Development of microsatellite markers in black tiger shrimp (Penaeus monodon Fabricius)

Microsatellites or Simple Sequence Repeats (SSRs)represent an abundant source for genetic markers in eukaryotic genomes. Nine synthesized repeat sequences labeled with biotin were used to create an enriched microsatellite library [(AG)(10), (TG)(10), (GAA)(10), (GAC)(10), (CAT)(10), (TAC)(10), (GACA)(8), (GATA)(8), and (TCAG)(8)] for Penaeus monodon. From a total of 2417 clones, only 406 clones (16.8%) were positive after colony hybridization against the nine repeat sequences. Those clones with insert sizes ranging from 300 to 1000 bp were isolated and characterized. The most abundant repeat sequences in the P monodon genome are (AG), and (CAT)(n) making up to 22% and 21%, respectively. A total of 102 from the 129 primer pairs (designed for 129 clones chosen) were able to amplify P monodon DNA. According to the sequences of the 102 clones, 27 loci, 17 loci, 4 loci, and 54 loci were dinucteotide, trinucleotide, tetranucleotide, and compound repeat sequences, respectively. Thirty microsatellite primer pairs were used to screen wild P monodon germplasm and the result revealed PIC values ranged from 0.4275 to 0.9264. Therefore, this set of microsatellite primers would provide a useful tool in P monodon breeding programs. (C) 2003 Elsevier Science B.V. All rights reserved.