基于微卫星评估草鱼放流亲本对野生群体遗传多样性的影响

利用筛选的13对草鱼多态性微卫星标记,开展了2011至2015年长江中游草鱼亲本增殖放流对野生群体遗传多样性的影响评估。通过对各位点的遗传多样性分析,13个微卫星位点的多态信息含量为0.8622(0.657~0.950),基因多样度为0.8555(0.675~0.936)。15个群体的有效等位基因数为7.4503~10.1536,等位基因丰度为11.483~15.204,说明15个草鱼群体的遗传多样性水平总体较高。遗传分化指数分析表明,群体间不存在显著遗传分化(FST5%)。通过贝叶斯聚类分析和主成分分析可将草鱼群体分为4个组群,根据分组结果以及来源划分分别对草鱼群体进行AMOVA分析,发现遗传变异大部分来自于群体内个体间,组间及组内群体间的分化水平较低(FCT5%,FSC5%),与FST分析结果一致。研究表明,当前草鱼亲本增殖放流模式对野生群体遗传结构影响不明显。     

Genetic characteristics of Pacific cod populations in Korea based on microsatellite markers

Pacific cod (Gadus macrocephalus) is a commercially important species in Korea. However, overfishing in the 1990s caused a strong decline in catch, and in response, artificially cultured juveniles have been released annually to enhance the stocks. Cod fishing has recently increased in Korea, and the variation within the cod population necessitates the study of their genetic characteristics. In this study, we utilized two newly developed and eight previously reported microsatellite markers to examine the genetic characteristics of Pacific cod populations. We compared the genetic diversity and genetic structure of three cod populations from the Korean coasts with three populations from the North Pacific Ocean. Genetic differences were identified in the eastern sea cod population from Korea. These genetic differences included a large number of alleles per locus, a large number of unique alleles, higher frequencies of the most common alleles, and lower gene diversity compared to the other Korean populations. Additionally, the eastern sea cod population was genetically significantly differentiated from the southern and western sea populations in Korea, in which no significant genetic differentiation was detected (F _ST = 0.033 and 0.031, respectively, P < 0.005).     

Microsatellite‐based genetic and growth analysis for a diallel mating design of two stocks of the clam,Meretrix meretrix

To determine the potential for productive efficiency and genetic improvement in the clam (Meretrix meretrix), four populations were produced from a diallel mating of two different geographical stocks (SD and JS). The genetic parameters at nine novel microsatellite loci indicated that the numbers of alleles, observed heterozygosity and polymorphic information content of the reciprocal cross populations (SDJS and JSSD) were larger than those of the pure populations (JSJS and SDSD). The values of Nei's unbiased genetic distance and F_ST revealed that the largest genetic divergence was between the two pure populations (D_C=0.2993, F_ST=0.1438) and the smallest was between the two reciprocal cross populations (D_C=0.1093, F_ST=0.0583). In addition, the mean shell lengths of the reciprocal cross populations were significantly larger than that of the pure populations by 1.577 mm (P<0.05), and the same trend was observed in the other traits. A significant maternal effect was revealed after analysis of the effects of egg origin and mating strategy on the four traits. Heteroses for all the traits were detected in the reciprocal cross populations. Our research implies an extensive development potential in productive efficiency and genetic improvement for M. meretrix.     

Genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus) revealed by DNA microsatellites

To assess the genetic diversity of Nile tilapia Oreochromis niloticus, a total of 250 fish from five Egyptian populations were genotyped using six microsatellite markers. Heterozygosity and Wright's F‐statistics (F_IS, F_ST, and F_IT) were calculated to determine the genetic variation within and between these populations. Observed heterozygosities were in the range of 0.4 (Burullus) to 0.96 (Qena), with F_IS values ranging from 0.082 to 0.282. The mean F_ST showed that approximately 96.5% of the genetic variation was within‐population and 3.5% was among populations. Standard genetic distances were used to classify the five populations into two major groups. The deeper lotic river Nile populations of Assuit and Cairo formed one group and the shallow less lotic Delta lakes populations of Manzalla and Burullus formed the second group, with the upstream Nile Qena population being an outgroup. The findings from the current study help understanding of the broad‐scale population structuring of the Nile tilapia (O. niloticus) allowing the population groupings identified to act as potential sources of genetic variation. These populations could be included in future Marker‐Assisted‐Selection programs for economically desired production traits.     

