Chul Min An

Isolation and characterization of 26 novel polynucleotide microsatellites from short barbeled grunter (Hapalogenys nitens) for genetic analysis

Short barbeled grunter, Hapalogenys nitens, is an important fishery resource and it has been regarded as a target marine fish species for prospective aquaculture diversification in Korea, but sustainable fry production is not yet possible. This delay has led to an increase in the need for genetic information about this species. Furthermore, it is necessary to conserve the wild stocks for the sustainable use of the species. In this study, we report 26 novel polymorphic microsatellites with a mean of 4.9 alleles per locus. The mean observed and expected heterozygosity per locus was 0.45 and 0.50, respectively. Cross-amplification revealed variability in others two Haemulidae species. These markers developed can be a valuable tool for conservation genetics and further genetic improvement of these species.

Characterization of 22 polymorphic microsatellite markers for seven-band grouper Epinephelus septemfasciatus developed using a 454 pyrosequencing approach

Seven-band grouper, Epinephelus septemfasciatus, is of considerable economic value and a candidate species of aquaculture in Eastern Asia. It is necessary to monitor the stocks for the sustainable use and aquaculture of the species. Monitoring genetic variation among marine resources necessitates the development of genetic markers. Here, we report 22 polymorphic microsatellite markers with 2–16 alleles per locus. The mean observed and expected heterozygosity per locus was 0.53 and 0.57, respectively. Cross-amplification revealed variability in Epinephelus bruneus and Epinephelus akaara. The 22 markers developed can be a valuable tool for genetic conservation of this species.

Genetic diversity and differentiation of the Korean starry flounder ( Platichthys stellatus ) between and within cultured stocks and wild populations inferred from microsatellite DNA analysis

The Korean starry flounder, Platichthys stellatus, is economically valuable coastal resident fish species. However, the annual catch of this fish has fluctuated and suffered major declines in Korea. We examined the genetic diversity and population structure for four wild populations and three hatchery stocks of Korean starry flounder to protect its genetic integrity using nine microsatellites. A group of 339 genotypes belonging to seven populations were screened. High degrees of polymorphism at the microsatellite loci were observed within both the wild and hatchery populations. Compared to the wild populations, genetic changes, including reduced genetic diversity and highly significant differentiation, have occurred in cultured stocks. Significant population differentiation was also observed in wild starry flounder populations. Similar degrees of inbreeding and significant Hardy–Weinberg equilibrium deviations were detected in both the wild and the hatchery populations. The genetic connectivity pattern identified four distinct metapopulations of starry flounder in Korea by clustering in the phylogenetic tree, Bayesian analyses, molecular variance analysis, PCA and multidimensional scaling analysis. A pattern of isolation-by-distance was not significant. This genetic differentiation may be the result of the co-effects of various factors, such as historic dispersal, local environment or anthropogenic activities. These results provide useful information for the genetic monitoring of P. stellatus hatchery stocks, for the genetic improvement of this species by selective breeding and for designing suitable management guidelines for the conservation of this species.

Genetic differences between wild and hatchery populations of red sea cucumber (Stichopus japonicus) inferred from microsatellite markers: implications for production and stocking programs design

Red sea cucumber Stichopus japonicus is the most important and valuable commercial sea cucumber species in Korea. Its farming and stock enhancement started in the early 2000s and is still rapid expansion in Korea. Therefore, the analyses of genetic status of wild and hatchery populations are necessary to maintain the genetic diversity of this valuable marine resource. In this study, possible genetic similarity and differences between the wild population and hatchery population in Jeju, Korea were accessed using multiplex assays with eight highly polymorphic microsatellite loci. High levels of polymorphism were observed between the two populations. A total of 93 different alleles were found. Although a considerable loss of unique alleles and relatively high inbreeding coefficient value were observed in the hatchery samples, no statistically significant reductions were found in heterozygosity or allelic diversity in the hatchery population, compared with the wild population. However, significant genetic heterogeneity was found between two populations. These results suggest that genetic drift has probably promoted differentiation between populations, and stocking intensity in wild populations may correlate with loss of genetic integrity. Therefore, the sustainable exploitation plans of the fishery resource should be developed by applying basic genetic principles combined with molecular monitoring. This genetic baseline information of Korean red sea cucumber has important implications for designing of genetically sustainable restocking programs and more efficient conservation management guidelines for these valuable genetic materials.

Isolation and characterization of polymorphic microsatellite markers from the Korean common squid Todarodes pacificus (Ommastrephidae)

The common squid, Todarodes pacificus, is an important fisheries species, but fluctuations in its abundance and its reproductive biology are poorly understood. To enable sustainable management of this resource, 21 novel polymorphic microsatellite loci were isolated using an enrichment method based on the magnetic/biotin capture of microsatellite sequences from a size-selected genomic library. To characterize each locus, 48 individuals from a natural T. pacificus population from the western coastal waters of Korea were genotyped. All of the microsatellite loci were highly polymorphic with 10–32 alleles per locus. The observed and expected heterozygosities ranged from 0.417 to 0.917 and 0.791 to 0.965, respectively. The high variability revealed in this study suggests that the microsatellite markers could be a useful tool for future conservation genetics studies and for the sustainable exploitation of this resource.