Polymorphisms of the growth hormone gene in domesticated red sea bream populations (Pagrus major) based on minisatellite genotypes and nucleotide sequences

The genetic diversity of the growth hormone gene in domesticated red sea bream (pmaGH) was evaluated using a minisatellite DNA marker located in intron 3 (pmaGH22) and nucleotide sequences. The number of alleles of pmaGH22 was largely decreased in domesticated strains of red sea bream, and the possibility of selection pressures was also detected based on the analysis of the Hardy–Weinberg equilibrium in some strains. However, each strain inherited a small number of alleles of pmaGH22, and the entire domesticated population (combining all strains) showed a large number of alleles (n = 17), similar to the allelic richness of the wild population (n = 18.5). Based on nucleotide sequencing analysis, three synonym mutations were found in the coding regions, and also several SNPs and indels were found in the noncoding regions. In addition, four genealogies of growth hormone haplotypes were identified based on principal coordinate analysis, and these genealogies of pmaGH partly reflected allele size ranges of pmaGH22. Several haplotypes shared alleles of pmaGH22, and also fragment size homoplasy in pmaGH22 was suspected. These alleles of pmaGH22 and the haplotypes will be a useful indicator for divergence of pmaGH and for broodstock individual selection with minimum inbreeding effect.     

Genetic diversity of red sea bream Pagrus major in western Japan in relation to stock enhancement

SUMMARY: Stock enhancement is used in Japan as a tool to help the replenishment of wild populations of red sea bream Pagrus major . In this study, we analyzed the genetic diversity and composition of wild red sea bream at seven locations around Shikoku Island, South-west Japan, using three microsatellite loci. This analysis was done to test the hypothesis that: (i) red sea bream comprises a single Mendelian population along Japan; and (ii) stock enhancement programs around Shikoku Island are causing genetic differentiation among wild stocks. The results indicated that some locations from the Shikoku area were not significantly different from the rest of Japan, supporting the hypothesis of a single Mendelian population. Significant departures from Hardy–Weinberg equilibrium and significant pairwise F_ST among locations indicated genetic instability within this region. We suggest that the stock enhancement programs made in the region are the possible cause of this genetic instability. A management scheme for the hatcheries involved in the stock enhancement of red sea bream is presented.     

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 changes in Oreochromis shiranus (Trewavas) associated with the early stages of national aquaculture development in Malawi

A study was carried out to investigate the genetic diversity during domestication of Oreochromis shiranus (Trewavas) and to see if it could be associated with events in the known history of aquaculture development in Malawi. Five polymorphic microsatellite loci were scored in 14 populations of O. shiranus and one population of O. mossambicus (Peters). The mean number of alleles per locus ranged from 4.4 ± 1.03 to 13.2 ± 3.31 and was higher in the wild populations than in the domesticated populations. Other measures of genetic diversity were also lower in the domesticated compared with the wild populations, and the decline in diversity was correlated with the time elapsed since the founding of the farm stocks. Ordination analysis grouped domesticated populations into three: (1) those that trace their genealogy from Lakes Chiuta and Chilwa populations and are now spread all over the country; (2) those that come from Lakes Malawi and Malombe; and (3) hybrids between O. shiranus and O. mossambicus. Genetic differentiation among farms was strongly influenced by the pattern of known exchanges among the farmers and introgressive hybridization that had occurred between O. shiranus and O. mossambicus in the farmers’ ponds. Thus, the process of genetic changes in the species subsequent to domestication are best explained and predicted by socio-economic factors that influence the behaviour of farmers, rather than by the time-and-distance models of standard population genetics.     

Spawning season,spawning grounds,and egg production of red sea bream in Hiuchi-nada,Seto Inland Sea

The spawning season and grounds of red sea bream in Hiuchi-nada, the central part of the Seto Inland Sea, were described using a new method based on monoclonal antibodies for identifying Pagrus major eggs, and the daily egg production (standardized by the incubation time and survival rate) was estimated. At the peak of spawning (May), the ranges of sea temperature, salinity, and chlorophyll a where red sea bream eggs occurred were 14.8–17.4°C, 32.0–33.0, 0.5–4.4 μg/L, respectively. The main spawning grounds of the red sea bream were confirmed as being the areas near the Geiyo Islands, Misaki Peninsula, Saijyo, Niihama. The spatial spread of red sea bream eggs increased with the egg developmental stage. The ranges of daily egg production in 2005 and 2006 were 0.3–19.3 and 0.2–6.7 × 10⁹ eggs/day, respectively. In Hiuchi-nada, aquaculture farms are located close to the spawning grounds, and the potential spawning population from the aquaculture farms equaled or exceeded that of the estimated spawning population obtained by the egg production method. Red sea bream eggs in Hiuchi-nada might be produced by both wild and aquaculture-based spawning populations.     