First microsatellite data on Proteus anguinus reveal weak genetic structure between the caves of Postojna and Planina

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Genetic characterization of naturalized populations of brown trout Salmo trutta L. in southern Chile using allozyme and microsatellite markers

This study describes the genetic structure of five naturalized populations of brown trout in southern Chile using allozyme and microsatellite markers to establish levels of intra‐ and interpopulation genetic variability and divergence. Fourteen enzymatic systems were used comprising 20 loci and three microsatellite loci specific to brown trout. The genetic variability values (allozymes, P=20–35%, average=27%, H_O=0.118–0.160, average=0.141; microsatellites, P=33.3–100%, average=66.66%, H_O=0.202–0.274, average=0.229) are similar to values described in other naturalized populations of brown trout present in Chile, but higher than those observed in European populations of this species. Values of total genetic diversity (H_T) (allozymes=0.1216 and microsatellites=0.3504) and relative genetic divergence (G_ST) (allozymes=9.5% and microsatellites=15%) were also similar to the results obtained in previous studies of Chilean populations of brown trout. These values, when compared with those obtained in Europe, proved to be similar for H_T but lower for G_ST. The low interpopulational genetic differentiation was in accordance with the small genetic distance observed between the populations analysed (D Nei=0.004–0.025). On the other hand, the high frequency of one of the two alternative alleles of the phylogeographic marker locus LDH‐5* in the populations analysed (LDH‐5*90>0.84) would indicate a European origin, in particular Atlantic as opposed to Mediterranean, for the brown trout introduced into Chile. The high levels of genetic variability suggest a mixed origin for the naturalized brown trout in Chile, which could have originated either before or during the introduction process. Nevertheless, the low level of genetic differentiation between populations could reflect the short lapse of time in evolutionary terms, during which populations introduced into Chile have been exposed to different evolutionary forces, and which has not been sufficiently long to produce greater genetic differentiation between populations.     

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.     

Genetic variability of cultured populations of the Pacific abalone (Haliotis discus hannai Ino) in China based on microsatellites

The genetic diversity of cultured populations of the Pacific abalone (Haliotis discus hannai Ino) from northern China was analysed using seven microsatellite markers. The microsatellite loci were polymorphic for all the populations, with an average of 8.7 alleles per locus (range 8.0–9.4). The mean observed and expected heterozygosities were 0.547 (range 0.500–0.596) and 0.774 (range 0.754–0.787) respectively. The allelic diversity in terms of number of alleles per locus was considerably lower than that previously found in wild populations (range 21.8–23.0), indicating that bottleneck effects occurred when each population was founded. Significant genetic differentiation among the five cultured populations was shown using F_st and R_st values, and pairwise comparison based on allelic distribution. A neighbour‐joining analysis of the genetic distance did not show a consistent relationship between the geographic and the genetic distances, suggesting the existence of exchanges of breeds and eggs between the hatcheries. The results obtained in this study are useful for a number of areas of interest for fisheries management and the aquaculture industry, especially with regard to breeding programmes.     

Effects of elevated pCO2 on the early development of the commercially important gastropod,Ezo abalone Haliotis discus hannai

We used an up‐to‐date, a high accuracy CO₂ manipulation system to investigate the sensitivity of organisms to CO₂ acidification, rearing marine calcifiers under elevated CO₂ in running water. We evaluated the effects of elevated partial pressures of carbon dioxide (pCO₂) in seawater on larvae of the commercially important marine gastropod Ezo abalone Haliotis discus hannai. In larval Ezo abalone, no effect of exposure to <1100 μatm pCO₂ seawater was observed in fertilization, malformation, or mortality rates until 15 h after fertilization. However, compared to control larvae in seawater (450 or 500 μatm pCO₂), the fertilization rate and the hatching rate (15 h after fertilization) decreased with increased pCO₂ exposure (1650 and 2150 μatm pCO₂) and the malformation rate increased significantly, with the larval shell length being smaller 75 h after hatching. These results suggest that ocean acidification will potentially impact the marine population of Ezo abalone as a human food source in the future.     

