Genetic relatedness and differentiation of hatchery populations of Asian seabass (Lates calcarifer) (Bloch, 1790) broodstock in Thailand inferred from microsatellite genetic markers

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population (RACF‐F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF‐F1, did not differ from those of wild populations (P > 0.05). RACF‐F1 had the lowest allelic diversity and effective population size (A_r = 6.99; N_e = 7.8) and highest relatedness values (mean r_xy = 0.075–0.204). Pairwise Φ_ST values, principal component analysis and model‐based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand (CHN, RACF, NSCF and SKCF), Southern Thailand (NICA) and the Andaman Sea (STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations.     

Genetic diversity and relatedness estimates for captive barramundi (Lates calcarifer,Bloch) broodstock informs efforts to form a base population for selective breeding

Aquaculture of barramundi or Asian seabass (Lates calcarifer) is growing in both Australia and Southeast Asia and there is substantial interest to improve production efficiency through selective breeding. The establishment of a large and genetically diverse base population is a prerequisite for a sustainable and long‐term productive breeding program. Before selective breeding programs can begin for Australian barramundi it is important to assess the overall genetic diversity of current captive broodstock populations. To address this question, 407 captive barramundi broodstock from eight separate Australian broodstock populations were genotyped using 16 polymorphic microsatellite DNA markers. A Bayesian STRUCTURE analysis indicated that captive Australian broodstock are broadly divided into two genetic stocks. Multivariate analysis between broodstock individuals and pairwise F_ST between broodstock populations also supported the existence of two stocks. Comparisons with data obtained from natural stocks suggested that hatchery individuals were either sourced from the two stocks or represented an admixture between them. Genetic diversity was low within each broodstock population (allelic richness ranged from 2.67 to 3.42 and heterozygosity ranged from 0.453 to 0.537) and relatedness estimates within hatcheries were generally low (average r was equal to 0.141). We recommend sourcing captive individuals according to high levels of neutral genetic diversity and low levels of relatedness for the establishment of a base population. We also make recommendations about including genetically diverse wild individuals.     

Genetic diversity within sea trout population from an intensively stocked southern Baltic river,based on microsatellite DNA analysis

Sea trout, Salmo trutta L., populations in the Slupia River basin have been affected by mass stocking with smolts and fry. This work is focused on a small‐scale differentiation in sea trout populations from one basin with a strong emphasis on the relationship between wild and hatchery origin fish. A total of 216 sea trout were genotyped at 10 microsatellite loci. Global F_ST obtained by amova was low at 0.0165. Pairwise F_ST were significant for all tests except wild and stocked adults. The highest pairwise difference was found between the hatchery sample and Kwacza (F_ST = 0.038). Analysis of the genetic structure revealed micro‐geographical differentiation with four subpopulations. The quality of the artificial spawning was found not to be adequate with a high risk of adverse effects to the whole population. All future stocking actions in the basin should consider the existing population structures.     

Microsatellite genetic variation in wild and hatchery populations of the sea cucumber (Apostichopus japonicus Selenka) from northern China

Farming of the sea cucumber Apostichopus japonicus (Selenka) started 20 years ago and is still in rapid expansion in China. In order to assess the genetic status of both wild and cultivated stocks of this species, we used eight microsatellite markers to estimate the level of genetic diversity within five hatchery stocks and two wild populations of A. japonicus, and compared the degree of genetic differentiation between them. High levels of polymorphism were observed over all loci. The mean alleles and expected heterozygosities over the seven stocks were 10.4–12.3 and 0.735–0.783 respectively. The results of the microsatellite survey provide no evidence to show that hatchery practice of the sea cucumber in China to date has significantly affected the genetic variability of the cultured stocks. Significant differentiation was found between most pairs of the hatchery stocks and wild populations (F_st range: 0.008–0.036), and no obvious difference was detected between the wild populations (F_st=0.008). The information on the genetic variation and differentiation obtained in this study can be applied for future genetic monitoring of A. japonicus aquaculture stocks and will be useful for future genetic improvement by selective breeding, and for designing suitable management guidelines for these genetic materials.     

