Hatchery Stocks Research Articles

Genetic diversity of hatchery stocks of giant freshwater prawn ( Macrobrachium rosenbergii) in Thailand

The culture of freshwater prawn in central Thailand has experienced low productivity despite the rapid expansion during the past several years. Deterioration of genetic variation and inbreeding depression were blamed for slow growth rate in farmed stocks. Six microsatellite DNA loci were used to assess genetic diversity from five hatchery stocks and two wild populations of freshwater prawn. Natural populations were collected from the ChaoPhaya River and the Kraburi River. Two local hatchery populations originated from the ChaoPhya River were collected from the provinces of Nakorn Pathom and Supanburi. Another ChaoPhya originating samples were obtained from a hatchery in Indonesia. An introduced stock of Myanmar origin was sampled from a hatchery in Nakhon Pathom province and samples of a commercial strain which originated from India were collected in Ratchaburi province. All hatchery and wild populations exhibited relatively high genetic variation and were similar with an average of 7.50 to 10.67 alleles per locus and average expected heterozygosity at all loci of 0.64 to 0.73. Pair-wise comparisons and the F ST values revealed significant genetic differentiation across all populations. Results indicated that poor performance of freshwater prawn due to deterioration of genetic variability and inbreeding was not an issue.

Genetic diversity of common carp ( Cyprinus carpio L.) in Vietnam using four microsatellite loci

Four highly variable microsatellite loci were used to investigate genetic diversity and population structure of common carp in Vietnam. A total of 968 fish were genotyped representing three groups comprising: three experimental lines from the Research Institute for Aquaculture No 1 (Bac Ninh); 11 hatcheries; and six wild populations from rivers and reservoirs giving 72 alleles over all loci. The mean number of alleles, per locus per population ranges from 4.25 to 11.00 and the mean observed heterozygosity at the four loci ranges from 0.40 to 0.83. An analysis of the distribution of genetic variation indicated within population variation is very high (90.6%), while among populations within groups and among groups is low (5.0% and 4.5% respectively). Highly significant deviations from Hardy–Weinberg, mostly due to deficits of heterozygotes, were found in both experimental and hatchery groups suggesting either inbreeding or recent stock mixing. Wild common carp populations exhibited more genetic diversity than cultured populations in term of allele richness and observed heterozygosity. Results from assignment tests for the 20 populations of carp indicated that the experimental common carp lines can be largely distinguish from one another and that mixing between indigenous and introduces carp is occurring in hatcheries and possibly also in wild populations. Multidimensional Scaling (MDS) and UPGMA analyses show that the experimental Vietnamese white carp line is closely related to wild common carp populations; the hatchery stocks are mostly closely related to the experimental Indonesian yellow carp line but with evidence of some mixing; and the domesticated Hungarian population is highly divergent and not closely related to any other carp populations.

Fine‐Scale Population Structure of Rainbow Trout in the Spokane River Drainage in Relation to Hatchery Stocking and Barriers

AbstractWe used 13 microsatellite loci to examine population structure in rainbow trout Oncorhynchus mykiss collected from 20 tributaries and 3 main stems in the greater Spokane River drainage. Populations displayed some excess homozygosity and linkage disequilibrium, which was more pronounced in upper tributary collections and probably the result of small effective population sizes or structuring within tributaries. In general, population structure followed geographic structure; collections from creeks within sub‐drainages were the most closely related, and collections from different tributaries were genetically distinct. Comparisons with cutthroat trout O. clarkii indicated little to no introgression. Comparisons with steelhead (anadromous rainbow trout), coastal rainbow trout O. mykiss irideus, and inland rainbow trout from hatcheries suggested introgression by hatchery fish into some wild populations. Introgression was suspected in populations from stocked tributaries and tributaries that lacked barriers to escaped hatchery fish. Populations from tributaries above barriers that had not been stocked were genetically distinct from hatchery fish and appeared to be native inland redband trout O. mykiss gairdneri.

