Isolation and characterization of microsatellite markers in the black tiger prawn Penaeus monodon

Abstract

Isolation and characterization of microsatellite sequences from the genome of the black tiger prawn Penaeus monodon are described. Ninety-seven (GT)(n) and 16 (CT)(n) microsatellites were isolated from partial genomic libraries composed of 18,000 and 5250 clones, respectively. The genomic library screening indicated that (GT)(n) microsatellites are more abundant than (CT)(n) in P. monodon genome. The microsatellite sequences were classified into three categories, perfect, imperfect, and compound. The predominant categories found in P. monodon microsatellites are imperfect repeats for both (GT)(n) and (CT)(n). Very long repeat arrays were found in P. monodon microsatellite clones, which resulted in difficulties in primer design. Two microsatellite loci, CUPmo 18 and CUPmo 386, were successfully amplified. The number of alleles of each locus was preliminarily determined. For the CUPmo 18 locus, Mendelian inheritance was tested by analysis of genotypic ratios in F1 offspring and their parents. The results of this study demonstrate the presence of highly polymorphic microsatellite markers in P. monodon. These markers will be useful in population studies and parental determination in P. monodon. However, the low abundance and difficulties in obtaining a large number of usable microsatellite loci indicated that these markers may not be appropriate for use in genome mapping of this species.