Isolation of microsatellite markers from Fenneropenaeus chinensis ESTs

By using the online bioinformatics software Repeatmasker, the ESTs database of Chinese shrimp was screened. 229 microsatellite sequences were obtained from 10446 ESTs sequences, about 2.19% in the whole database. A total of 146 dinucleotide repeats and 58 trinucleotide repeats were found in these 229 microsatellite sequences and most of them were perfect repeats, with (AT)n in dinucleotide repeats and (TAA)n in trinucleotide repeats being the most common, about 28.82% and 17.03% in the total microsatellite sequences respectively. Nineteen primer pairs were designed from microsatellites using computer program Primer Premier ( Version 5.00). Among the 16 primers that can be detected PCR products by electrophoresis, eight primers were polymorphic in about 20 Chinese shrimp samples by electrophoresis analysis. In these eight microsatellite loci, the alleles numbers distributed from 5 to 15, and the range of these alleles were between 165 to 305bp, similar to their predicted size. The expected heterozygosity and the PIC values of them distributed from 0.59 to 0.89 and 0.56 to 0.88, respectively. These values showed that these 8 microsatellite loci were suitable for genetic analysis.