Comparative genetic diversity of wild and hatchery-produced Pacific oyster (Crassostrea gigas) populations in Korea using multiplex PCR assays with nine polymorphic microsatellite markers

The Pacific oyster, Crassostrea gigas, is the most important and valuable commercial fishery species in Korea. Its farming started 20 years ago and is still rapid expansion in Korea. In this study, to maintain the genetic diversity of this valuable marine resource, possible genetic similarity and differences between the wild population and hatchery population in Tongyeong, Korea were accessed using multiplex assays with nine highly polymorphic microsatellite loci. A total of 250 different alleles were found over all loci. Despite a long history of hatchery practices, very high levels of polymorphism (mean alleles = 22.89 and mean heterozygosity = 0.92) were detected between the two populations. 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 provide no evidence to show that hatchery practice of Pacific oyster in Korea has significantly affected the genetic variability of the hatchery stock. Although further studies are needed for comprehensive determinations of the hatchery and wild populations with increased number of Pacific oyster sample collections, information on the genetic variation and differentiation obtained in this study can be applied for genetic monitoring of aquaculture stocks, genetic improvement by selective breeding and designing of more efficient conservation management guidelines for these valuable genetic materials.     

Genetic differentiation among populations and color variants of sea cucumbers (Stichopus japonicus) from Korea and China

The Far Eastern sea cucumber, Stichopus japonicus, is a favored food in Eastern Asia, including Korea, Japan, and China. Aquaculture production of this species has increased because of recent declines in natural stocks and government-operated stock release programs are ongoing. Therefore, the analyses of genetic structure in wild and hatchery populations are necessary to maintain the genetic diversity of this valuable marine resource. In addition, given that sea cucumber color affects market price, with the rare, possibly reproductively isolated, red type being the most valuable, an understanding of the genetic structure and diversity in color variation of green and red types is necessary. We analyzed the genetic structure of wild and hatchery-produced green type S. japonicus from Korea and China, and wild red type from Korea using 9 microsatellite makers. The number of alleles per locus ranged from 11 to 29 across all populations. The mean allele numbers of the green types from Korea (10.6) and China (10.1) were similar, but differed slightly from that of the red type (9.1). Pairwise multilocus F(ST) and genetic distance estimations showed no significant differences between the green types from Korea and China, whereas the differences between the green and red types were significant. This was clearly illustrated by a UPGMA dendrogram, in which the two close subclusters of green types were completely separated from the red type. In addition, the allele frequencies of the green and red types were significantly different. Assignment tests correctly assigned 100% (quality index 99.97%) of individuals to their original color types and demonstrated the feasibility of microsatellite analysis for discrimination between color types.     

Genetic differences between wild and hatchery populations of Korean spotted sea bass (Lateolabrax maculatus) inferred from microsatellite markers

The spotted sea bass, Lateolabrax maculatus, is popular in recreational fishing and aquaculture in Korea. Its natural population has declined during the past two decades; thus, beginning in the early 2000s stock-enhancement programs were introduced throughout western and southern coastal areas. In this study, genetic similarities and differences between wild and hatchery populations were assessed using multiplex assays with 12 highly polymorphic microsatellite loci; 96 alleles were identified. Although many unique alleles were lost in the hatchery samples, no significant reductions were found in heterozygosity or allelic diversity in the hatchery compared to the wild population. High genetic diversity (He = 0.724–0.761 and Ho = 0.723–0.743), low inbreeding coefficient (F _IS = 0.003–0.024) and Hardy–Weinberg equilibrium were observed in both wild and hatchery populations. However, the genetic heterogeneity between the populations was significant. Therefore, genetic drift likely promoted inter-population differentiation, and rapid loss of genetic diversity remains possible. Regarding conservation, genetic variation should be monitored and inbreeding controlled in a commercial breeding program.     

