The golden pompano Trachinotus ovatus belongs to the Carangidae family. It is distributed in tropical and subtropical areas of Southeast Asia and Mediterranean sea. Because of its delicious taste and rapid growth, it has been one of the most important marine fish commercially cultured in South China. However, the wild population of golden pompano has been rapidly decreasing due to overfishing in recent years, and the genetic status of its wild population is little known so far (Chen et al. 2007). Therefore, to facilitate a better understanding of genetic diversity and population structure of golden pompano for conservation, we have isolated and characterized 21 polymorphic microsatellites from T. ovatus, because microsatellites are the markers of choice for a variety of population genetic studies (Fernandez-Silva et al. 2013).

Total genomic DNA was extracted from one T. ovatus, using a phenol–chloroform extraction method (Ma and Chen 2009). Then the DNA was stored at −20 °C until used. All polymerase chain reactions (PCRs) were conducted on the Eppendorf PCR machine.

A (GT)n enriched genomic library of T. ovatus was constructed by employing the Fast Isolation by amplified fragment length polymorphism (AFLP) of Sequences Containing repeats (FIASCO) protocol which described detailed by Liao et al. (2007). Finally, 219 clones were sequenced successfully, but only 150 sequences contained the sufficient repeat motifs more than 5. 137 Primer pairs were designed using the PRIMER PREMIER 5.0 software, and forward primer of each pair was labeled with the FAM fluorescent dye.

Polymorphisms of each locus were assessed in the captive-bred population (48 individuals) of T. ovatus, which were collected from South China Sea, China. Total genomic DNA was isolated by phenol–chloroform extraction method. PCR amplifications were carried out in a 15-μL volume containing 1.5 μL 10 × PCR buffer (Mg2+ free), 1.5 mM MgCl2, 0.25 mM dNTPs, 0.2 μM of the forward and reverse primers, and 1.0 U Taq polymerase (Takara) and 50 ng template DNA. PCR programme consisted of an initial denaturation step of 5 min at 94 °C, followed by 35 cycles of denaturation at 94 °C for 45 s, annealing listed in Table 1 for 45 s and extension at 72 °C for 45 s, finally extension at 72 °C for 10 min. Finally PCR products were run on the 3130xl capillary DNA analyzer (Applied Biosystems), and the allele sizes were analyzed using GeneMapper V4.0.

Table 1 Characteristics of 21 polymorphic microsatellite loci from T. ovatus
Full size table

POPGENE32 was used to calculate the allele numbers, the observed heterozygosities (H O ), expected heterozygosities (H E ) and Hardy–Weinberg equilibrium (HWE). Software Cervus 3.0 was used to assess polymorphism information content (PIC).

108 of the 137 selected loci were successfully amplified in the captive-bred population of T. ovatus, and only 21 loci were shown to be polymorphic. The number of alleles ranged from 2 to 10, with an average of 4.48. The H O ranged from 0.083 to 0.792, and H E ranged from 0.081 to 0.886, with an average of 0.585 and 0.589, respectively,it indicates that the genetic diversity of the captive-bred population are high. The PIC value ranged from 0.0767 to 0.8623 (Table 1), twelve of the 21 loci showed a high degree of polymorphism information content (PIC > 0.5) (Botstein et al. 1980). 6 loci (TO33, TO47, TO67, TO80, TO132-1, TO145) showed significant deviations from HEW in this population (p < 0.01), possibly for the existence of subpopulations, the small sample size, the presence of the null alleles or the inbreeding of the captive-bred population. The 21 novel informative and polymorphic microsatellite loci will provide useful information for the study of the population structure, genetic variation, conservation genetics of the T. ovatus in the future.