The genetic structure of endangered indigenous populations of the amago salmon, Oncorhynchus masou ishikawae, in Japan

The amago salmon, Oncorhynchus masou ishikawae, is an endemic subspecies of O. masou in Japan. Owing to the extensive stocking of hatchery fish throughout Japan, indigenous populations of O. m. ishikawae are now on the verge of extinction. We examined the genetic effects of stocking hatchery fish on wild populations in the River Koza, Japan, using microsatellite and mitochondrial DNA (mtDNA) markers. For mtDNA, haplotype mt1, which is common in wild populations, was present exclusively in isolated wild populations assumed to be unaffected by previous stocking, while it was never observed in hatchery fish. Genetic diversity was much higher in wild populations in the stocked area, which shared many mtDNA haplotypes with hatchery fish, than in isolated wild populations with haplotype mt1. Pairwise FST estimates based on microsatellites showed significant differentiation among the isolated populations with many microsatellite loci monomorphic. Significant deviation from Hardy–Weinberg equilibrium was observed in wild populations in the area subject to stocking, where a Bayesian-based assignment test showed a high level of introgression with hatchery fish. These results suggest that wild populations with haplotype mt1, which became isolated through anthropogenic environmental change in the 1950–1960s, represent indigenous populations of O. m. ishikawae in the River Koza. They have low genetic diversity, most likely caused by genetic bottlenecks following damming and environmental deterioration, while stocking of hatchery fish over the past 30 years apparently had a large impact on the genetic structure of wild populations in the main channel of the River Koza.

Genetic Differences Between Hatchery Stocks and Natural Populations in Pacific Abalone (Haliotis discus) Estimated Using Microsatellite DNA Markers

Genetic variations within and between nine hatchery stocks and seven natural populations of abalone including Ezo-abalone (Haliotis discus hannai) and Kuro-abalone (H. d. discus) were assayed with nine microsatellite markers. Marked reductions of genetic variability in the hatchery stocks were recognized in the allelic diversity and mean heterozygosity compared with the natural populations. Thirteen of 16 significant HWE deviations in hatchery stocks revealed heterozygotes excess, while all natural populations did not show such a tendency. Highly significant F (ST) values were observed for all cases between the hatchery stocks, and between the hatchery stocks and natural populations. Genetic distance (D (A)) between each hatchery stock and the geographically proximal population (mean +/- SD, 0.108 +/- 0.035) were similar to those estimated for between the natural Ezo-abalone and Kuro-abalone (0.101 +/- 0.021). The self-assignment test, which allocated individuals to their own stock with a high success rate, provided evidence of solid genetic differences among the nine hatchery stocks. These results suggests that the allelic composition and diversity in the natural populations was not necessarily reflected in the hatchery stocks owing to population bottleneck and genetic drift through seedling process, and thus the seedling and stocking practice of these hatchery stocks should take much notice of the results to conserve the genetic diversity of natural populations.

Use of Otolith Microstructure to Discriminate Stocks of Juvenile Central Valley, California, Fall‐Run Chinook Salmon

AbstractWe examined the utility of otolith microstructure analysis as a means of discriminating among stocks and between rearing types of juvenile fall‐run Chinook salmon Oncorhynchus tshawytscha in California's Central Valley. Otolith samples were collected from 11 geographically discrete stocks of fall‐run Chinook salmon of river and hatchery rearing types over 2 years. Six measured otolith attributes and three statistics derived from these measurements served as dependent variables in a multifactor analysis of variance of paired river and hatchery stocks. Morphometrics that demonstrated no significant interaction between year and stock or rearing type were used as predictors in discriminant function analyses; 32% of samples were correctly classified by stock and 80% were correctly classified by rearing type. Measures of otolith size at fry emergence were the best predictors for distinguishing among both stocks and rearing types with discriminant function analysis. We hypothesize that observed differences in otolith size at emergence among stocks and rearing types reflect differential responses in development of Chinook salmon embryos reared under different temperature regimes. Although classification success among stocks was rather limited, results for correctly classifying fall‐run Chinook salmon by rearing type were encouraging. We suggest that observed differences in otolith microstructure between rearing types be augmented with thermal marking in Central Valley hatcheries to provide a fully reliable tool for determining the proportionate contribution of natural and hatchery production to spawner populations. This information alone would greatly advance stock management of Central Valley fall‐run Chinook salmon.

