Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing Ibrahim Celik • Visam Gultekin • Jens Allmer • Sami Doganlar • Anne Frary Received: 10 July 2013 / Accepted: 23 January 2014 / Published online: 6 February 2014 Ó Springer Science+Business Media Dordrecht 2014 Abstract Opium poppy (Papaver somniferum L.) is an important pharmaceutical crop with very few genetic marker resources. To expand these resources, we sequenced genomic DNA using pyrosequenc- ing technology and examined the DNA sequences for simple sequence repeats (SSRs). A total of 1,244,412 sequence reads were obtained covering 474 Mb. Approximately half of the reads (52 %) were assembled into 166,724 contigs representing 105 Mb of the opium poppy genome. A total of 23,283 non- redundant SSRs were identified in 18,944 contigs (11.3 % of total contigs). Trinucleotide and tetranu- cleotide repeats were the most abundant SSR repeats, accounting for 49.0 and 27.9 % of all SSRs, respec- tively. The AAG/TTC repeat was the most abundant trinucleotide repeat, representing 19.7 % of trinucleo- tide repeats. Other SSR repeat types were AT-rich. A total of 23,126 primer pairs (98.7 % of total SSRs) were designed to amplify SSRs. Fifty-three genomic SSR markers were tested in 37 opium poppy acces- sions and seven Papaver species for determination of polymorphism and transferability. Intraspecific polymorphism information content (PIC) values of the genomic SSR markers were intermediate, with an average 0.17, while the interspecific average PIC value was slightly higher, 0.19. All markers showed at least 88 % transferability among related species. This study increases sequence coverage of the opium poppy genome by sevenfold and the number of opium poppy- specific SSR markers by sixfold. This is the first report of the development of genomic SSR markers in opium poppy, and the genomic SSR markers developed in this study will be useful in diversity, identification, mapping and breeding studies in opium poppy. Keywords GS-FLX pyrosequencing technology Á Genetic diversity Á Genomic SSRs Á Microsatellites Á Papaver somniferum L. Introduction Opium poppy (Papaver somniferum L.) produces several pharmaceutically important alkaloids and is an economically important member of the family Pap- averaceae (Acharya and Sharma 2009). Benzyliso- quinoline alkaloids are extracted from opium poppy and have extensive medicinal properties, including analgesic and narcotic (morphine), antitumor (nosca- pine), antitussive (codeine) and muscle relaxant (papaverine) effects (Facchini and De Luca 2008; Ziegler et al. 2009; Winzer et al. 2012). In addition, poppy seeds and their oil are edible (Schulz et al. Electronic supplementary material The online version of this article (doi:10.1007/s11032-014-0036-0) contains supple- mentary material, which is available to authorized users. I. Celik Á V. Gultekin Á J. Allmer Á S. Doganlar Á A. Frary (&) Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir 35430, Turkey e-mail: annefrary@iyte.edu.tr 123 Mol Breeding (2014) 34:323–334 DOI 10.1007/s11032-014-0036-0