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.
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
© 2017 Institute of Molecular Biology, Slovak Academy of Sciences
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- Zoology
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- Zoology
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- Zoology
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