Abstract: Abstract：To develop efficient and practical EST-SSRs markers，10 179 EST sequences each of which
contained at least one SSR were obtained from 120 605 non-redundant EST in pepper，accounting for
8.44% in all EST. Mononucleotide，dinucleotide and trinuleotide were the main repeat types with a
percentage of 91.63% in all EST-SSRs. A/T was the most frequent motif with a frequency of 31.17%，
followed by TC/GA and CT/AG，accounting for 10.0% and 9.97% respectively. Twenty pairs of EST-SSRs
primers were designed and synthesized and were used to amplify 25 pepper varieties. The results showed
that 17 pairs of primers could amplify clear bands，and 12 out of 17 pairs could amplify 42 polymorphic
bands with an average of 3.5 bands per pair of primer. The polymorphic information content of primers
screened were between 0.21 and 0.95. The clustering results of 25 pepper varieties based on EST-SSRs
markers were in agreement with morphological and biological classification，it is indicated that EST-SSRs
markers developed in the study could be used for germplasm resources genetic diversity analysis in pepper.

Key words: pepper, EST-SSR, molecular marker, genetic diversity