Characterization of mirosatellite DNA in giant tiger prawn Penaeus monodon genome

Abstract

This research had the objectives to isolate and characterize microsatellites in the giant tiger prawn, Penaeus monodon, genome and to develop genetic markers for use in various applications including population genetic studies, selective breeding and genome mapping etc. One hundred and thirty one microsatellites were isolated and characterized from partial genomic libraries of the giant tiger prawn (P. monodon) by screening with an oligonucleotide probe (GT)15. These microsatellites were classified as perfect, imperfect and compound repeats. With 51.9%, imperfect repeats were the predominant category of microsatellites in P. monodon genome found in this study. A total of 97 (GT)n microsatellites were isolated and the frequency of the (GT)n repeats in the genome was estimated. The average distance between neighbouring (Gt)n microsatellites was 92.8 kb. The most common size class in all categories contained sequences between 30-35 repeats in length. PCR primers were designed from the unique flanking sequences of 7 microsatellites, 2 pairs for (AT)n and 5 pairs for (GT)n microsatellites. By testing 8 individual prawns from krunturg, the Andaman Sea and Angsila, the Gulf of Thailand with the PCR amplification, it was found that 3 of 7 microsatellite primer sets, namely, Pmo 18, Pmo 386 and Pmo 14, produced fragments whose sizes were in the expected range, the others gave nonspecific amplifications. Two microsatellite loci, Pmo 18 and Pmo 386, yielded scorable PCR products and showed high level of polymorphism indicating their potential use in DNA typing of P. monodon