Genetic variation measured by microsatellites among three strains of domesticated rainbow trout (Oncorhynchus mykiss, Walbaum)

Genetic variation fuels selective change in natural and captive populations. In establishing a broodstock for selective improvement, the level of genetic diversity is an important consideration because it provides an indication of the scope for selective progress. Three domesticated strains of rainbow trout, Oncorhynchus mykiss (Walbaum), were examined at nine polymorphic microsatellite loci to assess detectable levels of allelic diversity and heterozygosity within and differentiation among the strains. A total of 126 alleles were observed to segregate into unique multilocus genotypes for each of the 152 individuals assayed. There was an average heterozygosity of 71.5% at these nine loci, and an average of 14 alleles at a locus. Each locus was represented by alleles unique to at least two of the three strains. Deviations from Hardy–Weinberg expectations of genotype frequencies were detected in each strain. Subsequent analysis indicated sub‐structuring within strains leading to Wahlund effects that caused these deviations. Significant differences in genotype frequencies and pairwise F_ST values demonstrated that all strains were unique. The overall F_ST of 0.089 provides additional evidence of unique genetic diversity present in each strain, and agrees well with the degree of genetic variation found in rainbow trout across broad geographical ranges. The genetic diversity contributed by each population suggests that there is greater scope for selective improvement of numerous traits within a synthetic strain combining these three strains than within any individual strain.     

Genetic population structure of the Pacific bluefin tuna Thunnus orientalis and the yellowfin tuna Thunnus albacares in the North Pacific Ocean

The genetic population structure of the Pacific bluefin tuna (PBF) Thunnus orientalis and the yellowfin tuna (YFT) T. albacares in the North Pacific Ocean was investigated. The polymorphism of microsatellite (SSR) loci and sequences of mitochondrial DNA control region (mtCR) were analyzed for 71 samples of PBF from Japan and Mexico and 45 samples of YFT from Japan and Panama. In the SSR analyses, both single-locus (?0.010 to 0.008 in PBF and ?0.023 to 0.020 in YFT) and global multilocus (0.003 in PBF and ?0.002 in YFT) F _ST values among the geographic populations were low and not significant in these species. In the mtCR analyses, neither the neighbor-joining tree nor the minimum spanning network showed genetic differentiation among the geographic populations in each species. The pairwise F _ST values among the geographic populations of them (?0.005 in PBF and ?0.020 to ?0.014 in YFT) were low and not significant. Our SSR and mtCR data suggested that genetic differentiations were not evident among the eastern and western populations in the North Pacific Ocean either in PBF or in YFT. Mismatch distributions, demographic parameters, and neutrality tests suggested that sudden population expansion of PBF and YFT in the North Pacific Ocean occurred 628,000–731,000 and 450,000–525,000 years ago, respectively.     

Population genetics of cobia (Rachycentron canadum) in the Gulf of Thailand and Andaman Sea: fisheries management implications

