Characterization of Tri- and Tetranucleotide Microsatellites in the Black Tiger Prawn, Penaeus monodon

In order to characterize triand tetranucleotide microsatellites in the black tiger prawn, Penaeus monodon, a genomic library of P. monodon was screened with the repeats (GAA)n, (GATA)n, (GGAT)n, (GGAA)n and (CACC)n. In the 79 positive clones isolated, the repeats (GATA)n was found at the highest frequency, followed by the (GAA)n while the other sequence types were rare or not found. Sequencing of the microsatellite positive clones revealed that the predominant category of (GAA)n and (GATA)n microsatellites were perfect repeats, with the number of repeats ranging from 5 to 45 for (GAA)n and 4 to 16 for (GATA)n. Primers were designed for seven microsatellite loci and 6 pairs of primers produce scorable PCR products. Analysis of polymorphism in wild P. monodon caught off the Gulf of Thailand revealed that all six microsatellite loci were highly polymorphic with 21 to 29 alleles and heterozygosities of 16 to 89%. Cross-amplification using these microsatellite markers on related penaeid shrimps suggested low level of sequence similarity in microsatellite regions among penaeids.