Screening and characterization of novel microsatellite loci in Lateolabrax japonicus.

Lateolabrax japonicus, an economically important species, is widely consumed in the offshore coasts of China, Korea, and Japan. We identified 10 new L. japonicus microsatellite markers, using a modified protocol of fast isolation by AFLP of sequences containing repeats. Thirty L. japonicus individuals were collected from Xiamen, China, to evaluate the degree of polymorphism. The number of identified alleles ranged from three to five. The polymorphism information content varied from 0.267 to 0.711, whereas the observed and expected heterozygosities ranged from 0.249 to 0.706 and 0.294 to 0.751, respectively. One of the 10 loci (L10) deviated from the Hardy-Weinberg equilibrium. These new microsatellite markers will provide a useful tool for the determination of population genetic structure and genetic diversity in L. japonicus.

Development of novel polymorphic microsatellite markers in Siganus fuscescens.

Rabbitfish, Siganus fuscescens, is widely distributed in the Indo-Pacific regions and eastern Mediterranean. Its dwelling place includes reef flats, coral reef regions, and seagrass meadows in tropical area and reef areas or shallow waters in locations at high latitudes. In the present study, 10 new polymorphic microsatellite markers were screened from 30 wild S. fuscescens individuals, using a method of fast isolation protocol and amplified fragment length polymorphism of sequences containing repeats. The number of polymorphic alleles per locus was 3 to 5 with a mean of 4.3, while the value of polymorphic information content ranged from 0.283 to 0.680. The values of the observed and expected heterozygosities were in the range 0.3333-0.8462 and 0.3011-0.7424, respectively. Deviation from Hardy-Weinberg equilibrium was not observed in this study. These polymorphic loci are expected to be effective in evaluating the genetic diversity, population structure, and gene flow and in determining the paternity in S. fuscescens, as well as for conservation management.

Isolation and characterization of microsatellite markers in Ruditapes philippinarum.

Ruditapes philippinarum is considered a commercially valuable species, which is commonly found in tidal flats along West Pacific coasts. In China, it is mainly distributed in the southeast sea. In this study, 16 novel microsatellite loci from the R. philippinarum genome were developed, using the protocol of fast isolation by amplified fragment length polymorphism of sequence containing repeats. Thirty-two wild-caught individuals were used to evaluate the degree of polymorphism of these markers. Our results show that there were 10 polymorphic loci and 6 monomorphic loci. The number of alleles per locus and the polymorphism information content ranged from 2 to 6 and from 0.199 to 0.751, respectively. The observed and expected heterozygosities varied from 0.1333 to 0.6207 and 0.1603 to 0.7412, respectively. Of all loci, only one locus was found to deviate significantly from Hardy-Weinberg equilibrium after Bonferroni correction. The loci identified here will provide useful information for future population genetic studies of R. philippinarum.

Isolation and characterization of eight novel microsatellite markers in Acanthopagrus schlegelii.

Acanthopagrus schlegelii is a warm temperate demersal fish, which inhabits the sediment substrate or rocky reefs in shallow seas. As this fish is a nutritionally endowed species with good palatability, it is a highly valuable commercial species for aquaculture and has a long historical standing in Western Pacific countries. Because the population of this fish is currently declining in China, studies and measures aimed at addressing this decline are needed. In this study, eight microsatellite markers were screened from 30 wild A. schlegelii fishes through the FIASCO method, whereby sequences containing repeats were obtained from amplified fragment length polymorphisms. The allelic number ranged from 3 to 5, with a mean number of 3.625. The average observed heterozygosity was 0.6290, ranging from 0.3214 to 0.8966, while the expected heterozygosity was 0.5435, ranging from 0.3452 to 0.6721. The value for polymorphism information content ranged from 0.313 to 0.666. These results show this population has moderate genetic variation and low genetic diversity. These novel polymorphic loci will be useful for future genetic studies of A. schlegelii.

Isolation and characterization of microsatellite markers in Atrina vexillum Born.

Atrina vexillum Born is an economically valuable species, widely distributed in the coastal waters of temperate and tropical areas of the Asia Pacific region. Twenty one novel microsatellite loci were identified in the genome of A. vexillum Born using the protocol for fast isolation by amplified fragment length polymorphism of sequence containing repeats. Thirty-two wild type individuals were used to evaluate the degree of polymorphism of these markers. We identified 13 polymorphic and 8 monomorphic loci with the number of alleles per locus and the polymorphism information content ranging from 2 to 5 and 0.141 to 0.664, respectively. The observed and expected heterozygosity varied from 0.1250 to 0.7000 and 0.1223 to 0.6216, respectively. Two loci deviated significantly from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction, whereas the other loci were in HWE. These loci are expected to provide useful information for population genetic studies of A. vexillum Born.

Isolation and characterization of novel microsatellite markers in Mercenaria mercenaria.