尼罗罗非鱼人工驯养、选育群体遗传多样性及瓶颈效应

人工驯养和选育是家养动物适应性进化的主要动力之一,中国大陆尼罗罗非鱼引进群体经历了长期的人工驯养和选育,是研究鱼类在驯养、选育条件下适应性进化的良好材料。本实验以尼罗罗非鱼1个埃及土著群体为对照组,以中国大陆具有代表性的尼罗罗非鱼5个驯养群体和4个选育群体为实验组,采用12个多态性微卫星位点分析了驯养群体和选育群体的遗传多样性和瓶颈效应。结果显示,土著群体、驯养群体和选育群体平均每个位点的有效等位基因数(AE)分别为5.433、5.113~6.515和3.239~6.734,期望杂合度(HE)分别为0.812、0.796~0.859和0.657~0.858,多态信息含量(PIC)分别为0.768、0.753~0.819和0.601~0.818,近交系数(FIS)分别为0.323、0.166~0.342和0.249~0.314。LSDt检验结果显示,受人工选择的群体(驯养群体、选育群体)与土著群体间遗传多样性水平(AE和HE)无差异,3个驯养群体(EGY群体、WY群体和GD群体)的遗传多样性水平(HE)显著高于1个选育群体(XJF群体)。瓶颈效应分析显示,尼罗罗非鱼土著群体、驯养群体和选育群体在历史上都曾发生过群体缩小的现象。其中,土著群体、2个驯养群体(WY、EGY)、2个选育群体(JNM、XJF)在近期可能经历过遗传瓶颈,其他群体在新的突变和基因流的作用下,群体规模可能已恢复。有效群体大小分析显示,土著群体、驯养群体和选育群体的有效群体数量分别为177、29~117(平均值为57.4)和84~123(平均值为102.8)。本研究结果不仅为尼罗罗非鱼驯养群体的持续利用和选育群体的进一步遗传改良提供了有价值的信息,而且为鱼类在驯养和选育条件下群体遗传结构和种群动态研究提供了新的参考依据。     

Molecular evidence for the lack of transmission of the monogenean Sparicotyle chrysophrii (Monogenea, Polyopisthocotylea) and isopod Ceratothoa oestroides (Crustacea, Cymothoidae) between wild bogue (Boops boops) and cage-reared sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax)

In the Mediterranean area, wild fish have often been suggested as either the reservoirs of the causative agents or at least the carriers of the pathogens responsible for disease outbreaks in cultured fish. However, no epidemiological investigations on actual pathogen/disease interactions between farmed and wild fish have been conducted even for the most important fish pathogens. Only sporadic isolations and identifications of various pathogens in wild fish have been done and real associations with the pathological conditions that exist within the farm environment and vice versa have not been established. Monogenean ectoparasite Sparicotyle chrysophrii and isopod Ceratothoa oestroides are commonly found in the Mediterranean cage-reared sea bream and sea bass and in the surrounding wild fish population. Both species were recognized as pathogens that seasonally inflict serious losses in fingerlings and juveniles of sea bream and sea bass, being potentially propagated and exchanged during wild and caged fish interaction. In order to evaluate the degree of pathogens transfer between wild and farmed fish, we investigated genetic population structures of these two important parasitic pathogens inferred by mtDNA cytochrome oxidase I locus. Parasites isolated from wild and farmed fish on the two most productive Adriatic fish farms showed genetic heterogeneity, contradicting widely accepted hypothesis of cross-contamination, at least in case of S. chrysophrii and C. oestroides. As far as we know, this is the first report that in a study of pathogen transfer molecular evidence was employed to asses the genetic population structure of shared parasites.     

Population genetic structure of sea cucumber, Stichopus japonicus in Korea using microsatellite markers

Sea cucumber ( Stichopus japonicus ) is a commercially valuable species in Korea. We examined the genetic characteristics of sea cucumber populations in Korea using microsatellite markers. A total of 144 sea cucumbers from five populations were typed for nine polymorphic microsatellite loci. A total of 139 different alleles were found over all loci and many alleles were unique. The average number of allele per locus ranged from 6 to 18.4. The average observed and expected heterozygosities ranged from 0.532 to 0.626 and from 0.719 to 0.789 respectively. All populations showed significant departure from Hardy–Weinberg equilibrium at almost all loci except one (Psj2409). This deviation was in the direction of heterozygote deficit. A phylogenetic tree revealed two distinct clusters. One cluster was formed by the eastern sea population. A second cluster consisted of the subpopulations of the western and southern sea populations. The eastern sea population showed genetic differences such as a larger number of alleles per locus, a larger number of unique alleles and a smaller number of the most common alleles, suggesting a higher genetic diversity in this population. These results provide basic information on natural population genetic structure of S. japonicus in Korea.     

