We isolated novel dinucleotide, trinucleotide, and tetranucleotide microsatellites from the genome of Asian sea bass (Lates calcarifer). Two genomic DNA libraries were established, one was enriched for (CA)n repeats, while the other for (GATA)n, (GACA)n, and (AAC)n repeats. Sixty clones containing an insert between 250 and 1000 bp in size were sequenced from each library; altogether 50 (43%) of them contained microsatellites. Forty microsatellites were characterized in 16 unrelated Asian sea bass individuals. Twenty-eight of them (70%) showed specific amplification and polymorphism. The allele number per loci varied between 2 and 20 with an average of 5.3, while expected heterozygosity ranged from 0.31 to 0.95 with an average of 0.64. At some loci allele sizes spread over a wide range (>100 bp). No significant correlation (r = 0.23, df = 31, P > 0.05) was found between the repeat number and the number of alleles. A whole broodstock containing 170 individuals was analyzed by using 8 selected polymorphic microsatellites. The average number of alleles per locus was 11.8 (range, 4–21). The expected heterozygosity ranged from 0.57 to 0.90 with an average of 0.75, while the fixation index was 0.02. Genetic similarity between individuals ranged from 0 to 0.72. Comparison of allele frequencies between the broodstock and the 24 nonrelated individuals revealed some unique alleles.
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