Startseite Forensic application of EST-derived STR markers in opium poppy
Artikel
Lizenziert
Nicht lizenziert Erfordert eine Authentifizierung

Forensic application of EST-derived STR markers in opium poppy

  • Veronika Mičianová , Katarína Ondreičková , Darina Muchová , Lenka Klčová , Martina Hudcovicová , Michaela Havrlentová , Daniel Mihálik und Ján Kraic EMAIL logo
Veröffentlicht/Copyright: 30. Juni 2017
Veröffentlichen auch Sie bei De Gruyter Brill
Biologia
Aus der Zeitschrift Biologia Band 72 Heft 6

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.


e-mail:

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.2009.148.153Suche 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-2016-0111Suche 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/BF02788051Suche 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.2007.330Suche 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/gks1195Suche 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/s11032-016-0469-8Suche 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/s11032-014-0036-0Suche 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.2012.08.002Suche 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: 412–696.10.1155/2008/412696Suche 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.2008.799.9Suche 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.0170522Suche 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.xSuche 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.Suche 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/s10535-011-0129-0Suche in Google Scholar

Kraic J. 2005. Relevancy of genomic and gene-based variation in distinguishing of elite barleys. Biologia 60: 675–680.Suche 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.xSuche 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.xSuche 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: 424.10.1186/1471-2164-8-424Suche 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/bti282Suche 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-2015-0020Suche 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-1003-39Suche 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/bts460Suche 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).Suche 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/155.2.945Suche 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.Suche 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/cropsci2001.4151596xSuche 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/B408930HSuche 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.12059Suche 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/s00122-002-1031-0Suche 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/f8030081Suche 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: 253.10.1186/1471-2105-9-253Suche 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

Artikel in diesem Heft

  1. Cellular and Molecular Biology
  2. Forensic application of EST-derived STR markers in opium poppy
  3. Botany
  4. Phylogeny and maternal donor of Elymus (Triticeae: Poaceae) in China based on chloroplast matK sequences
  5. Botany
  6. Isolation and characterization of regulators involved in PHOT1-mediated inhibition of hypocotyl phototropism in Arabidopsis
  7. Botany
  8. Isolation and functional characterization of a Lonicera japonica hydroxycinnamoyl transferase involved in chlorogenic acid synthesis
  9. Botany
  10. Salt stress resilience potential of a fungal inoculant isolated from tea cultivation area in maize
  11. Zoology
  12. Distribution of the genus Veigaia (Mesostigmata: Veigaiidae) in Romania with notes on the species ecology
  13. Zoology
  14. The effect of grassland management on diversity and composition of ground-dwelling spider assemblages in the Mátra Landscape Protection Area of Hungary
  15. Zoology
  16. Downstream effect of a pumped-storage hydropower plant on river habitat conditions and benthic life – a case study
  17. Zoology
  18. Parasites as biological tags of divergence in Central European gudgeon populations (Actinopterygii: Cyprinidae: Gobioninae)
  19. Zoology
  20. Chromosomal characteristics of rDNA in a conserved karyotype of two Sternopygus macrurus (Gymnotiformes: Sternopygidae) populations from upper Paraná River basin
  21. Zoology
  22. Habitat suitability and patterns of sex-biased migration of the Iranian long-legged wood frog, Rana pseudodalmatina (Anura: Ranidae)
  23. Cellular and Molecular Biology
  24. Blebbistatin induces chondrogenesis of single mesenchymal cells via PI3K/PDK1/mTOR/p70S6K pathway
  25. Cellular and Molecular Biology
  26. Direct interaction between troponin and myosin enhances the ATPase activity of heavy meromyosin
Heruntergeladen am 3.10.2025 von https://www.degruyterbrill.com/document/doi/10.1515/biolog-2017-0076/html
Button zum nach oben scrollen