Genetic variation in farmed populations of the gilthead sea bream Sparus aurata in Greece using microsatellite DNA markers

Genetic variation in seven reared stocks of gilthead sea bream Sparus aurata, originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of two natural populations from the Ionian and the Adriatic Seas. The total number of alleles per marker ranged from 11 to 19 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic diversity and expected heterozygosity. The global genetic differentiation for the cultivated samples was significant as indicated by F_st analysis, which might indicate random genetic drift and inbreeding events operating in the hatcheries. On the contrary, no significant difference was found between the two wild populations. Population pairwise tests between farmed and wild stocks were also significant, with the exception of one hatchery sample, the Central Greece 1, which was not significantly different from the two wild samples perhaps due to its recent use in aquaculture from wild‐caught animals. The UPGMA tree topology grouped the wild samples together with the Central Greece 1 stock, and showed a clear division between wild and farmed sample sets for the six remaining hatchery samples. Knowledge of the genetic variation in S. aurata cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for the proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.     

Genetic monitoring of broodstocks of the marine shrimp Litopenaeus vannamei in a closed rearing system in Pernambuco,Brazil

Loss of genetic variability can be detrimental to a population's survival traits and fitness. These effects are likely to be maximized in shrimp closed broodstock rearing systems where post‐larvae are often produced from crosses of breeders collected from an associated grow‐out farm after mass selection. Longtime broodstock management in closed systems is also expected to lead to reduction in or even complete eradication of genetic variability. The present work aimed at monitoring the genetic variability of a Litopenaeus vannamei hatchery in the state of Pernambuco (Brazil), during three successive replacements, using microsatellite markers. No significant genetic diversity losses have been observed through the values of mean heterozygosity (H_o=0.460 and H_e=0.660 in the first sample; H_o=0.420 and H_e=0.620 in the second sample; and H_o=0.600 and H_e=0.660 in the third sample). However, some alleles appear to have been lost after three replacements. The diversity level was considered to be high and is comparable to those reported for wild populations, suggesting that the original imported founder stock of Brazilian L. vannamei is likely to have had a high genetic diversity, possibly due to multiple origins.     

Genetic structure and genetic relatedness of a hatchery stock of Senegal sole (Solea senegalensis) inferred by microsatellites

Solea senegalensis is a fish species in an early stage of domestication. A commercial hatchery in southern Spain experienced a dramatic failure in spawning and embryo survival, after incorporation into the broodstock of fish reared in their hatchery. To assess the impact of management on the stock quality, a population genetics study was made of adult broodstock present at this hatchery in 2000. The broodstock was composed of a group of fish of wild origin and two more groups from F₁ progeny. A set of eight microsatellite loci was used to compare genetic variability among the three groups and to establish the relationships between pairs of individuals within each group.Individuals from F₁ origin showed a substantial reduction in genetic variability when compared to those from the wild. There was a greater than 50% decrease in the number of alleles per locus corrected by sample size and 16% and 26% reductions in H_e values in the two F₁ groups, respectively. The degree of genetic relationship between individuals, evaluated by the relatedness estimator, rxy, and by graphical approaches, revealed a high proportion, almost 75%, of full-sibs and half-sibs in both F₁ groups, which might account for the reduction in overall variability. The high proportion of siblings also suggests a reproductive pattern in this stock in which few individuals breed successfully. This mating behaviour, along with factors inherent to selection and management systems, might be responsible for the negative effects on the reproductive capacity of the stock.     

Genetic variation of hatchery and wild stocks of the pearl oyster <Emphasis Type="Italic">Pinctada fucata martensii</Emphasis> (Dunker, 1872), assessed by mitochondrial DNA analysis

In order to provide baseline information for the genetic resources, genetic variation in wild and cultured Pinctada fucata martensii from southern Korea and Japan was studied using nucleotide sequence analysis of 379 base pairs (bp) in the mitochondrial cytochrome oxidase subunit I gene (COI). The study included three hatchery stocks from Korea (Tongyeong) and Japan (Mie and Tsushima) and one wild stock from Korea (Geoje). A total of 3 haplotypes were identified in hatchery stocks of 78 individuals, of which 63 individuals shared 1 haplotype. Overall, nucleotide diversity (π) was low, ranging from 0.000 to 0.002, and haplotype diversity (h) ranged from 0.000 to 0.541. Considerably low haplotype and nucleotide diversities in hatchery stock indicated that low effective population size and consecutive selective breeding of P. fucata martensii could be responsible for the reduction in genetic variation. The wild stock exhibited low haplotype diversity (0.507 ± 0.039) with two shared haplotypes. The results of the present study with first record of wild pearl oyster in Korea support the possibility that the transplanted pearl oyster for overwintering experiments could have survived in winter. In order to enhance and/or maintain genetic diversity in the hatchery stock, further research should be directed toward genetic monitoring and evaluation of the hatchery and wild pearl oysters.     