Aggression Level in Different Water Velocities Depends on Population Origin in Grayling, Thymallus thymallus

AbstractPhenotypic plasticity is recognized as an important mechanism of adaptation. However, because of its potential costs and limits, it has been hypothesized to be reduced and ultimately become lost when there is no selection for its maintenance. Heterogeneous environments in particular are expected to favour and thus maintain plastic phenotypes. Lakes and rivers differ in their flow regimes. In addition to higher average water velocity, rivers are characterized by distinct spatial and temporal variation in water flow, whereas lakes can be regarded as quite uniform in this respect. We studied whether behaviour, which is generally considered to be highly plastic, shows differences in the degree of plasticity between lake and river populations of the European grayling, Thymallus thymallus, fry in response to different water velocities. Given that aggressive behaviour in fish has been shown to relate to ambient flow regime, we compared aggressiveness of hatchery‐reared grayling originating from hatchery stocks of two lake and two river populations in still and flowing water. River fish showed higher aggressiveness in flowing water compared with still water, whereas aggressiveness of lake fish did not appear to vary according to water velocity. The higher plasticity of aggressiveness evoked in river fish by different water velocities may thus represent an adaptation to more variable flow and presumably related feeding conditions in their natural environment.

Genetic variation losses in Atlantic salmon stocks created for supportive breeding

Conservation of genetic variability is of priority for hatchery stocks employed to supplement natural populations. Supportive breeding of Atlantic salmon is carried out in order to enhance wild populations at the south of the European distribution (northern Spain). In this study we demonstrated that adult breeders chosen for creating hatchery stocks by artificial spawning preserved all genetic variants present in wild Spanish populations for six microsatellite loci. However, significant losses of genetic variability were found in juveniles released to the native rivers. An inadequate strategy of crosses was the cause of genetic variation decrease in these hatchery stocks. Unbalanced sex ratio was identified as one of the causes of genetic erosion. Increasing the number of breeder males was suggested to maximize fidelity of hatchery stocks to native wild genetic patterns.

Microsatellite variability and differentiation of hatchery stocks of chum salmon Oncorhynchus keta Walbaum in Sakhalin

Variability at eight microsatellite loci was examined in five populations of chum salmon Oncorhynchus keta Walbaum from Sakhalin hatcheries. The population of Kalinino hatchery had the lowest heterozygosity and the lowest average number of alleles per locus. The populations examined exhibited significant differentiation, theta ST = 0.026 on average per locus. The maximum genetic differences were found between the populations of the Kalinino and the Ado-Tymovo hatcheries; the latter differs from the remaining populations also by the highest number and high frequencies of specific alleles. The genetic features of the Taranai hatchery population, observed at microsatellite loci, reflect its "mixed" origin.

Mitochondrial DNA Variation in the Endangered Colorado Pikeminnow: A Comparison among Hatchery Stocks and Historic Specimens

AbstractThe Colorado pikeminnow Ptychocheilus lucius is a federally endangered species restricted to the Colorado River. Dexter National Fish Hatchery and Technology Center, Dexter, New Mexico, maintains three separate captive stocks of the Colorado pikeminnow: 1974YC (Yampa River), 1981YC (Green–Colorado rivers), and 1991YC (Colorado River). We surveyed mitochondrial DNA diversity in these three stocks (879 base pairs [bp]; ND‐4L and ND‐4 genes; N = 30) and in museum specimens collected from 1890 to 1976 (450 bp; ND‐4; N = 11). All individuals had the same haplotype except for a 1‐bp variant detected in 2 of the 12 fish from 1981YC. The low variation is postulated to be the result of a post‐Pleistocene bottleneck in the wild and small sizes of the hatchery founder populations.