Population genetics has been recognized as a key component of policy development for fisheries and conservation management and aquaculture development. This study aims to evaluate the genetic diversity and population structure of native cobia (Rachycentron canadum) in the Gulf of Thailand and Andaman Sea, establishing the existing population distributions and contributing information to aid in the development of policy, prior to extensive aquaculture development. Microsatellite analysis of natural cobia populations in these two ocean basins shows similar levels of gene diversity at 0.844 and 0.837, respectively. All populations and almost all microsatellite loci studied show significant heterozygote deficiency. Genetic differentiation between local populations is low and mostly not significant (R _ST = ?0.0109 to 0.0066). The population shows no marked structure over the long geographic barrier of the Thai–Malay peninsula, either when analyzed using pairwise genetic differences or evaluated without predefined populations using STRUCTURE. Additionally, a Mantel test shows no evidence of isolation by distance between the population samples. The significant heterozygote deficiency at most of the loci studied could be explained by the possibility of null alleles. Alternatively, given the behavior of forming small spawning aggregations, seasonal migration, and hitchhiking on large marine animals, the population genetics could be complex. The population of cobia at each location in Thai waters may be inbred, as a result of breeding between relatives, which would reduce heterozygosity relative to Hardy–Weinberg frequencies, while some of these populations could be making long distance migrations followed by admixture between resident and transient groups. This migration would cause population homogeneity in allele frequencies on a larger geographic scale. The results suggest that fisheries management for this species should be considered at both national and international levels, and until the possibility of local adaptation is fully investigated, policy development should apply the precautionary principle to ensure the preservation of genetic diversity and the sustainability of local and regional fisheries.     

Genetic variation and population structure of the caramote prawn Penaeus kerathurus (Forskäl) from the eastern and western Mediterranean coasts in Tunisia

Ten populations of Penaeus kerathurus (Forskäl), a prawn of high commercial value, were sampled from the eastern and western Mediterranean coastal waters of Tunisia and screened electrophoretically for genetic variation at 13 allozyme loci. Four among the six polymorphic loci were out of Hardy–Weinberg equilibrium (H–WE) in at least one population. In the same way, the multilocus test showed deviation from H–WE in six populations. These populations showed heterozygote deficiency whereas the average heterozygosity for the four remaining ones is quite similar to the expected levels. Genetic variability was low. The number of alleles per locus ranged from 1.2 to 1.5 (average=1.3), and the observed heterozygosity varied between 0.010 and 0.048 (average=0.021). Significant population differentiation (F_ST=0.076, P<0.05) in the total data set reflected the differentiation of the two populations, which were at the margins of the range sampled, from all the others (Pairwise F_ST values ranged from 0.035 to 0.208). Although there was no significant differentiation among the other populations (pairwise F_ST values ranged from ?0.006 to 0.201, P>0.05). Our data suggest a population structure consistent with separation by Mediterranean Sea basins that might reflect different local biogeographical zones.     

Genetic Diversity and Population Structure in the Heavily Exploited Korean Rockfish,Sebastes schlegeli,in Korea

The Korean rockfish, Sebastes schlegeli, is a valuable and intensively exploited species in Korea. We discuss the genetic diversity and genetic structure of four Korean rockfish populations using eight microsatellite loci. In total, 161 different alleles from 138 individuals were observed. Average allele number per locus ranged from 2.5 to 23 and allelic richness varied from 13.38 to 14.63 within a population. Despite a long history of stocking practices, we found very high levels of polymorphism (mean heterozygosity = 0.810), which is comparable to other congeneric species. No significant difference in genetic diversity and molecular genetic variance (F_ST and R_ST) was observed among four local samples (P > 0.1). Little indication of contemporary inbreeding (F_IS= 0.051) or population structure (K = 1) was detected. This absence of differentiation may reflect high levels of gene flow along the coast of Korea. Our study demonstrates that rockfish in Korea should be managed as a single unit. Currently, the species does not appear to be genetically threatened, but the potential for a rapid loss of genetic diversity remains. This information on the genetic characteristics of Korean rockfish populations has important implications for fisheries management and conservation efforts, and will aid in the sustainable exploitation of the fishing resources and the preservation of biodiversity.     

Population genetic structure and gene flow in the Japanese sea cucumber Apostichopus japonicus across Toyama Bay, Japan

The Japanese sea cucumber Apostichopus japonicus has a pelagic-lecithotrophic larva. Here, we clarify larval dispersal among Japanese sea cucumber populations by describing the levels of distinctiveness and gene flow among red and green variant populations of A. japonicus across Toyama Bay using 11 polymorphic microsatellite markers. Samples of Japanese sea cucumber populations were collected from three localities (Noto, Shinminato, and Uozu) around Toyama Bay. Geographically separated populations of red and green variants were determined to be genetically distinct, supported by phylogenetic analysis and the distinctiveness range values of pairwise multilocus estimates of F _ST. Contemporary migration analyses indicated that the majority of estimated migration events occurred within A. japonicus populations comprised of only either red or green variants. In a historical gene flow analysis, two best-fit models (n-island and stepping stone models) showed circulation for the gene migration in Toyama Bay among red variant populations. Our results provide useful information on the genetic structure of Japanese sea cucumber populations and will be helpful for genetic conservation and fisheries management of sea cucumber populations in Toyama Bay.     

