Development of SSR Markers in Aquatic Plant Nymphoides peltata (Menyanthaceae) Based on Information from Transcriptome Sequencing

Using the program MISA, a total of 12319 EST-SSRs were sought out from 79536 ESTs of aquatic plant Nymphoides peltata. Dinucleotide and trinucleotide SSRs were the two main motif types, accounting for 57.31% and 30.87%, respectively. The most abundant di-and tri- motifs were AG/CT (29.76%) and AAG/CTT (8.66%), respectively. We randomly selected 130 primer pairs to evaluate their application and polymorphism across two populations of N. peltata. Seventy-eight SSR markers were amplified successfully, yielding clear and discernible bands, among which 37 were found to be polymorphic and the polymorphic rate was 47.44%. Using the polymorphic SSR markers, a total of 114 alleles were detected. The number of alleles per locus ranged from 2 to 6 (mean 3.08). Observed heterozygosity (H_o) and expected value (H_e) per locus varied from 0.229 to 1.000 and from 0.351 to 0.756, respectively. Polymorphism information content (PIC) ranged from 0.286 to 0.698, with an average of 0.495.The results indicated that the development of SSR molecular markers from the EST dataset generated by next generation sequencing in the aquatic plant N.peltata is valuable and effective. These newly generated SSR makers will provide new tools for studying genetic diversity and population genetic structure of N.peltata.