Parental Contributions in a Japanese Flounder Hatchery Inferred from Mitochondrial DNA Haplotypes

We analyzed a portion of the mitochondrial genome of hatchery Japanese flounder Paralichthys olivaceus to compare the genetic characteristics between maternal parents and their offspring. The maternal parents consisted of 11 subcultured fish (broodstock taken from hatchery-raised fish) and 41 wild fish. A 1098 base pair region extending from the 3'half of the cytochrome b gene to the central domain of the control region of mtDNA was amplified by PCR and analyzed using 11 restriction endonucleases. We also analyzed the number of copies of tandem repeats in the control region from the sizes of the PCR products. Each female parent had a unique haplotype, but only 31 of them were observed among the 66 offspring examined. From these results, we estimated that about 60% of the maternal parents in the hatchery contributed to the offspring we surveyed. The distribution of the family sizes of the wild fish was Poisson, which is consistent with expectation from a randomly mating population. In contrast, the distribution of family sizes of the subcultured fish deviated from a Poisson distribution. One of the sources of the deviation was that none of the six oldest fishes contributed to offspring production, which is consistent with observation that the spawning peaks later in the spawning season for older fish in flounder hatcheries. Uneven contribution of the female flounders in the hatchery has the potential to reduce substantially the genetic diversity in the offspring. Our results suggest that the misuse of subcultured fish as broodstock is an important cause of reduced genetic diversity in hatchery-raised flounder juvenile.     

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.     

Parentage assignment in hatchery population of brown sole <Emphasis Type="Italic">Pleuronectes herzensteini</Emphasis> by microsatellite DNA markers

ABSTRACT:   Five loci ( Phz2 , Phz6 , Phz7 , Phz12 , and Phz14 ) of microsatellite DNA markers developed in a previous study for parentage assignment in the hatchery population generated by mating among 61 broodstock fish (35 females and 26 males) in a spawning tank, were selected. After natural spawning in the same tank, larvae collected at three different times were categorized into early phase (EP), middle phase (MP), and late phase (LP) groups. In the parental broodstock, the mean number of alleles per locus was 21.8 and expected heterozygosity ( H _E ) was 0.813. In the progeny, the mean number of alleles per locus decreased to 11.6 (EP), 14.4 (MP), and 6.4 (LP) and H _E to 0.796 (EP), 0.833 (MP), and 0.681 (LP). Parental assignment determined eight dams and six sires as major parents for the EP group. In the MP group, 13 dams and ten sires genetically contributed to spawning, but only three dams and two sires were involved in LP group progeny. In the hatchery population produced from a limited number of parental fish such as the LP group, genetic variability was apparently decreased.     

Microsatellite pedigree analysis reveals high variance in reproductive success and reduced genetic diversity in hatchery-spawned northern abalone

The northern (or pinto) abalone, Haliotis kamtschatkana, is a broadcast-spawning marine gastropod that was recently listed as endangered in Canada. To aid in species recovery, a captive-breeding and supplementation program is underway in Barkley Sound, British Columbia. We genotyped first generation progeny for five microsatellite loci and used a pedigree reconstruction program (Pedigree 2.2) to identify their genealogical relationships in the absence of information on parental genotypes. We analyzed progeny from three separate group-spawning events and inferred considerable variation in the number of offspring produced by each parent; in the most severe case a single male sired all the progeny produced during one spawning event. After only one generation of captive-breeding we found a 55–60% reduction in allelic richness and a 17–18% reduction in heterozygosity relative to the diverse wild source population. This study illustrates the difficulty of managing genetic diversity in hatchery populations of a broadcast-spawning species, even when gametes are collected separately from each individual broodstock.     

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.     

Application of Polymorphic Microsatellite Loci in a Channel Catfish Ictalurus punctatus Breeding Program

Abstract.— In order to monitor spawning success in earthen ponds, individual channel catfish Ictalurus punctatus broodfish were identified prior to stocking by genotype analysis with polymorphic microsatellite DNA markers. Individual spawns were collected and reared in a hatchery, and eight sac-fry per spawn were sampled for genotype analysis. Mendelian inheritance of microsatellite alleles was used to identify parents of each spawn. The probability of detecting a falsely matched offspring and spawning pair was >99%. Average spawning success was 44% (17–80%). Multiple spawning by males was found in seven of the eight ponds sampled. In these ponds, 47% of the males fertilized 2–6 egg masses over 1–8 wk, although most were 2–3 wk apart. Four different spawns were identified as two full-sib families and were probably due to interrupted spawning. Parent/offspring genotype analysis will be useful for production of half-sib families for estimation of genetic components of variation, estimation of effective breeding population, and selection of broodstock for multiple reproductive traits under natural spawning conditions.     