Identification of differential broodstock contribution affecting genetic variability in hatchery stocks of Atlantic salmon (Salmo salar)

Supportive breeding of Atlantic salmon (Salmo salar) is commonly employed to maintain numbers of fish where the species has become locally endangered. Increasingly, one of the main aims of population management is the preservation of natural genetic diversity. If the stocks employed in supportive breeding exhibit reduced variation they can alter the natural pattern of genetic variation observed in wild populations. In northern Spain, wild adult salmon are caught every year from local rivers and artificially crossed in order to create supportive stocks. The offspring are hatchery reared until the juvenile stage, then released into the same river where their parents were caught. In the current study, our findings demonstrate that although adult broodstock exhibit a pattern of variation similar to the wild populations, variability at microsatellite loci was drastically reduced in the juveniles released into one of three rivers analyzed. The contribution of broodstock to this juvenile stock was examined by pedigree analysis. A restricted number of females contributing to the hatchery stock was identified as the main cause of loss in genetic variation, possibly due to overmaturity of some multi-sea-winter females. We suggest that better monitoring and control of parental contribution will help in solving the problem of loss of genetic diversity in hatchery populations.     

Monitoring of the genetic variability of the hatchery and recaptured fish in the stock enhancement program of the rare species barfin flounder <Emphasis Type="Italic">Verasper moseri</Emphasis>

ABSTRACT:   In relation to the stock enhancement program for barfin flounder, hatchery juveniles produced in 2001 were genotyped using microsatellite DNA markers (msDNA) and then released to natural waters. Subsequently, recaptured individuals, designated as 'tentative recaptured', were examined using msDNA. In order to evaluate the effectiveness of the stock enhancement program, pairwise F _ST and genic differentiation tests were used to estimate the genetic divergence between the wild samples, the hatchery broodstock, and the tentative recaptured samples. Analysis showed significant differentiation among these three groups. Pedigree determination by msDNA was used to establish the origin of the tentative recaptured individuals, in order to elucidate whether they were hatchery produced, 'real recaptured', or wild specimens. Wild individuals were not found. The effective population size of the real recaptured stock was very low ( N _e = 16.6). Equal family survivability was observed between the released and real recaptured stocks, indicating that the genetic variability of the released stock was maintained in the natural environment. Future broodstock management, breeding designs, and family contribution equalization of the offspring to be released will be required in this rare species to avoid unintended genetic differentiation between the wild population and the hatchery broodstock.     

Genetic diversity of cultured and wild populations of the giant freshwater prawn Macrobrachium rosenbergii (de Man, 1879) based on microsatellite analysis

Freshwater prawn (Macrobrachium rosenbergii) culture in the Western Hemisphere is primarily, if not entirely, derived from 36 individual prawns originally introduced to Hawaii from Malaysia in 1965 and 1966. Little information is available regarding genetic variation within and among cultured prawn stocks worldwide. The goal of the current study was to characterize genetic diversity in various prawn populations with emphasis on those cultured in North America. Five microsatellite loci were screened to estimate genetic diversity in two wild (Myanmar and India‐wild) and seven cultured (Hawaii‐1, Hawaii‐2, India‐cultured, Israel, Kentucky, Mississippi and Texas) populations. Average allelic richness ranged from 3.96 (Israel) to 20.45 (Myanmar). Average expected heterozygosity ranged from 0.580 (Israel) to 0.935 (Myanmar). Many of the cultured populations exhibited reduced genetic diversity when compared with the Myanmar and the India‐cultured populations. Significant deficiency in heterozygotes was detected in the India‐cultured, Mississippi and Kentucky populations (overall F_is estimated of 0.053, 0.067 and 0.108 respectively) reflecting moderate levels of inbreeding. Overall estimate of fixation index (F_st = 0.1569) revealed moderately high levels of differentiation among the populations. Outcome of this study provide a baseline assessment of genetic diversity in some available strains that will be useful for the development of breeding programmes.     