Comparative genetic diversity of wild and hachery populations of Korean threadsail filefish Stephanolepis cirrhifer using cross-species microsatellite markers

The threadsail filefish Stephanolepis cirrhifer is a highly commercial fisheries resource in Korea that suffers intensive anthropogenic pressure across much of its range. For basic information about its current genetic status in relation to stock enhancement, the level and distribution of genetic variation between a wild and a hatchery-bred population were investigated using 10 microsatellite markers developed for Thamnaconus modestus. High levels of polymorphism were observed between the two populations. A total of 95 different alleles were found at all loci, with some alleles being unique. The allelic variability ranged from six to 13 in the wild population and from five to 13 in the hatchery one. The average observed and expected heterozygosities were estimated to be 0.72 and 0.80 in the wild sample and 0.70 and 0.79 in the hatchery one, respectively. These results showed similar genetic variability in the hatchery population, as compared with the wild population and significant genetic differentiation between the wild population and the hatchery samples (F _ST = 0.016, P < 0.05). Genetic drift in the intensive breeding practices for stock enhancement has probably promoted differentiation between populations. Significant deviations from Hardy-Weinberg equilibrium were detected in both populations. Our results indicate that further studies using species-specific microsatellite markers will be necessary for a more reliable assessment of genetic diversity of the species.     

New polymorphic microsatellite markers in Pacific abalone Haliotis discus hannai and their application to genetic characterization of wild and aquaculture populations

Seven new microsatellite markers were developed for the Pacific abalone (Haliotis discus hannai, Haliotidae), and allelic variability was compared between a wild population and a hatchery population in Yeosu, Korea. All loci amplified readily and demonstrated allelic variability, with the number of alleles ranging from 6 to 15 in the wild population and from 3 to 12 in farmed populations. Average observed and expected heterozygosities were estimated at 0.65 and 0.77 in the hatchery samples, and 0.79 and 0.87 in the wild samples. These results indicated lower genetic variability in the hatchery population, as compared with the wild population and significant genetic differentiation between the wild population and the hatchery samples (F _ST=0.055, p<0.001). These microsatellite loci may be valuable for future population genetic studies and for tracking hatchery samples used in stock enhancement programs.     

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.     

Population genetic structure of wild and hatchery black rockfish Sebastes inermis in Korea, assessed using cross-species microsatellite markers

The population structure of the black rockfish, Sebastes inermis (Sebastidae), was estimated using 10 microsatellite loci developed for S. schlegeli on samples of 174 individuals collected from three wild and three hatchery populations in Korea. Reduced genetic variation was detected in hatchery strains [overall number of alleles (N(A)) = 8.07; allelic richness (A(R)) = 7.37; observed heterozygosity (H(O)) = 0.641] compared with the wild samples (overall N(A) = 8.43; A(R) = 7.83; H(O) = 0.670), but the difference was not significant. Genetic differentiation among the populations was significant (overall F(ST) = 0.0237, P < 0.05). Pairwise F(ST) tests, neighbor-joining tree, and principal component analyses showed significant genetic heterogeneity among the hatchery strains and between wild and hatchery strains, but not among the wild populations, indicating high levels of gene flow along the southern coast of Korea, even though the black rockfish is a benthic, non-migratory marine species. Genetic differentiation among the hatchery strains could reflect genetic drift due to intensive breeding practices. Thus, in the interests of optimal resource management, genetic variation should be monitored and inbreeding controlled within stocks in commercial breeding programs. Information on genetic population structure based on cross-species microsatellite markers can aid in the proper management of S. inermis populations.     

Population genetic structure in wild and hatchery populations of white cloud mountain minnow (Tanichthys albonubes): Recommendations for conservation

We used mitochondrial (mt) cytochrome b gene (cyt b) to compare the genetic variability in three hatchery broodstocks of white cloud mountain minnow with the variability in six wild populations sampled in two river drainages. A total of 43 haplotypes in 102 specimens were observed, with no haplotype shared between wild and hatchery populations. The nucleotide diversity of the wild samples (0.048) was significantly higher than that of the hatchery ones (0.007), but the haplotype diversity was almost similar between them. Two major phylogenetic haplotype groups were revealed and estimated to diverge about 6.531 myr (million years) ago. Significant genetic differentiation was revealed between wild and hatchery populations as well as among nine sampled populations, suggesting at chance effect during the founding process for the hatchery population and a subsequent genetic drift. According to the network, the connection between wild and hatchery populations indicates that present hatchery populations originated from single wild population. We suggested that two regions (Pearl River system and Lu River) identified by reciprocal mtDNA monophyly and SAMOVA should be regarded as three different ESUs and two different MUs in South China, respectively.     