Pedigree analysis of recaptured fish in the stock enhancement program of spotted halibut Verasper variegatus

ABSTRACT:   Spotted halibut Verasper variegatus hatchery juveniles produced in 2002 were genotyped using three microsatellite DNA markers (msDNA) and then released into natural waters. Subsequently, recaptured individuals were examined using msDNA. In order to evaluate the effectiveness of the stock enhancement program, from the genetic point of view, a pairwise F _ST test was implemented to estimate the genetic divergence between the wild captive broodstock, the hatchery offspring and the recaptured samples. The analysis showed significant differentiation between the broodstock and recaptured samples. Pedigree determination using msDNA was used to calculate the effective population size of the recaptured stock, which was found to be very low ( N _e ≈ 8). Equal family survivability was observed between the two recaptured stocks, but not between the released and recaptured stock. The number of identified families was higher and more equalized in the hatchery offspring compared to the recaptured samples, where the number of families declined. This fact was caused by an unequal family survivability just before or just after release. Separately, the number of contributing parents to the hatchery offspring was lower than the broodstock census number. Consequently, these two facts caused the genetic divergence of the recaptured stock from the broodstock.     

Genetic drift in a hatchery and the maintenance of genetic diversity in hatchery-wild systems

ABSTRACT:   Loss of within-population genetic diversity by genetic drift is related to stocking. In order to reduce it, selective use of wild-born individuals for hatchery broodstock is proposed. Its effectiveness is evaluated by the analytical method and numerical simulation. Results indicated that it is effective, especially when the ratio of released hatchery-produced individuals is high in the natural population. Loss of within-population genetic diversity by a few other strategies of broodstock preparation is also analyzed by numerical simulation and the effectiveness of these is also discussed.     

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.     

An Assessment of Hatchery Cohort Growth Rates of South African Abalone,Haliotis midae,Across Four Commercial Environments

The abalone, Haliotis midae (commonly referred to as “perlemoen”), is an important aquaculture species in South Africa, accounting for the highest percentage of total aquaculture production revenue. The industry largely makes use of wild, undomesticated broodstock and thus a consortium of top producers was formed to develop a genetic improvement program to increase efficiency and sustainability of the industry. As such, the current study aimed to evaluate growth trait performance (wet weight and shell length) of four hatchery‐derived cohorts of South African abalone, across four differing production environments. No significant cohort‐by‐location effects were found for weight and length traits; however, differences were detected between respective cohorts and locations. It is concluded that a single synthetic population comprised of all hatchery cohorts under a single breeding goal is suitable for production at all test locations. Furthermore, advances in artificial reproductive technologies, genetic markers, and individual identification hold promise for genetic improvement of the species.     

Evaluating spawning performance among captive Florida pompano Trachinotus carolinus broodstock using microsatellite‐based parentage assignment

Florida pompano has been identified as a promising candidate for commercial‐scale aquaculture production, but to date, little information is available regarding captive broodstock spawning characteristics. Genetic markers were tested for their power in monitoring mating outcomes and potential in analysing heritability of rapid growth trait in Trachinotus carolinus. A total of 20 unrelated adults (10 females and 10 males) were chosen for a hormone‐induced mass spawning event. The 515 fastest growing and 485 slowest growing fish of the total 4852 offspring were considered a selected progeny stock, and fish were collected at 45 days post hatch based on their growth traits. Parentage analyses based on the 20 breeders and 1,000 selected progeny were performed using a total of nine microsatellite markers, a 100% assignment rate was achieved, and a four‐marker set was the minimum number for the parentage assignment. The effective breeding number for the selected progeny was 11 (six females and five males), among which three females and two males were predominant contributors with the total contribution of 95.8% and 94.7% respectively. The proportion of fast‐growing offspring from broodfish and each mating cross (sire/dam) was used for detecting whether variation in growth of the offspring was related to parental stocks. Results showed that three adults and their mated combination exhibited the greatest fast‐growing offspring proportion (69.73% and 55.95%). This research provided new information regarding spawning performance and parental contribution during mass spawning events; both important first steps towards developing improved management strategies for captive Florida pompano broodstock.     