A Genetic Assessment of a Red Drum,Sciaenops ocellatus,Stock Enhancement Program

The South Carolina Department of Natural Resources began a stock enhancement research program for red drum, Sciaenops ocellatus, as a possible management strategy for augmenting the availability of juveniles for recreational harvest in South Carolina estuaries. Between 1999 and 2011, approximately 6 million juveniles and 260 million larvae were stocked into the Charleston Harbor (CH) estuary, and proportions of stocked fish were found through standardized sampling as high as 49.6% within a subadult year‐class and up to 12% within the spatially separate spawning population. This study evaluated the genetic influences of stocking on the spawning population, using microsatellite loci, and examined any changes in genetic diversity metrics over the course of the stock enhancement program. Percent contribution of stocked fish among subadult and adult collections was compared against measures of genetic diversity. No statistically significant correlations were found among genetic diversity metrics, suggesting that responsible stocking of red drum as small juveniles has not altered the genetic diversity of adults spawning offshore the CH. Life‐history characteristics likely play a large role in mitigating changes in genetic diversity, despite high contributions of stocked fish in some years, because red drum exhibit a long adult life span and benefit from overlapping generations.     

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 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.     

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.     

Comparison of the swimming performance of farmed and wild gilthead sea bream, Sparus aurata

Farmed gilthead sea bream, Sparus aurata, frequently escape from the sea cages and interact with wild populations. The impact of these interactions on the wild populations will depend, in part, on differences in performance of the bream. This study compared the swimming performance of the wild and farmed fish in a current channel. The absolute critical swimming speed (U_crit) increased with increasing size while the relative U_crit decreased. Even at the same length there were noticeable performance differences between the individuals. The wild sea bream have significantly higher (P<0.05) absolute U_crit performance (0.86±0.01 m s⁻¹) than the farmed fish (0.79±0.01 m s⁻¹) and significantly higher (P<0.05) relative U_crit performance (4.52±0.05 BL s⁻¹) than the farmed fish (4.21±0.05 BL s⁻¹). The present study suggests that cultured sea bream may not have the ability to compete with wild sea bream in native seawaters.     

Loss of genetic variability in the captive stocks of tambaqui,Colossoma macropomum (Cuvier, 1818), at breeding centres in Brazil,and their divergence from wild populations

The loss of variability in farmed populations and the risks of interactions with wild populations support the need for the genetic monitoring of species farmed throughout the world. In Brazil, the tambaqui is the most widely farmed native fish species. Despite this, there are no data on the pedigree of the farmed stocks, and the potential for interactions with wild populations in the Amazon basin has raised concerns with regard to the genetic variability of these stocks. The present study analysed sequences of the mitochondrial Control Region and 12 microsatellites to characterize the genetic variability of seven historically important commercial tambaqui breeding centres located in four different regions of Brazil, and compared these sequences with those obtained from individuals collected from a wild population. High levels of genetic diversity were found in the wild population, whereas genetic diversity was reduced in both markers in most captive populations, except for the broodstock located near the Amazon River. High F_ST and D_EST indices were recorded between the wild population and most of the captive stocks analysed. The drastic reduction in genetic diversity found in most captive stocks and the difference between these stocks and the wild population may have been the result of the small size of the founding populations and the absence of breeding management. The renewal of the broodstocks and the application of breeding management techniques are recommended. In the Amazon region, in addition, the use of broodstocks that are genetically very different from local wild populations should be avoided.     

Forecasting the genetic influences of red drum stock enhancement in South Carolina

The South Carolina Department of Natural Resources (SCDNR) began stocking red drum, Sciaenops ocellatus (Linnaeus), in 1989 to augment the abundance of juveniles available for recreational harvest in South Carolina estuaries. While stock enhancement can help supplement wild populations under high fishing pressure, releasing hatchery‐raised fish into the wild also presents the risk of decreased genetic diversity. An individual‐based model (IBM) was developed to forecast the genetic influences of stocking on the wild spawning population to inform responsible stocking strategies. Model results indicated the SCDNR red drum stock enhancement programme should maintain mean contributions of stocked fish no greater than 30% per year class over a 45‐year stocking period, coupled with at least 10 effective breeders in the hatchery replaced annually, to maintain current levels of genetic diversity estimated in the wild population. The IBM is a useful tool for hatchery managers to guide responsible stock enhancement.     

