Analysis Of Microsatellites In The ESTs And Entire Tribolium Castaneum Genome Database And Isolation Of Polymorphic Microsatellite Loci

Tribolium castaneum serves as a prominent species in a wide range of research area such as hostparasite interaction, sexual selection, and population genetics. By using bioinformatics method and a downloaded software(SSRfinder), ESTs and entire Tribolium castaneum genome database were screened. The criteria used in SSRFinder to dentify microsatellites is: motifs that are more than12bp.52886(include 37683 mononucleotide) microsatellites were obtained from ESTs and 43791(include 2050 mononucleotide) microsatellites in the whole genome database. The frequency of microsatellite in ESTs is 1/0.87kb, and in genome is 1/3.65kb. As there is too many mononucleotide in the ESTs, it has an immense effect on the frequency of microsatellite in ESTs, which also affect the result profoundly. When we removed mononucleotide, the frequency of microsatellite in ESTs is 1/3.01kb, and in genome is 1/3.82kb.In the study, the author analyzed the abundance and density of various microsatellite types in the Tribolium castaneum ESTs and in the whole genome sequence. The density of poly(A)or poly(T) is 9 times more than that of poly(G) or poly(C) in the both ESTs and genome. Analysis of the densities of dinucleotide repeats showed that AT and CA repeats had the highest desity. TAA(genome)and CTA(ESTs) had the highest density in trinucleotide repeats. TAAA and TAAAA is the highest in tetranucleotide and pentanucleotide repeats. While, TAATAT(ESTs)and TAAA(genome) had the highest density in hexanucleotide repeats. In conclusion, Both ESTs and genome contain abundance A-rich or T-rich repeat in SSRs.Thirty primer pairs were designed from microsatellites using computer program Primer Premier (Version 5.00). Of the 25 primers that produced product, nine primers were polymorphic. In these nine microsatellite loci, the alleles numbers distributed from 2 to 5, and the range of these alleles were 100 to 300bp and similar with their predicted size. The expected heterozygosity and the PIC values of them distributed from 0.494 to 0.791 and 0.368 to 0.631, respectively. These values showed that these 8 microsatellite loci were suitable for genetic analysis.