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.     

Decreased genetic diversity and a reduced effective population size in cultured silver-lipped pearl oysters (Pinctada maxima)

Before selection programmes for aquaculture species can commence, a fundamental knowledge of how the culture process affects genetic diversity is requisite. “South Sea” pearl production, through the culture of the silver-lipped pearl oyster, Pinctada maxima, stands to gain substantially from genetic selection. Aquaculture techniques for P. maxima have progressed vastly, to a point where the majority of current operations are based on hatchery-propagated stock; however, there has been no investigation on how the culture process is affecting the genetic diversity of this species. To address this deficiency, we investigated the genetic diversity and effective population sizes (N_e) in three wild and five hatchery-produced P. maxima populations. Using six microsatellite DNA markers, cultured populations exhibited low N_e (3.5–9.2) and reduced allelic richness (29–44%) compared with their wild progenitors. Observed heterozygosities were not affected greatly, however, an increased mean pairwise genetic relatedness was observed in all cultured populations. The practice of mass spawning was identified as a major factor in the reduction of diversity, although diversity was not necessarily maintained when a more controlled spawning approach was utilised. Pedigree reconstructions revealed genetic diversity and N_e is affected by large skews in full-sib family representations (up to 40% from a single family, in a cohort using 28 broodstock), and could be due to differential survival rates amongst communally reared families. In order to maximise future selective breeding efforts, further research should be directed towards identifying critical stages of the culture process in which genetic diversity is lost.     

Influence of Hatchery Protocols on Mitochondrial DNA Variation in Japanese Flounder Juveniles

The Japanese flounder Paralichthys olivaceus is a commercially important fish that is stocked extensively from hatchery rearing programs in Japan. To examine the genetic variability of hatchery-raised juveniles of the Japanese flounder that are used for stocking into natural waters, we analyzed a portion of the mitochondrial genome. The mtDNA region extending from the 3'half of the cytochrome b gene to the central domain of the control region was PCR amplified and analyzed using 11 restriction endonucleases. We identified 34 polymorphic cleavage sites out of a total of 61 sites, which resulted in 67 different haplotypes in a total of 265 offspring, examined from eight hatchery stocks. Haplotype diversity of offspring at each of the eight hatcheries ranged from 0.49 ± 0.09 (SE) to 0.94 ± 0.03 (SE). Also, we observed 40 polymorphic sites out of a total of 59 sites, which resulted in a total of 50 haplotypes in 60 wild flounder. Haplotype diversity of the wild population was 0.98 ± 0.01 (SE). The use of subcultured fishes as broodstock appears to be one of the most important causes of reduced genetic diversity in hatchery-raised flounder juvenile. Our results suggest that the use of wild fish for broodstock is an effective way to maintain genetic variability in Japanese flounder offspring.     

Production Management of Double-Net Tilapia Oreochromis spp. Hatcheries in a Eutrophic Tropical Reservoir

Abstract.— A floating, double-net hatchery system for a red tilapia hybrid Oreochromis spp. was developed and tested in a eutrophic reservoir in West Java, Indonesia. Objectives of the studies were to test the effects of different male and female broodstock rotation times on fingerling production and compare production of the double-net system with other studies using a multiple regression model. Two experiments (EXP1 and EXP2) were conducted in four separate double-net hatchery systems comparing three broodstock rotation times over 12 spawning periods in EXP1 and 21 in EXP2. In both experiments, shorter broodstock rotation times (14–16 d in EXP1 or 10–15 d in EXP2) produced significantly ( P < 0.05) higher numbers of fingerlings (6.24 in EXP1 and 14.52 fingerlings/female per d in EXP2). A multiple regression model was developed to summarize results of six studies which included 31 spawning periods. A significant ( r² = 0.651, P < 0.05) relationship was found between tilapia seed production in net hatcheries as the dependent variable and initial female broodstock densities (−), initial female body weight (−), female/male stocking ratio (−), and feed protein content (±) as independent variables.     

