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An, Hye-Suck,Kim, Eun-Mi,Lee, Jang-Wook,Kim, Dae-Jung,Kim, Yi-Cheong The Korean Society for Integrative Biology 2012 Animal cells and systems Vol.16 No.1
Eighteen new polymorphic microsatellite markers were developed for the Korean mi-iuy croaker ($Miichthys$ $miiuy$, Perciformes, Sciaenidae), and allelic variability was compared between a wild population in Mokpo, Korea, and a hatchery population in Tongyeong, Korea. All loci were amplified readily and demonstrated allelic variability, with the number of alleles ranging from 5 to 37 in the wild population, and from 4 to 12 in the farmed population. The average observed and expected heterozygosities were estimated, respectively, to be 0.74 and 0.78 in the hatchery population samples, and 0.79 and 0.86 in the wild samples. These results indicate lower genetic variability in the hatchery population compared with the wild population, and significant genetic differentiation between the wild population and the hatchery samples ($F_{ST}$=0.058, P<0.001). These microsatellite loci may be valuable for future population genetic studies, monitoring changes in the genetic variation within stocks in a commercial breeding program, conservation genetics, and molecular assisted selective breeding of the mi-iuy croaker in the future.
An, Hye Suck,Kim, Byeong Hak,Lee, Jang Wook,Dong, Chun Mae,Kim, Shin Kwon,Kim, Yi Cheong Molecular Diversity Preservation International (MD 2011 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.12 No.9
<P>Pen shell (<I>Atrina pectinata</I>) is a popular food source with a high commercial value in a number of Asian Pacific areas. The natural <I>A. pectinata</I> population has been declining continuously over the past several decades. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of pen shell populations. In this study, 20 polymorphic microsatellite (MS) DNA markers were identified from a partial genomic pen shell DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery pen shell populations in Korea. A total of 438 alleles were detected at the 20 MS loci in the two populations. All loci were easily amplified and demonstrated allelic variability, with the number of alleles ranging from 5 to 35 in the wild population and from 5 to 22 in the farmed population. The average observed and expected heterozygosities were 0.69 and 0.82, respectively, in the hatchery samples and 0.69 and 0.83, respectively, in the wild samples. Statistical analysis of fixation index (<I>F</I><SUB>ST</SUB>) and analysis of molecular variance (AMOVA) showed minor, but significant, genetic differences between the wild and hatchery populations (<I>F</I><SUB>ST</SUB> = 0.0106, CI<SUB>95%</SUB> = 0.003–0.017). These microsatellite loci may be valuable for future aquaculture and population genetic studies for developing conservation and management plans. Further studies with additional pen shell samples are needed to conclusively determine the genetic diversity between the wild and hatchery populations.</P>
An, Hye Suck,Lee, Jang Wook,Kim, Hyun Chul,Myeong, Jeong-In Molecular Diversity Preservation International (MD 2011 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.12 No.8
<P>The Pacific abalone, <I>Haliotis discus hannai</I>, is a popular food in Eastern Asia. Aquacultural production of this species has increased because of recent resource declines, the growing consumption, and ongoing government-operated stock release programs. Therefore, the genetic characterization of hatchery populations is necessary to maintain the genetic diversity of this species and to develop more effective aquaculture practices. We analyzed the genetic structures of five cultured populations in Korea using six microsatellite markers. The number of alleles per locus ranged from 15 to 64, with an average of 23.5. The mean observed and expected heterozygosities were 0.797 and 0.904, respectively. The inbreeding coefficient <I>F</I><SUB>IS</SUB> ranged from 0.054 to 0.184 (mean <I>F</I><SUB>IS</SUB> = 0.121 ± 0.056). The genetic differentiation across all populations was low but significant (overall <I>F</I><SUB>ST</SUB> = 0.009, <I>P</I> < 0.01). Pairwise multilocus <I>F</I><SUB>ST</SUB> tests, estimates of genetic distance, and phylogenetic and principal component analyses did not show a consistent relationship between geographic and genetic distances. These results could reflect extensive aquaculture, the exchange of breeds and eggs between hatcheries and/or genetic drift due to intensive breeding practices. Thus, for optimal resource management, the genetic variation of hatchery stocks should be monitored and inbreeding controlled within the abalone stocks that are being released every year. This genetic information will be useful for the management of both <I>H. discus hannai</I> fisheries and the aquaculture industry.</P>
An, Hye Suck,Kim, Eun Mi,Lee, Jang Wook,Dong, Chun Mae,Lee, Bai Ik,Kim, Yi Cheong Molecular Diversity Preservation International (MD 2011 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.12 No.6