Mitochondrial DNA variation and population genetic structure in the small yellow croaker at the coast of Yellow Sea and East China Sea

Small yellow croaker is one of the most important fishery species in China. The mass–scale artificial propagation of this fish species was initially developed in 2015 with the aim of facilitating the fish production stock enhancement and aquaculture programs in the future. In the present study, the wild broodfish and its corresponding progeny along with three other wild populations were sampled and subjected to sequence analysis of the mitochondrial cytochrome c oxidase subunit I gene. The genetic diversity and population genetic structure were evaluated with a total sample size of 141 individuals representing the populations of the Yellow Sea (Qingdao and Lvsi populations) and the East China Sea (Xiangshan and Ningde populations). The wild populations were characterized by high haplotype diversity (0.925–0.976) and low nucleotide diversity (0.376%–0.560%). The hierarchical analysis of molecular variance (AMOVA) analysis and the values of pairwise Ф-statistics (Ф_ST) indicated non-significant genetic differentiation among the four wild populations. The hatchery stock XSH exhibited lower indices of genetic diversity compared with the wild populations that could be attributed to the small effective population size. The findings of the present study have valuable insight to the sustainable management and utilization of this resource.     

Population structure of the olive flounder (Paralichthys olivaceus) in Korea inferred from microsatellite marker analysis

The population structure of olive flounder Paralichthys olivaceus was estimated using nine polymorphic microsatellite (MS) loci in 459 individuals collected from eight populations, including five wild and three hatchery populations in Korea. Genetic variation in hatchery (mean number of alleles per locus, A = 10·2–12·1; allelic richness, A_R = 9·3–10·1; observed heterozygosity, H_O = 0·766–0·805) and wild (mean number of alleles per locus, A = 11·8–19·6; allelic richness, A_R = 10·9–16·1; observed heterozygosity, H_O = 0·820–0·888) samples did not differ significantly, suggesting a sufficient level of genetic variation in these well‐managed hatchery populations, which have not lost a substantial amount of genetic diversity. Neighbour‐joining tree and principal component analyses showed that genetic separation between eastern and pooled western and southern wild populations in Korea was probably influenced by restricted gene flow between regional populations due to the barrier effects of sea currents. The pooled western and southern populations are genetically close, perhaps because larval dispersal may depend on warm currents. One wild population (sample from Wando) was genetically divergent from the main distribution, but it was genetically close to hatchery populations, indicating that the genetic composition of the studied populations may be affected by hydrographic conditions and the release of fish stocks. The estimated genetic population structure and potential applications of MS markers may aid in the proper management of P. olivaceus populations.     

Determination of genetic diversity of wild and cultured topmouth culter (Culter alburnus) inhabiting China using mitochondrial DNA and microsatellites

The topmouth culter (Culter alburnus) is one of the most commercially important freshwater fish species inhabiting China. However, very limited information is available regarding its genetic diversity and population structure, thus hindering the effective management of this fish stock. Understanding the genetic diversity of wild and cultured topmouth culter populations is highly relevant for successful hatchery management. This study evaluated the genetic diversity and structure of five wild and two cultured populations of topmouth culter in China by using microsatellites and mitochondrial DNA. The genetic diversity of wild populations was found to be lower than that of cultured populations. This finding indicates that wild topmouth culter resources should be protected to prevent further degeneration and extinction. Moreover, it demonstrated that cultured populations have greater breeding potential than wild ones. Subdivisions among wild populations were observed, which should be considered as different units for conservation and hatchery management.     

Do hatchery-reared sea urchins pose a threat to genetic diversity in wild populations?

In salmonids, the release of hatchery-reared fish has been shown to cause irreversible genetic impacts on wild populations. However, although responsible practices for producing and releasing genetically diverse, hatchery-reared juveniles have been published widely, they are rarely implemented. Here, we investigated genetic differences between wild and early-generation hatchery-reared populations of the purple sea urchin Paracentrotus lividus (a commercially important species in Europe) to assess whether hatcheries were able to maintain natural levels of genetic diversity. To test the hypothesis that hatchery rearing would cause bottleneck effects (that is, a substantial reduction in genetic diversity and differentiation from wild populations), we compared the levels and patterns of genetic variation between two hatcheries and four nearby wild populations, using samples from both Spain and Ireland. We found that hatchery-reared populations were less diverse and had diverged significantly from the wild populations, with a very small effective population size and a high degree of relatedness between individuals. These results raise a number of concerns about the genetic impacts of their release into wild populations, particularly when such a degree of differentiation can occur in a single generation of hatchery rearing. Consequently, we suggest that caution should be taken when using hatchery-reared individuals to augment fisheries, even for marine species with high dispersal capacity, and we provide some recommendations to improve hatchery rearing and release practices. Our results further highlight the need to consider the genetic risks of releasing hatchery-reared juveniles into the wild during the establishment of restocking, stock enhancement and sea ranching programs.     