Oocyte and embryo quality in Crassostrea gigas (Portuguese strain) during a spawning period in Algarve,South Portugal

Egg quality is one of the most important factors determining larval viability. The study of oocytes released by `wild' broodstock will contribute to the definition of quality criteria applied to hatcheries as well as being an indicator of the oyster reproduction potential and aquaculture ongrowing systems. The aim of this study was to determine the relationship between condition of Crassostrea gigas spp. angulata (Portuguese strain) from `wild' broodstock (condition index, gonadal maturity and number of oocyte released), oocyte biochemistry and hatching rate of eggs during the spring/summer of 1995. Stages of gonadal maturity and condition index indicated that natural spawning of this species occurred between April and August with the highest spawning intensity occurring in June. Analyses demonstrated that C. gigas oocyte organic matter consist of 44–74 % proteins, 16–38 % lipids and 7–12 % carbohydrates. A significant relationship was observed between some biochemical parameters – organic matter and lipid content – and broodstock condition index and hatching rate. It seems that these two oocyte parameters (organic matter and total lipids) could be used to define quality of oocyte and thus larval viability. The oocyte protein content was also found to be associated with broodstock and larval quality. In summary, these data are a contribution to the knowledge of the reproductive cycle of oysters in Europe and may be useful in improving hatchery management of this species.     

Spawning Frequency Analysis of Wild and Pond-Reared Pacific White Shrimp Penaeus vannamei Broodstock under Large-Scale Hatchery Conditions

Second generation Penaeus vannamei broodstack, pond-reared and wild populations, were compared for spawning frequency and several variables associated with reproductive performance. For this purpose, 470 pond-reared and 237 wild-caught individually tagged females were stocked with males of the same origin in ten maturation tanks in a commercial hatchery, and several productivity variables were recorded over time. Results of the analysis indicate that wild shrimp had higher mating and spawning frequencies compared to pond-reared broodstock. The number of nauplii per spawn was higher for wild shrimp, but fertilization and hatching rates were higher for pond-reared spawners. A larger proportion of nonmating females were found in pond-reared shrimp; whereas, wild females had a higher potential for multiple matings. The spawn quality (fertilization and hatching rates, percentage of viable spawns, and number of nauplii) in consecutive matings did not decline substantially. The present study indicates that selection of females with multiple spawning capabilities can be an important commercial strategy to improve nauplii production over the short term. Pond-reared broodstock can be an adequate source for applying this strategy because of their year-round availability and an overall acceptable reproductive performance.     

Reproductive strategies in small populations: using Atlantic salmon as a case study

Abstract –  Wild salmonid populations with only a few breeding adults may not exhibit a significant reduction in genetic variability compared with larger populations. Such an observation suggests that effective population sizes are larger than population size estimates based on direct adult counts and/or the mating strategy maximises outbreeding, contributing to increased heterozygosity. In the case of wild Atlantic salmon Salmo salar populations, stratification by age classes and sexes on the spawning grounds avoids inbreeding and increases genetic variability. We studied the breeding composition of four Spanish salmon populations. Over a 7-year period we concluded that the probability of within-cohort mating is very low: females generally reproduce after two sea-winters whereas males reproduce mostly as one sea-winter ( grilse ) and/or mature parr. Considering different levels of contribution of mature parr to spawning derived from field surveys, we developed a simple model for estimating effective population sizes and found that they doubled with 65% parr contribution expected for rivers at this latitude (43°N), and ranged from 100–800 individuals. The effect of between-cohort mating was modelled considering different ranges of differences in allele frequencies between cohorts and resulted in 28–50% increases in heterozygosity when considering a 65% parr contribution. The complex mating strategy of Atlantic salmon contributes to explain the high levels of genetic variability found for small populations of this species. This model can probably be extended to other animal species with mating strategies involving different cohorts.     

Genetic comparison of experimental farmed strains and wild Icelandic populations of Atlantic cod (Gadus morhua L.)

Microsatellite DNA loci and the Pantophysin locus (Pan I) were used to investigate levels of genetic diversity within farmed strains of Atlantic cod Gadus morhua and to compare them with the wild source population. A total of 282 farmed samples originating from a spawning ground off the south-west coast of Iceland were sampled in the years 2002 and 2003, and 258 wild cod were collected at the same spawning ground in the same years. The farmed strains exhibited a lower mean number of alleles and allelic diversity than the wild samples at the microsatellite loci. Significant differences were observed between wild and farmed samples both in allele and genotype frequencies at the Pan I locus. We argue that the genetic divergence of wild and farmed samples of Atlantic cod may be due to a small number of effective founding breeders contributing to the genetic variation of the farmed strains, inducing a reduction in allelic diversity. We discuss the potential effect of breeding practices on the genetic diversity of Atlantic cod.     

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.