Genetic diversity and structure of domesticated strains of red sea bream,Pagrus major,inferred from microsatellite DNA markers

The genetic diversity and structure of nine domesticated strains of red sea bream used in a private hatchery were studied and compared to a wild population. A total of 313 individuals were genotyped at eight microsatellite loci. Average number of alleles per locus ranged from 5.5 to 9.4 in domesticated strains, but that of the wild population was 28.4. Heterozygosity of domesticated strains (ranged 0.697–0.804) was also lower compared to the wild population (0.952). Estimated Ne also decreased in all domesticated strains (ranged 10.3–126.0) compared to the wild population (1422.5). The UPGMA tree and 3‐D FCA showed that there were two main clusters containing domesticated strains, and the wild population was at the middle of both of the domesticated clusters. The STRUCTURE analysis also supported the phylogenetic analysis, and revealed three sub‐clusters in the domesticated strains. Pairwise F_ST revealed that all domesticated strains were statistically different from the wild population, and also the differentiation between domesticated strains was all statistically significant. Information on genetic diversity and structure of domesticated strains of red sea bream obtained in this study will be useful for future broodstock management and selective breeding programmes.     

Parentage assignment of stocked black sea bream <Emphasis Type="Italic">Acanthopagrus schlegelii</Emphasis> in Hiroshima Bay using microsatellite DNA markers

The genetic contribution of 51 broodstock, comprising 29 females and 22 males, reared at Hiroshima City Marine Products Promotion Center for the production of stocked black sea bream was monitored during two consecutive years using seven microsatellite DNA loci. The high discrimination ability of these markers was reflected in the polymorphic identification content (PIC=0.831), the exclusion probability (Q≈1), and the low probability of identity index (I=3.635⁻¹⁰). The total number of breeders contributing to the mating process was estimated at 32 (62.7%) in 2000 and 30 (58.8%) in 2001. On pedigree reconstruction, 69.3% of the offspring were successfully assigned to a single broodstock pair. Loss of alleles accounted for 16.9% during seed production; nevertheless, 90.9% of males and 69.0% of females participated in the mating process. Based on microsatellite genetic tagging, 58.9% of the fish sampled during the two months after release were identified as hatchery stock, presenting no significant differences from wild conspecifics in either fork length or body weight.     

Enhancement of reproductive performance in shrimp Litopenaeus vannamei (Boone, 1931) by supplementation of Ulva clathrata meal in maturation diet in two commercial hatcheries

The effect of supplementing dehydrated seaweed Ulva clathrata (20 g/kg) in the squid fraction of a formulated fresh diet on the reproductive performance of Litopenaeus vannamei broodstock was evaluated in two commercial hatcheries (A and B). The origin of broodstock, use of ablation on females, tank/culture conditions (for maturation, spawning, and larval rearing) were different between hatcheries. Daily mortality was higher (p < .01) for females in the control group compared to Ulva‐fed group of hatchery A, where females were ablated. No differences in mortality were found for unablated females in hatchery B, or with males from either hatchery. In hatchery A, broodstock fed Ulva produced more eggs (an increase in +5% compared to control, p < .05) and nauplii per female (+18%, p < .01). In hatchery B, broodstock fed Ulva produced significantly more eggs (+26%, p < .05) and nauplii per day (+33%, p < .05). In hatcheries A and B, eggs from broodstock fed Ulva had increased hatching rates (+13 and +7%, respectively, p < .001 in both cases). The number of spawns per day had a tendency to be higher in broodstock fed Ulva in both hatcheries, but the difference did not reach statistical significance (+14% for hatchery A and +20% for hatchery B). Dehydrated U. clathrata appears therefore as a functional additive in L. vannamei maturation diets that enhances the reproductive performance at commercial scale, regardless of the management conditions.     

