In Silico Retrieving of Opium Poppy (Papaver Somniferum L.) Microsatellites

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Repetitive tandem sequences were retrieved within nucleotide sequences of opium poppy (Papaver somniferum L.) genomic DNA available in the GenBank® database. Altogether 538 different microsatellites with the desired length characteristics of tandem repeats have been identified within 450 sequences of opium poppy DNA available in the database. The most frequented were mononucleotide repeats (246); nevertheless, 44 dinucleotide, 148 trinucleotide, 62 tetranucleotide, 28 pentanucleotide and 5 hexanucleotide tandem repeats have also been found. The most abundant were trinucleotide motifs (27.50%), and the most abundant motifs within each group of tandem repeats were TA/AT, TTC/GAA, GGTT/AACC and TTTTA/ TAAAA. Five hexanucleotide repeats contained four different motifs.

ACHARYA, H. - SHARMA, V. 2009. Molecular characterization of opium poppy (Papaver somniferum) germplasm. In American Journal of Infection Diseases, vol. 5, pp. 148 -153.

BENSON, D.A. - CAVANAUGH, M. - CLARK, K. - KARSCH-MIZRACHI, I. - LIPMAN, D.J. - OSTEL, J. - SAYERS E.W. 2013. GenBank. In Nucleic Acids Research, vol. 41, pp. D36-D42. DOI: 10.1093/nar/ gks1195.

ҪELIK, I. - GÜLTEKIN, V. - ALLMER, J. - DOĞANLAR, S. - FRARY, A. 2014. Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing. In Molecular Breeding, vol. 34, pp. 323-334. DOI: 10.1007/s11032-014-0036-0.

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. In Internation- al Journal of Plant Genomics, Article ID 412696. DOI:10.1155/2008/412696.

DITTBRENNER, A. - LOHWASSER, U. - MOCK, H.P. - BÖRNER, A. 2008. Molecular and phytochemical studies of Papaver somniferum in the context of intraspecific classification. In GROENDIJK-WILDERS, N. - ALEXANDER, C. - VAN DEN BERG, R.G. - HETTERSCHEID, W.L.A. (Eds). Proceedings of the 5th International Symposium on the Taxonomy of Cultivated Plants. Wageningen : Netherlands, October 15 - 19, 2007. (Series: Acta Horticulturae, Vol. 799) Leuven: ISHS (2008) 81-88. DOI: 10.17660/Acta- Hortic.2008.799.9.

GUPTA, P.K. - RUSTGI, S. - SHARMA, S. - SINGH, S. - KUMAR, N. - BALYAN, H.S. 2003. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. In Molecular Genetics and Genomics, vol. 270, pp. 315-323. DOI: 10.1007/s00438-003-0921-4.

GUPTA, P.K. - VARSHNEY, R.K. 2000. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. In Euphytica, vol. 113, pp. 163-185. DOI: 10.1023/A:1003910819967.

GÜÇLÜ, G.B. - GÜRKÖK, T. - KOYUNCU, M. - ARSLAN, N. - PARMAKSIZ, İ. 2014. Genetic characterization of Turkish commercial opium poppy (Papaver somniferum L.) cultivars using ISSR and SSR markers. In Journal of New Results in Science, vol. 7, pp. 48 -57.

HARI, S. - SHARMA, A. - SHARMA, V. 2009. Molecular characterization of opium poppy (Papaver somniferum) germplasm. In American Journal of Infection Diseases, vol. 2, pp. 155-160.

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. In Journal of Forensic Sciences, vol. 55, pp. 1002-1008. DOI: 10.1111/j.1556-4029.2010.01423.x.

LEE, E.J. - JIN, G.J. - LEE, K.L. - HAN, M.S. - LEE, Y.H. - YANG, M.S. 2011. Exploiting expressed sequence tag database for the development of gene-derived simple sequence repeat markers in opium poppy (Papaver somniferum L.) for forensic applications. In Journal of Forensic Sciences, vol. 56, pp. 1131-1135. DOI: 10.1 111/j.1556-4029.2011.01810.x.

LITT, M. - LUTY, J.A. 1989. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. In American Journal of Human Genetics, vol. 44, pp. 388-396.

MORGANTE, M. - OLIVIERI, A.M. 1993. PCR-amplified microsatellites as markers in plant genetics. In Plant Journal, vol. 3, pp. 175-182.

PARMAKSIZ, I. - OZCAN, S. 2011. Morphological, chemical, and molecular analyses of Turkish Papaver accessions (Sect Oxytona). In Turkish Journal of Botany, vol. 35, pp. 1-16. DOI: 10.3906/bot-1003-39.

RAJENDRAKUMAR, P. - BISWAL, A.K. - BALACHANDRAN, S.M. - SUNDARAM, R.M. 2008. In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships. In In Silico Biology, vol. 8, pp. 87-104.

SARMAH, R. - SAHU, J. - DEHURY, B. - SARMA, K. - SAHOO, S. - SAHU, M. - BAROOAH, M. - SEN, P. - MODI, M.K. 2012. ESMP: A high-throughput computational pipeline for mining SSR markers from ESTs. In Bioinformation, vol. 8, pp. 206-208. DOI: 10.6026/97320630008206.

SAUNDERS, J.A. - PEDRONI, M.J. - PENROSE, L.D.J. - FIST, A.J. 2001. AFLP analysis of opium poppy. In Crop Science, vol. 41, pp. 1596-1601.

ŞELALE, H. - ҪELIK, I. - GÜLTEKIN, V. - ALLMER, J. - DOĞANLAR, S. - FRARY, A. 2013. Development of EST - SSR markers for diversity and breeding studies in opium poppy. In Plant Breeding, vol. 132, pp. 344-351. DOI: 10.1111/pbr.12059.

SHARMA, P.C. - GROVER, A. - KAHL, G. 2007. Mining microsatellites in eukaryotic genomes. In Trends in Biotechnology, vol. 25, pp. 490-498. DOI:10.1016/j. tibtech.2007.07.013.

SUÁREZ, M.C. - BERNAL, A. - GUTIÉRREZ, J. - TOHME, J. - FREGENE, M. 2000. Developing expressed sequence tags (ESTs) from polymorphic transcript- derived fragments (TDFs) in cassava (Manihot esculenta Crantz). In Genome, vol. 43, pp. 62-67. DOI: 10.1139/g99-073.

TANG, J. - BALDWIN, S.J. - JACOBS, J.M.E. - VAN DER LINDEN, C.G. - VOORRIPS, R.E. - LEUNISSEN, J.A.M. - VAN ECK, H. - VOSMAN, B. 2008. Large-scale identification of polymorphic microsatellites using an in silico approach. In BMC Bioinformatics, vol. 9, pp. 374. DOI:10.1 186/1471-2105-9-374.

TEMNYKH, S. - DECLERCK, G. - LUKASHOVA, A. - LIPOVICH, L. - CARTINHOUR, S. - MCCOUCH, S. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. In Genome Research, vol. 11, pp. 1441-1452. DOI: 10.1101/gr.184001.

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.). In Theoretical and Applied Genetics, vol. 106, pp. 411-422. DOI: 10.1007/s00122-002-1031-0.

Wang, X. - LU, P. - LUO, Z. 2013. GMATo: A novel tool for the identification and analysis of microsatellites in large genomes. In Bioinformation, vol. 9, pp. 541-544. DOI: 10.6026/97320630009541.

Agriculture (Pol'nohospodárstvo)

The Journal of National Agricultural and Food Centre

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