Mercenaria mercenaria, also known as the hard clam, is widely distributed in the coastal waters of temperate and tropical areas in the Asian Pacific region. This species is widely popular in the international market, especially in the United States, Europe, and other Western countries, because of its high protein value, taste, and simple farming requirements. In this study, 17 novel microsatellite loci from the M. mercenaria genome were developed using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol. Thirty-two wild individuals were used to evaluate the degree of polymorphism of these markers. Results indicated that there were 11 polymorphic loci and six monomorphic loci, and the number of alleles per locus and the polymorphism information content ranged from two to six and from 0.059 to 0.498, respectively. The observed and expected heterozygosity varied from 0.0625 to 0.5333 and 0.0615 to 0.4977, respectively. The Y1-4 locus deviated significantly from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction was applied, while the other loci were in HWE. These loci will provide useful information for M. mercenaria population genetic studies.

Isolation and characterization of new microsatellite loci in Fenneropenaeus penicillatus.

Fenneropenaeus penicillatus is one of the major economic shrimp species in China. In this study, 14 novel microsatellite loci were developed using the fast isolation protocol with amplified fragment length polymorphism of sequences containing repeats (FIASCO). Polymorphisms were tested in 30 individuals from a single-wild population. The results showed that the number of alleles at each locus ranged from two to four, and the polymorphism information content varied from 0.314 to 0.692. The observed and expected heterozygosities ranged from 0.3343 to 0.6542 and from 0.3458 to 0.6657, respectively. Three loci deviated significantly from Hardy-Weinberg equilibrium after a Bonferroni correction was applied, while no deviations were detected in the other 11 loci. The new microsatellite loci identified in this study could be useful in future F. penicillatus population genetic, conservation research, population structure assessment, and linkage map construction studies.

Isolation and characterization of new microsatellite markers in red tail prawn, Fenneropenaeus penicillatus, an endangered species in China.

Until recently, Fenneropenaeus penicillatus was considered a commercial shrimp species. However, in 2005, it was included on the Red List as an endangered species by the Chinese government. In this study, 19 new microsatellite markers in F. penicillatus were developed and tested in samples of 32 wild individuals from Nanao, China. Twelve loci were polymorphic and 7 were monomorphic. Of the 12 polymorphic loci, the number of alleles per locus ranged from 3 to 6, with an average of 4.42 alleles per locus. The polymorphism information content ranged from 0.302 to 0.670, with a mean of 0.4817. The observed and expected heterozygosities ranged from 0.2250 to 0.8889 and from 0.1111 to 0.7750, respectively. Significant deviations from Hardy-Weinberg equilibrium (HWE, adjusted P < 0.0042) after a Bonferroni correction were observed in 3 loci (NA-9, NA-57, and NA-64), whereas the other 9 loci were in HWE. These new microsatellite markers will be useful in further research on the population genetic structure of F. penicillatus.

Isolation and characterization of microsatellite loci in hybrid giant tiger grouper.

The hybrid giant tiger grouper is a fish that has considerable commercial value and has become increasingly important for aquaculture in South East Asia since 2008. In order to prevent any reduction in genetic diversity in hybrid grouper as a result of aquaculture, we have identified 21 microsatellite markers that can be used to estimate genetic variation in the fish population. The number of alleles at polymorphic microsatellite loci ranged from 2 to 7, and observed and expected heterozygosities varied from 0.0323 to 0.9643 and 0.0921 to 0.7174, respectively. Polymorphism information content values ranged from 0.088 to 0.737. Nineteen of the 21 loci were in Hardy-Weinberg equilibrium (P > 0.005) after application of the Bonferroni correction (k = 10), the exceptions being ZZLD35 (P < 0.005) and ZZLD36 (P < 0.001). No linkage disequilibrium was detected. These 21 microsatellite markers are potentially of great value for analyzing genetic diversity to provide essential information for sustainable management of these fish.

Screening and characterization of novel polymorphic microsatellite markers from sea cucumber Holothuria leucospilota.

The sea cucumber Holothuria leucospilota has high me-dicinal value and rich nutritional edible value, and thus is a commercially important aquatic product in China. Microsatellite loci were developed and screened using a fast isolation protocol and amplified fragment length polymorphism of sequences containing repeats. In this study, 16 novel polymorphic microsatellite markers in H. leucospilota were identified, and the relevant genetic variability index was assessed using 30 individu-als from a wild population. The polymorphic information content ranged from 0.183 to 0.668, and the number of alleles per locus varied from 3 to 5. The observed and expected heterozygosities were 0.0370-0.5000 and 0.0776-0.6250, respectively. With the exception of 3 loci (Y1-15, Y11-1, and Y28), the polymorphic loci were in Hardy-Weinberg equilibrium (P > 0.003125). These polymorphic microsatellite loci will contribute to studies of genetic diversity, the research of population structure, and the design of conservation strategies for H. leucospilota.