GENETIC DIVERSITY OF THE EUROPEAN OYSTER (OSTREA EDULIS L.) IN NOVA SCOTIA: COMPARISON WITH OTHER PARTS OF CANADA, MAINE AND EUROPE AND IMPLICATIONS FOR BROODSTOCK MANAGEMENT

The European oyster (Ostrea edulis) was introduced to the Nova Scotia aquaculture industry 30 years ago using stocks imported from naturalized populations in Maine whose ancestors originated in the Netherlands. This study used 5 microsatellites to assess the level of genetic diversity in several hatchery stocks and naturalized populations from Nova Scotia, New Brunswick, British Columbia and Maine. Some genetic erosion was shown to have occurred in the Maritimes populations, with the largest loss of alleles being experienced by the hatchery stocks. In spite of this loss, genetic diversity and heterozygosity in the Maritimes populations are still relatively high. Relationships within and between the populations and the existence of kin groups within the collections were overall consistent with our knowledge of the historical transfers of oysters between different locations. Furthermore, the established database allowed to assign with good confidence unknown oyster samples to their geographic origin. This would be a useful forensics tool in the case of an illegal transfer from a diseased area.

Polymorphic microsatellite primers developed from DNA of the endangered Mekong giant catfish, Pangasianodon gigas (Chevey) and cross‐species amplification in three species of Pangasius

AbstractThe critically endangered Pangasianodon gigas is endemic to the Mekong River. Despite its importance, little is known about its genetic diversity and conservation efforts are hampered. Ten polymorphic dinucleotide microsatellite primer pairs were developed from DNA of P. gigas. The analysis of 20 individuals from hatchery stocks using these primers resulted in two to six alleles/locus; HO = 0.05–0.95; HE = 0.05–0.81. All but one locus (Pg‐3) conformed to Hardy–Weinberg expectation. Eight, six and seven primer pairs were amplified with the DNA from Pangasianodon hypophthalmus, Pangasius larnaudii and Pangasius sanitwongsei, respectively. These markers will be useful for genetic monitoring of wild and hatchery stocks of these pangasiids.

The role of genetics in shellfish restoration

Restoration of shellfish populations is becoming an increasingly common practice worldwide, as natural fisheries succumb to pressures of overharvesting, habitat loss or degradation, and challenges from invasive competitors and pathogens. Primary genetic concerns relevant to shellfish restoration projects are reviewed, using the cupped oysters Crassostrea gigas and Crassostrea virginica as case studies. Molecular genetic tools can be used to delineate the geographic distribution of germ plasm diversity at the species and intraspecific levels, enabling more informed selection of genetic material for hatchery breeding and production. Maintenance of genetic variability and prevention of excessive inbreeding in hatchery stocks may be facilitated by the use of genetic markers for regular pedigree monitoring. The effect of hatchery supplementation on the effective population size of a recipient wild population (Ryman-Laikre effect) is reviewed in light of the population biology of bivalve molluscs, and appears to be minimal. Deployment of selected enhancement stocks may be a valuable tool for improvement of degraded wild populations, reversing the negative effects of generations of selective harvesting. Molecular genetic tools can be used effectively to monitor restoration programs, when the discriminatory power of the marker(s) is high and high-throughput scoring methods currently available are used.

Genetic diversity of common carp in Vietnam using direct sequencing and SSCP analysis of the mitochondrial DNA control region