中华绒螯蟹长江、黄河和辽河水系野生和养殖群体的遗传多样性

中华绒螯蟹(Eriocheirsinensis)是中国最重要的淡水养殖蟹类,广泛分布于东亚地区,养殖区域主要集中在长江、黄河和辽河流域。本研究基于线粒体DNAD-loop区评估辽河野生群体(LW)和养殖群体(LC)、黄河野生群体(HW)和养殖群体(HC)及长江野生群体(YW)和养殖群体(YC)的遗传多样性和种群结构。结果显示:(1)用于本研究的D-loop基因片段长度为477 bp,共包含234个变异位点和131个简约信息位点, 6个群体的262个个体中共有110个单倍型,包括90个独有单倍型和20个共享单倍型;(2)6个种群的单倍型多样性指数(Hd)范围为0.88889～0.96522,核苷酸多样性指数(π)范围为0.00887～0.01602,养殖和野生群体遗传多样性水平依次为:HCYCLC及HWLWYW;(3)6个群体的遗传距离(Da)范围为0.0119～0.0173,不论是养殖群体还是野生群体,辽河群体和长江群体之间的遗传距离均最小,且6个群体间遗传分化指数FST为0.12938。对6个群体进行中性检验显示Tajima’s D和Fu’s Fs的值均为负值。综上,基于线粒体D-loop基因的研究结果表明,三水系养殖和野生群体均具有较高的遗传多样性,且辽河和长江水系中华绒螯蟹的亲缘关系相对较近,该研究为中华绒螯蟹的种质资源评估、保护和开发提供了参考。     

Susceptibility,behaviour, and retention of the parasitic salmon louse (Lepeophtheirus salmonis) differ with Atlantic salmon population origin

Atlantic salmon populations across the world have diverse ecological and evolutionary histories, from wild anadromous or landlocked, to domestication and genetic modification. The natural host behaviours confer protection from infestation by ectoparasitic salmon lice Lepeophtheirus salmonis, yet whether genetic origin results in different behaviours and thus susceptibility to infestation is unknown. In common garden experiments, we tested antiparasite behaviours, susceptibility and retention of salmon lice in wild anadromous, wild landlocked, domesticated and genetically modified domesticated strains. Within domesticated strains, we tested two infestation histories (previously infested and naïve) and a new phenotype (albino colouring). Farmed stocks initially acquired 24%–44% higher levels of parasite density than the wild and landlocked strains. Burst swimming and displacement behaviours were higher in the domesticated groups, and jumping was more prevalent in the domesticated strains. At 34 days post‐infestation, domesticated strains and the wild anadromous strain did not differ significantly from each other; however, landlocked salmon had increased infestation levels considerably. Domesticated strains lost ~20% (±9.9%–16.5%; 95% CI) of their initial parasite load, while parasite load increased by 5.5% (±30.1%) for wild salmon and 20.1% (±28.5%) in landlocked salmon. This study provides early evidence for diverged host–parasite interactions associated with domestication in this system.     

Development of microsatellite markers and evaluation of genetic diversity of the Amazonian ornamental fish Pterophyllum scalare

The objective of the present work was to develop species-specific microsatellite markers for P. scalare and to analyze the diversity and genetic structure of a wild population, from the Amazon River, and three commercial stocks (common, marble, and clown morphological variants), from farmers in Vieras-Minas Gerais. Through microsatellite-enriched genetic libraries, 11 microsatellite markers with adequate amplification patterns were characterized. Population genetic analysis identified eight polymorphic loci that generated 66 alleles ranging from two alleles (PSCA1B3) to nine (PSCA2H1). The polymorphic information content ranged from 0.031 to 0.827. High genetic differentiation was observed between the wild population and the stocks, and moderate differentiation between the three stocks. Deviation in the Hardy-Weinberg equilibrium was observed in one locus in the wild population, in five loci in the common morphological variant, in two in the marble, and in two in the clown morphological variant. Bayesian analysis of genetic structure revealed the existence of two clusters, one represented by the natural population and the other by the stocks. The developed microsatellite markers serve as a tool for the analysis of diversity and genetic structure and conservation studies of P. scalare.

     

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.     

基于SSR-seq技术评估中间球海胆多代选育群体和普通养殖群体的遗传多样性

为明确不同选育群体中间球海胆的遗传多样性和遗传结构,利用SSR-seq技术和15个微卫星位点,对1个家系选育群体(FP)、1个群体选育群体(IP)和1个未经选育的普通养殖群体(CP)的遗传多样性及遗传结构进行了分析。结果显示,15个微卫星位点共检测出112个等位基因,FP、IP、CP 3个群体的平均观测等位基因数(N_a)分别为5.077、5.133和6.133个,平均有效等位基因(N_e)分别为2.816、2.873和3.638个,平均观测杂合度(H_o)分别为0.522、0.441和0.501,平均期望杂合度(H_e)分别为0.595、0.599和0.667,平均多态性信息含量(PIC)分别为0.546、0.543和0.623。家系选育群体(FP) H_e与H_o的差值(0.073)低于IP (0.158)和CP (0.166),平均固定指数(F)(0.115)低于IP (0.248)和CP (0.246)。3个群体间遗传分化系数(F_st)介...