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Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing

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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 pyrosequencing 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 tetranucleotide repeats were the most abundant SSR repeats, accounting for 49.0 and 27.9 % of all SSRs, respectively. The AAG/TTC repeat was the most abundant trinucleotide repeat, representing 19.7 % of trinucleotide 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 accessions 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.

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Acknowledgments

The authors thank Dr. Hüseyin Camci, Dr. Arzu Köse and Dr. Ferda Kosar from the Anatolia Agricultural Research Institute for providing plant material. We are also grateful to Ali Üncü and Ayşe Dülger Üncü for SSR validation by sequencing. This study was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) project no. 109O797.

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Authors and Affiliations

  1. Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, 35430, Turkey

    Ibrahim Celik, Visam Gultekin, Jens Allmer, Sami Doganlar & Anne Frary

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  1. Ibrahim Celik
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  2. Visam Gultekin
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  3. Jens Allmer
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  4. Sami Doganlar
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  5. Anne Frary
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Correspondence to Anne Frary.

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Celik, I., Gultekin, V., Allmer, J. et al. Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing. Mol Breeding 34, 323–334 (2014). https://doi.org/10.1007/s11032-014-0036-0

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  • DOI: https://doi.org/10.1007/s11032-014-0036-0

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