<P>In this study, we developed 20 polymorphic microsatellite markers for the Korean black scraper, <I>Thamnaconus modestus</I> (Günther, 1877), Monacanthidae, and used them to compare allelic variation between wild and hatchery populations in Korea. All loci were readily amplified and demonstrated allelic variability, with the number of alleles ranging from 5–35 in the wild population and 5–22 in the farmed population. The average observed and expected heterozygosities were estimated, respectively, as 0.74 and 0.80 in the hatchery samples and 0.78 and 0.81 in the wild ones. These results indicate lower genetic variability in the hatchery population than in the wild population and minor, but significant, genetic differentiation between the two populations (<I>F</I><SUB>ST</SUB> = 0.005, <I>P</I> < 0.01). Additionally, cross-amplification was tested in another monacanthid species, <I>Stephanolepis cirrhifer</I>; many loci were found that yielded useful information. The high degree of polymorphism exhibited by the 20 microsatellites will be useful in future aquaculture and population genetic studies for developing conservation and management plans.</P>
An, Hye-Suck,Kim, Jae-Woo,Lee, Jang-Wook,Kim, Shin-Kwon,Lee, Bae-Ik,Kim, Dae-Jung,Kim, Yi-Cheong The Korean Society for Integrative Biology 2012 Animal cells and systems Vol.16 No.1
Kelp grouper ($Epinephelus$ $bruneus$ Bloch 1793) is a commercially important fish in Korea. In recent years, the catch of kelp grouper in the coastal waters of Korea has significantly declined. Despite its importance, little is known about its genetic diversity and conservation efforts are hampered. In this study, we isolated and characterized 12 microsatellite loci using an enrichment method based on magnetic/biotin capture of microsatellite sequences from a size-selected genomic library. All loci were readily amplified and contained TG/CA denucleotide repeats. To characterize each locus, 30 individuals from a natural E. bruneus population in the coastal waters of Jeju Island, Korea, were genotyped. All loci except three, KEm118, KEm154, and KEm219, were polymorphic, with an average of 8.1 alleles per locus (range 2-18). The mean observed and expected heterozygosities were 0.47 (range 0.19-1.00) and 0.61 (range 0.29-0.92), respectively. A significant deviation from Hardy-Weinberg equilibrium was observed at three loci (KEm134, KEm184, and KEm283). These findings will be useful for effective monitoring and management of genetic variation of kelp grouper as well as for the implementation of a fisheries conservation program.
An, Hye Suck,Lee, Jang Wook Molecular Diversity Preservation International (MD 2012 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.13 No.8
<P><I>Mytilus coruscus</I> (family Mytilidae) is one of the most important marine shellfish species in Korea. During the past few decades, this species has become endangered due to the loss of habitats and overfishing. Despite this species’ importance, information on its genetic background is scarce. In this study, we developed microsatellite markers for <I>M. coruscus</I> using next-generation sequencing. A total of 263,900 raw reads were obtained from a quarter-plate run on the 454 GS-FLX titanium platform, and 176,327 unique sequences were generated with an average length of 381 bp; 2569 (1.45%) sequences contained a minimum of five di- to tetra-nucleotide repeat motifs. Of the 51 loci screened, 46 were amplified successfully, and 22 were polymorphic among 30 individuals, with seven of trinucleotide repeats and three of tetranucleotide repeats. All loci exhibited high genetic variability, with an average of 17.32 alleles per locus, and the mean observed and expected heterozygosities were 0.67 and 0.90, respectively. In addition, cross-amplification was tested for all 22 loci in another congener species, <I>M. galloprovincialis.</I> None of the primer pairs resulted in effective amplification, which might be due to their high mutation rates. Our work demonstrated the utility of next-generation 454 sequencing as a method for the rapid and cost-effective identification of microsatellites. The high degree of polymorphism exhibited by the 22 newly developed microsatellites will be useful in future conservation genetic studies of this species.</P>
An, Hye Suck,Lee, Jang Wook,Kim, Hee Yong,Kim, Jong Bin,Chang, Dae Soo,Park, Jung Youn,Myeong, Jeong In,An, Chul Min Springer-Verlag 2014 Genes & Genomics Vol.36 No.2
Population genetics has been recognized as a key component of policy development for fisheries and conservation management. In this study, natural sea bass (Lateolabrax japonicus) populations in three ocean basins in Korea were assessed using multiplex assays with 12 highly polymorphic microsatellite loci; 203 alleles and similarly high levels of genetic diversity [mean number of alleles (N-A) = 14.43, mean expected heterozygosity (He) = 0.84] were detected. All populations showed significant heterozygote deficiency at four loci, which could be explained by the presence of null alleles. The genetic population subdivision was low and was significantly different according to F-statistics (overall F (ST) = 0.003, R (ST) = 0.005). However, this substructure was not supported by an analysis of molecular variance test, analyses of isolation by distance or Bayesian analysis. The passive dispersal of eggs/larvae via the main currents appears to facilitate gene flow. The possibility of a recent genetic bottleneck was observed in all three populations of L. japonicus, indicating that overfishing and degradation of the environment in recent years has led to a decline in the sea bass populations in Korea. Our study demonstrates that sea bass in Korea do not appear to be genetically partitioned and should be managed as a single unit; however, the potential for a rapid loss of genetic diversity remains. Information regarding the genetic characteristics of Korean sea bass populations has important implications for fishery management and conservation efforts and will aid in the sustainable exploitation of fishing resources and the preservation of biodiversity.