Strategies for the retention of high genetic variability in European flat oyster (<Emphasis Type="Italic">Ostrea edulis</Emphasis>) restoration programmes

The native European flat oyster Ostrea edulis is listed in the OSPAR Convention for the Protection of the Marine Environment of the North-East Atlantic (species and habitat protection) and in the UK Biodiversity Action Plan. Once extremely abundant in the nineteenth century, European stocks of O. edulis have declined during the twentieth century to rare, small, localised populations due to overexploitation, habitat degradation and, most recently, the parasitic disease bonamiosis. Selective breeding programmes for resistance to bonamiosis have been initiated in France and Ireland. High genetic diversity and bonamiosis-resistance would be important features of any sustainable restoration programmes for O. edulis. Oysters were sampled across Europe from four hatchery sources, four pond-cultured sources and four wild, but managed fisheries and were genotyped at five microsatellite loci. Hatchery-produced populations from small numbers of broodstock showed a significant loss of genetic diversity relative to wild populations and pedigree reconstruction revealed that they were each composed of a single large full-sib family and several small full-sib families. This extremely low effective population size highlights the variance in reproductive success among the potential breeders. Pond-cultured oysters were intermediate in genetic diversity and effective population size between hatchery and wild populations. Controlled hatchery production allows the development of bonamiosis-resistant strains, but at the expense of genetic diversity. Large scale pond culture on the other hand can provide a good level of genetic diversity. A mixture of these two approaches is required to ensure a healthy and sustainable restoration programme for O. edulis in Europe.     

Analysis of microsatellite DNA markers reveals no genetic differentiation between wild and hatchery populations of Pacific threadfin in Hawaii

Pacific threadfin, Polydactylus sexfilis, is popular fish in recreational fishing, as well as aquaculture in Hawaii. Its natural population has been continuously declining in the past several decades. Microsatellite DNA markers are useful DNA-based tool for monitoring Pacific threadfin populations. In this study, fifteen Microsatellite (MS) DNA markers were identified from a partial genomic Pacific threadfin DNA library enriched in CA repeats, and six highly-polymorphic microsatellite loci were employed to analyze genetic similarity and differences between the wild population and hatchery population in Oahu Island. A total of 37 alleles were detected at the six MS loci in the two populations. Statistical analysis of fixation index (F(ST)) and analysis of molecular variance (AMOVA) showed no genetic differentiation between the wild and hatchery populations (F(ST) = 0.001, CI(95%) = -0.01-0.021). Both high genetic diversity (H(o) = 0.664-0.674 and H(e) = 0.710-0.715) and Hardy-Weinberg equilibrium were observed in the wild and hatchery populations. Results of genetic bottleneck analysis indicated that the hatchery was founded with sufficient numbers of brooders as inbreeding coefficient is very low (F(IS) = 0.052-0.072) in both wild and hatchery populations. Further studies are needed for comprehensive determinations of genetic varieties of primary founder broodstocks and successive offspring of the hatchery and wild populations with increased number of Pacific threadfin sample collections.     

Microsatellite DNA variation in wild populations and farmed strains of turbot from Ireland and Norway: a preliminary study

Turbot Scophthalmus maximus is the focus of a rapidly expanding aquaculture industry, while at the same time wild catches appear to be in decline. As a preliminary investigation into the effects of hatchery rearing, genetic variation at three polymorphic microsatellite loci was assessed in two wild populations and two farmed strains of turbot, from Ireland and Norway. Although a considerable loss of rare alleles was observed in the Irish farmed strain, no statistically significant reductions were found in mean heterozygosity or allelic diversity in farmed strains compared to wild populations. Significant genetic heterogeneity was found between wild and farmed samples from each country but not between the two wild populations. Genetic differentiation between the farmed strains was presumed to be caused by drift in the hatcheries. The utility of these particular microsatellite loci in comparing these samples and the importance of molecular genetic testing of farmed strains is stressed.     

