Objective: To provide powerful tools for molecular marker-assisted breeding and resources protection by analyzing the simple sequence repeat (SSR) information in the transcriptome of Fritillariae Cirrhosae Bulbus. Method: The Illumina HiSeq2000 technology platform was used for high throughput sequencing of the bulbs and leaves of Fritillariae Cirrhosae Bulbus

and MISA software was used for SSR loci analysis of Unigene. Result: 3 817 SSR loci were found in a total of 44 973 unigenes obtained from the transcriptome

distributing in 3 367 unigenes in the examined sequences. Frequency of occurrence for SSRs was 8.49%

and the density of distribution was 1/10.37 kb on average. Tri-nucleotide and di-nucleotid repeats were predominated with an occurrence frequency of 56.51%and 27.06%

respectively. CCG/CGG of Tri-nucleotide was the most frequent one among all the repeat types

followed by AG/CT of di-nucleotid repeats. The number of SSR repeats was mainly between 4-12 times

and the sequence length of 24.55%SSR was higher than 20 bp. Conclusion: The SSR loci in the transcriptome of Fritillariae Cirrhosae Bulbus show high frequency

rich types

and high polymorphism

which will might be applied in the study on the candidate gene mining and marker-assisted breeding.