Genetic diversity and population history of Tanichthys albonubes (Teleostei: Cyprinidae): Implications for conservation

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Conservation genetics of the Mary River turtle (Elusor macrurus) in natural and captive populations

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Unanticipated departures from breeding designs can be detected using microsatellite DNA parentage analyses

Using microsatellite analysis, a partial pedigree was constructed from an experiment designed to evaluate differences between hatchery Chinook salmon (Oncorhynchus tshawytscha) and their wild donor stocks. First generation (F₁) progeny were created by crossing both hatchery and wild females with hatchery and wild males to create hybrid and control lines. The pedigree analysis revealed an accidental switch of a half-sib control and hybrid F₁ family, which most likely occurred during incubation and led to the misclassification of individuals in those families. The experimental error propagated into the F₂ lines. The pedigree also revealed a number of unintended full-sib matings in the F₂ crosses. This resulted from the small numbers (5 females, 14 males) of wild fish available for the experiment and differential family survival of the F₁ fish. Because researchers used group-specific physical marks to track typed crosses and not family groups, and because physical marks cannot detect inadvertent movement of fish until they are large enough to mark, experimental error occurred that would have influenced the results had a DNA-based analysis not been employed to verify the integrity of the experiment.     

Effect of introducing wild paternity on stock performance of hatchery-reared ayu

The domestication of ayu Plecoglossus altivelis, in which breeding has been carried out for multiple generations without the introduction of exotic broodstock (purebred-styled cultivation), causes rapid loss of genetic variability, and is problematic for resource management programs. The introduction of wild paternity to enhance genetic variability was examined for its effects on the performance of the newly hybridized stock using the Gunma population (hatchery strain), which has been inbred for 29 generations since its origin. Principal component analysis showed that hybridization could modify the stock performance, moderately affecting behavior and morphometrics. Reinforcement of aggressiveness as well as transformation to a long-nosed shape in the hybrid population contribute drevised performance that was acceptable to sports fishers as an artificial stock. To reduce genetic stress for native ayu populations, the introduction of wild paternity is proposed through sperm from wild caught specimens to hybridize with eggs from the pure-bred hatchery population.     

Productivity benefits of selectively breeding Black Tiger shrimp (Penaeus monodon) in Australia

Advances in the domestication and selective breeding of Australian Black Tiger shrimp, Penaeus monodon, opens the opportunity for world producers to reconsider the benefits of farming this species. Just over a decade ago this species was the world's most farmed shrimp species, however, difficulty in its domestication, in part, led to the widespread establishment of Penaeus vannamei (Pacific White shrimp) as the most farmed shrimp species in the world. This study empirically evaluates the productivity benefits of commercially domesticating P. monodon against production from wild broodstock of the same species. The evaluation compared the relative production from commercial ponds stocked with the progeny of wild P. monodon broodstock and ponds stocked with the progeny of domesticated stocks. The production data were from 164 ponds of domesticated stocks and 30 ponds of wild stocks, collected over 4 years (2009–2013) from two separate farm sites of the same Australian shrimp farming company. The wild stocks were sourced from the east coast of Australia. The results suggested that the productivity of the selectively bred stocks was 39% greater compared with production from wild stocks given equivalent amounts of feed and other inputs. Furthermore, productivity was additionally enhanced depending on the choice of feeds and whether stocking took place in September rather than later in the year (i.e. in early spring rather than late spring/early summer in the Southern hemisphere). This suggests that there is significant potential to further enhance the productivity of P. monodon farms via integrating advances in domestication, feeds and management practices.     

Genetic evidence for a single stock of giant tiger prawns Penaeus monodon in demarcated prawn fishing zones of Tanzania

Tanzania demarcated three prawn fishing zones along its coast to spread fishing pressure and help the prawn fishery to recover. However, it is unknown whether the demarcated zones correspond to the genetic stock structure of the world's most commercially important prawn, the giant tiger prawn (Penaeus monodon). Thus, this study used partial mitochondrial control region sequences (534 base pairs) to test the hypotheses that (1) giant tiger prawns in Tanzania's demarcated prawn fishing zones are a single stock and (2) the giant tiger prawns on the Tanzanian coast experienced a recent demographic expansion. The sequences showed high haplotype diversity (h = 0.998–1.0) and low nucleotide diversity (θ_π = 1.89%–2.24%). The neutrality test and mismatch analysis showed that the hypothesis of recent demographic expansion could not be rejected. The analysis of molecular variance revealed low and insignificant fixation indices between the zones (F_ST = 0.00025, p > 0.05; Φ_ST = −0.00027, p > 0.05), suggesting that the three demarcated fishing zones constitute a single stock and that fishers may be targeting the same stock. Furthermore, it was discovered that Zone 2 has the potential to replenish depleted areas; thus, it should be prioritised in future conservation planning.