Abstract:   【Objective】The aims of this study is to characterize the distribution of simple sequence repeats (SSR) in the transcribed regions of Panax ginseng, and to develop genomic SSR (G-SSR) and unigene derived microsatellite (UGMS) markers in Panax ginseng. 【Method】A data set of 7 649 expressed sequence tags (ESTs) of P. ginseng downloaded from NCBI was assembled to obtain the unigenes. SSR-containing unigenes and genome were selected to characterize the SSR distribution in ginseng genome. A set of UGMS and G-SSR primers was designed to amplify genomic DNA of ginseng and other Araliaceae species. 【Result】A total of 4 869 unigenes with a length of 2.72 Mb were predicted. From 488 SSR-containing unigenes (10.02%), 724 UGMS were identified with a density of 1 per 3.75 kb of unigenes. Dinucleotide repeats (48.06%) were the most abundant followed by mono (29.28%) and tri-nucleotide repeats (19.06%). The motifs of AT/TA and AAG/CTT were mostly distributed in untranslated region and protein coding region, respectively. Among the 100 UGMS and 44 G-SSR primer pairs, 86 and 44 ones showed amplifications in a set of 9 ginseng accessions. Polymorphisms between the accessions were found to be 42.0% and 43.2%, respectively. The transferability of ginseng UGMS marker to P. guinquefolius, P. notoginseg and E. senticosus was 100%, 87.2% and 75.6%, while 95.5%, 72.7% and 40.9% for G-SSR, respectively. 【Conclusion】The SSR shows higher frequency in ginseng and the most abundant motif is dinucleotide. The distribution of UGMS was non-random with respect to different genic regions. UGMS markers detected a lower polymorphism but a higher level of transferability than those derived from genomic SSR.

Key words: Panax ginseng, UGMS, genomic SSR