Abstract:  In order to explore the polymorphism of EST-SSR markers in silkworm, we retrieved and analyzed 4 465 expressed sequence tags (ESTs) on linkage group 12 of the silkworm, Bombyx mori. After splicing and jointing, we obtained 581 non-redundant ESTs with the total length about 480 kb. A total of 154 simple sequence repeats (EST-SSRs) were detected in 122 ESTs which accounted for 2.73% of all the investigated ESTs, meaning one EST-SSR per 3.12 kb on average. Trinucleotide repeats and tetranucleotide repeats were the main classes， which accounted for 36.36% and 28.57% of all detected EST-SSRs, respectively. The average length of nucleotide repeats was 16.2 bp, and the maximum was 30 bp. Homologous sequences of 26 EST-SSRs were retrieved in NCBI database, which contained 40 SSRs. Among them, 14 SSRs (35.0%) were located in the 5′-UTR, 11 SSRs (27.5%) in the 3′-UTR and 15 SSRs (37.5%) in the coding sequences (CDSs). Eleven primer pairs were designed for the screened EST-SSRs and 8 of them showed polymorphic bands. The primer ES1204 showed polymorphism among 8 silkworm strains. The results suggest that it is feasible to find SSR markers through searching of silkworm EST databases.

Key words: Silkworm (Bombyx mori), linkage group, expressed sequence tags (ESTs), EST-SSR markers, polymorphism