
Published in Print: 2017-6-27

© 2017 Institute of Molecular Biology, Slovak Academy of Sciences

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