The aquaculture of common carp ( Cyprinus carpio L.) in Vietnam is based upon both indigenous and introduced stocks which have not been subject to study using modern molecular genetic methods to any significant extent. Twenty strains or populations of common carp in Vietnam represented by 968 fish were screened for variation in mitochondrial control region fragments using a combination of direct DNA sequencing and Single Strand Confirmation Polymorphism (SSCP) analysis. Common carp samples from China, Japan, Indonesia, and Hungary were analysed for comparison. Sequencing revealed that Vietnamese common carp have high haplotype, but low nucleotide diversity and represent a mixture of indigenous and introduced strains. The SSCP procedure resolved eight haplotypes that distinguished Indonesian, Hungarian and Vietnamese strains and which varied significantly among hatchery and wild Vietnamese common carp populations. Intra-population diversity was least in experimental common carp lines, maintained at the Research Institute for Aquaculture No 1 and greatest within hatchery stocks. Relationships among populations based on SSCP haplotype frequencies showed that the RIA1 Vietnamese white common carp strain is closely related to wild populations, which in turn are closely related to six of the eleven hatchery stocks. The other five hatchery stocks had higher levels of interpopulation variation and mostly showed a closer relationship to Indonesian yellow carp strains. The Hungarian carp strain was highly divergent from all other populations suggesting that this strain has not contributed significantly to the establishment of cultured stocks in Vietnam, based on this maternally inherited marker. The SSCP procedure shows considerable potential for rapid genotyping and genetic characterization of common carp and therefore, for investigation of diversity in wild stocks and broodstock management.

Intra- and Interspecific Competition in Hatchery Landlocked Salmon and Brown Trout in Semi-Natural Streams

I studied inter- and intraspecific competition in two hatchery stocks: landlocked salmon with long-hatchery background and a heterogenic brown trout stock. These species are potential competitors in the natural environment when landlocked salmon is being restored to wild by stocking hatchery juveniles. Behavioural responses were studied in four indoor laboratory flumes (400 cm long and 37 cm wide) and habitat use in six semi-natural outdoor streams (26 m long and 1.5 m long). Video recordings were used to monitor fish behaviour and electrofishing for fish positioning in the outdoor channels. The study design included five treatments: two densities of brown trout and salmon in solitary and both species together. The results of the study demonstrated that juvenile brown trout changed their behaviour in laboratory streams in response to presence of the landlocked salmon and the density of the conspecifics also tended to alter the habitat use by brown trout in semi-natural streams. Landlocked salmon juveniles showed no response to treatments. I conclude that possible poor adaptive ability to conditions outside hatchery by the hatchery salmon together and more competitive brown trout stocks may limit the success of management action in restoring landlocked salmon back to their natural streams of stocking.

The Effect of an Introduced Summer Steelhead Hatchery Stock on the Productivity of a Wild Winter Steelhead Population

AbstractWe investigated the effect of a hatchery program for summer steelhead Oncorhynchus mykiss on the productivity of a wild winter steelhead population in the Clackamas River, Oregon. We used a suite of Ricker and Beverton–Holt stock–recruitment models that incorporated species interaction variables to demonstrate that when high numbers of hatchery summer steelhead adults were present the production of wild winter steelhead smolts and adults was significantly decreased. We found that large releases of hatchery smolts also contributed to the decrease in wild adult productivity. Averaged over the results of our models, a 50% decline in the productivity parameter (the number of recruits per spawner at low densities) and a 22% decline in the maximum number of recruits produced in the basin were observed when high numbers of hatchery fish were present. We concluded that over the duration of the hatchery program, the number of hatchery steelhead in the upper Clackamas River basin regularly caused the total number of steelhead to exceed carrying capacity, triggering density‐dependent mechanisms that impacted the wild population. The number of smolts and adults in the wild winter steelhead population declined until critically low levels were reached in the 1990s. Hatchery fish were removed from the system in 2000, and early results indicate that the declining trends have reversed.

