Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/5548
Title: Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing
Authors: Çelik, İbrahim
Gültekin, Visam
Allmer, Jens
Doğanlar, Sami
Frary, Anne
Çelik, İbrahim
Gültekin, Visam
Allmer, Jens
Doğanlar, Sami
Frary, Anne
Izmir Institute of Technology. Molecular Biology and Genetics
Keywords: Genetic diversity
Genomic SSRs
GS-FLX pyrosequencing technology
Microsatellites
Papaver somniferum L.
Issue Date: Aug-2014
Publisher: Springer Verlag
Source: Çelik, İ., Gültekin, V., Allmer, J., Doğanlar, S. , and Frary, A. (2014). Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing. Molecular Breeding, 34(2), 323-334. doi:10.1007/s11032-014-0036-0
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.
URI: http://doi.org/10.1007/s11032-014-0036-0
http://hdl.handle.net/11147/5548
ISSN: 1380-3743
1572-9788
Appears in Collections:Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

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