Selection and genetic drift in captive versus wild populations: an assessment of neutral and adaptive (MHC-linked) genetic variation in wild and hatchery brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) populations

Captive bred individuals are often released into natural environments to supplement resident populations. Captive bred salmonid fishes often exhibit lower survival rates than their wild brethren and stocking measures may have a negative influence on the overall fitness of natural populations. Stocked fish often stem from a different evolutionary lineage than the resident population and thus may be maladapted for life in the wild, but this phenomenon has also been linked to genetic changes that occur in captivity. In addition to overall loss of genetic diversity via captive breeding, adaptation to captivity has become a major concern. Altered selection pressure in captivity may favour alleles at adaptive loci like the Major Histocompatibility Complex (MHC) that are maladaptive in natural environments. We investigated neutral and MHC-linked genetic variation in three autochthonous and three hatchery populations of Austrian brown trout (Salmo trutta). We confirm a positive selection pressure acting on the MHC II β locus, whereby the signal for positive selection was stronger in hatchery versus wild populations. Additionally, diversity at the MHC II β locus was higher, and more uniform among hatchery samples compared to wild populations, despite equal levels of diversity at neutral loci. We postulate that this stems from a combination of stronger genetic drift and a weakening of positive selection at this locus in wild populations that already have well adapted alleles for their specific environments.     

真鲷自然群体和人工繁殖群体的遗传多样性

采用RAPD技术对真鲷野生群体及人工繁殖群体各23个个体进行了DNA多态性检测。实验选取OPK组16个10 bp随机引物用于两群体的遗传多样性分析。在野生群体和人工繁殖群体中分别获得131和123条扩增片段,两群体的多态片段比例分别为62.60%和54.47%,平均杂合度分别为0.4786和0.3633,可见真鲷野生群体及人工繁殖群体的遗传多样性较为丰富,在选择育种和遗传改良方面具有较大的潜力。人工繁殖群体的多态片段比例和平均杂合度都低于野生群体,意味着在生产过程中要采取行之有效的管理保护措施以避免或减少遗传多样性水平的降低,确保真鲷增养殖业的可持续发展。     

Wild and aquaculture populations of the eastern oyster compared using microsatellites

Five new microsatellite markers were developed for the eastern oyster (Crassostrea virginica), and allelic variability was compared between a wild Chesapeake Bay population (James River) and a hatchery strain (DEBY). All loci amplified readily and demonstrated allelic variability with the number of alleles ranging from 16 to 36 in the wild population and from 11 to 19 in the DEBY strain. Average observed and expected heterozygosities were estimated at 0.66 and 0.80 in the hatchery sample. The corresponding estimates were 0.91 and 0.75 in the wild sample. Results indicated lower genetic variability in the DEBY strain and significant genetic differentiation between the wild population and hatchery strain. These microsatellite loci will prove valuable for future population genetic studies and in tracking of hatchery strains used in restoration.     

Genetic Structure of Different Populations of Walking Catfish (Clarias batrachus L.) in Bangladesh

Information on genetic variation is essential for conservation and stock improvement programs. Seven dinucleotide microsatellite loci were analyzed to reveal genetic variability in three wild populations (Kella beel, Hakaluki haor, and Shobornokhali beel) and one hatchery population of the freshwater walking catfish, Clarias batrachus, in Bangladesh. Upon PCR amplification, the alleles were separated on polyacrylamide gel using a sequencing gel electrophoresis system and visualized by the silver-staining method. The loci were polymorphic (P95) in all the populations. Differences were observed in number and frequency of alleles as well as heterozygosity in the studied populations. Current gene diversity (He) was higher than expected under mutation-drift equilibrium, significantly in the Hakaluki haor and Shobornokhali beel populations, indicating a recent genetic bottleneck. Population differentiation (FST) values were significant (P<0.05) in all the population pairs. A relatively high level of gene flow and a low level of FST values were found between wild population pairs compared to hatchery-wild pairs. The unweighted pair group method with averages dendrogram based on genetic distance resulted in two major clusters: the hatchery population was alone in one cluster whereas the three wild populations made another cluster. The results reflect some degree of genetic variability in C. batrachus populations indicating potentialities for improving this species through a selective breeding program. The results revealed a recent bottleneck in some wild populations of C. batrachus. Protection of habitat may help increase the population size and lower the risk of vulnerability of the species in the future.     

Population genetic structure of the sea bass (Lateolabrax japonicus) in Korea based on multiplex PCR assays with 12 polymorphic microsatellite markers

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.