Genetic relationship between broodstocks of olive flounder, Paralichthys olivaceus (Temminck and Schlegel) using microsatellite markers

For the first generation of a selective breeding programme, it is important to minimize the possibility of inbreeding. This mostly occurs by mating between closely related individuals, while proper mating can provide an opportunity to establish the base families with wide genetic variation from which selection for subsequent generations can be more effective. Genotyping with microsatellite-based DNA markers can help us determine the genetic distances between the base populations. The genetic markers further facilitate the identification of the correct parents of the offspring (parentage assignments) reared together with many other families after hatching. We established a genetic analysis system with microsatellite DNA markers and analysed the genetic distances of three farmed stocks and a group of fish collected from wild populations using eight microsatellite markers. The averaged heterozygosity of the farming stocks was 0.826 and that of the wild population was 0.868. The hatchery strains had an average of 8.6 alleles per marker, which was less than a wild population that carried an average of 14.3 alleles per marker. Significant Hardy–Weinberg disequilibrium (HWDE) was observed in two farming stocks (P<0.05). Despite relatively low inbreeding coefficiency of the hatchery populations, the frequency of a few alleles was highly represented over others. It suggests that the hatchery stocks to some extent have experienced inbreeding or they originated from closely related individuals. We will develop a selective program using the DNA markers and will widen the usage of the DNA-based genetic analysis system to other fish species.

Genetic Diversity among Hatchery Stocks and Established Populations of Rainbow Trout in Missouri

AbstractIntroduction of rainbow trout Oncorhynchus mykiss in Missouri over the last 125 years has established numerous self‐sustaining populations. While many populations have been repeatedly stocked, some have received few fish beyond the original releases, and it is possible that those populations currently represent their source lineages. There is angler interest in fishing “wild” rainbow trout populations both for historical purposes and for the fighting ability of hooked fish. A genetic inventory was conducted to determine the extent to which Missouri's wild fish differ from hatchery stocks. Haplotype diversity in the mitochondrial DNA (mtDNA) cytochrome b gene and allele frequencies at four microsatellite loci were examined. Significant differences in mtDNA genotypes were found among several wild and hatchery sources, indicating that multiple sources of rainbow trout were probably represented. Crane Creek—long considered a stronghold of McCloud River (California) redband trout O. mykiss stonei in Missouri—and its tributary, Spring Creek, were characterized as having a large proportion of unique haplotypes. Microsatellite diversity was largely shared among individuals within populations, and average heterozygosity was high. By including this information in decisions about regulations and stocking, the Missouri Department of Conservation can manage rainbow trout to satisfy angler interests with respect to both historical and performance‐related population characteristics.

Genetic diversity in a Tasmanian hatchery population of Atlantic salmon (Salmo salar L.) compared with its Canadian progenitor population

The level of genetic diversity in a cultured Atlantic salmon (Salmo salar) population from Tasmania, Australia was examined at 11 microsatellite loci and compared with that in its progenitor population from the River Philip in Nova Scotia, Canada. The reference progenitor population consisted of archived scales collected from wild River Philip salmon in 1971 and 1972, not long after salmon from this river were imported into Australia in the mid-1960s. The Tasmanian hatchery stock had a significant reduction in the mean number of alleles (31–43%) and mean allelic richness (28–39%) across all microsatellite loci compared with the wild Canadian population. Mean heterozygosity levels remained unchanged. Estimates of per-generation effective population sizes for the Tasmanian population, based on allele frequency temporal variance with the wild progenitor population, ranged from 102–207 individuals and reflected hatchery records.

Variation of Morphology among Juvenile Chinook Salmon of Hatchery, Hybrid, and Wild Origin

AbstractBody morphology differed significantly between juvenile hatchery Chinook salmon Oncorhynchus tshawytscha that have experienced five generations of hatchery culture and juveniles derived from the wild founding stock and cultured in the same environment. All lines tested were raised in a similar hatchery environment. Thin‐plate spline analysis was used to characterize the morphometric variation among these lines of fish. Hatchery fish had a more compressed body, a narrower head, shorter maxillae, and a longer and narrower caudal peduncle than wild fish. Canonical discriminant analysis was able to correctly classify 88% of hatchery fish and 90% of wild fish. Second‐generation hybrids of the two lines were morphologically intermediate to but significantly different from both the hatchery and wild lines, and they appeared to be more similar to the wild line. These results suggest that the differences observed between lines are largely genetic in origin and may be a result of the divergence of the hatchery stock from the founding wild stock. In addition, family of origin had a significant effect on body morphology.