Development of SSR markers in poppy (Papaver somniferum L.)

Abstract

The opium poppy (Papaver somniferum L.) belongs to the family Papaveraceae. Opium poppy is an important agronomic plant due to its production of more than 80 different alkaloids. In addition, poppy oil and seeds are used in food. The number of molecular markers for opium poppy is limited. To date, molecular characterization of opium poppy has been done using general marker systems such as AFLP, RAPD, ESTSSR and ISSR. However, development of other molecular markers systems is essential for more comprehensive analysis of the opium poppy genome. A genomic library was constructed from opium poppy DNA. Genomic DNA was sequenced by Roche 454 SequencingTM platform. Genomics reads were clustered by MIRA software. Di-, tri-, tetra-, penta- and hexanucleotide SSR repeats were identified and flanking primers were designed by Batchprimer3 software. A total of 1399 contigs containing 3284 SSRs were identified. A total of 1820 primer pairs which fulfilled the criteria for primer design were designed from flanking sequence of SSRs. A total of 100 SSR primers were tested in six Papaver somniferum accessions. No polymorphism was found among the Papaver somniferum accessions. Transferability of the markers was tested in seven Papaver species. SpSSR-6, spSSR-8 and spSSR-23 detected polymorphic alleles in these species. These markers are the first set of opium poppy-specific SSR markers derived from genomic sequence of this crop. These markers can be used for assessment of genetic diversity, mapping and marker assisted selection in opium poppy.