Genetic differentiation of wild and hatchery Oujiang color common carp: potential application to the identification of escapees

The escape or release of cultured and domesticated organisms into the wild poses a threat to the genetic integrity of natural populations. Based on data from 17 microsatellite loci, the genetic differentiation between wild and hatchery Oujiang color common carp Cyprinus carpio var. color was investigated, and its potential application for identifying the escapees of hatchery strains was assessed using Bayesian genetic assignment. No significant differences were observed between pooled hatchery and pooled wild populations in terms of allelic richness (A _R), observed heterozygosity (H _O), and inbreeding coefficient (F _IS). Analysis of molecular variance and pairwise F _ST comparisons suggested significant genetic differentiation between hatchery strains and between hatchery and wild populations, which was further confirmed by principal components analysis and Bayesian clustering analysis. Bayesian genetic alignment showed high self-assignment accuracy (ranging from 86.0 to 96.0%) in the original populations, demonstrating the ability of this technique to identify hatchery Oujiang color common carp escapees in the wild population.     

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.     

大泷六线鱼放流群体与野生群体遗传多样性比较

基于线粒体DNA控制区高变区部分序列和4对微卫星标记,对大泷六线鱼放流群体及自然海域群体的遗传多样性与遗传差异进行了比较分析。线粒体DNA控制区序列分析的结果显示,413尾个体共检测到单倍型117种,其中仅Hap₃、 Hap₇和Hap₁7为共享单倍型,占总单倍型数目的 2.5%;放流、野生群体特有单倍型分别为20种和66种,分别占总单倍型数的17.09%和56.41%,放流群体特有单倍型数明显低于野生群体;放流群体和野生群体核苷酸多样性分别为0.005 1～0.006 7和0.005 8～0.007 5,单倍型多样性分别为0.856 7～0.949 9和0.883 1～0.954 9,遗传多样性均较高。微卫星标记分析结果显示,放流、野生群体平均等位基因数(Na)分别为13～44和13～27,平均多态信息含量为0.885 6和0.874 0,均具较高的遗传多态性;群体遗传结构分析结果表明,放流、野生群体间遗传分化水平较低。研究表明,山东近海大泷六线鱼放流群体与野生群体均具有较丰富的遗传多样性,且遗传结构未存在显著的群体分化...     

Identification of Two Channel Catfish Stocks,Ictalurus punctatus,Cultivated in Northeast Mexico

The channel catfish farming in Mexico began in the 1970s. One of the most important areas of production is its northeastern region. Traditionally, the channel catfish farmers have attempted to preserve their original genetic stock. After more than 30 yr of production, the genetic relationship between stocks has not been assessed. The goal of this study was to evaluate the genetic differentiation between five channel catfish farm populations, using 13 microsatellite markers. A total of 154 fin clip samples were collected from five channel catfish farms in Tamaulipas. We also included 31 individuals of the commercial strain NWAC103. In each population, we calculated parameter of genetic variability: inbreeding coefficient (F_IS), pairwise differentiation (F_ST), and genetic distance (D_C). For the inference of populations and individual assignment two Bayesian methods were used. Genetic variability parameters were N_A = 9.54–11.08 and A_E = 5.40–6.67. Hardy–Weinberg equilibrium deviations were observed for all farm populations examined, and a deficit of heterozygotes was found. Signals of inbreeding were observed, particularly for the ACU (Acuamex) hatchery. Populations EKA (Empresas Karol) and ACU showed higher genetic differentiation values with respect to the commercial strain (F_ST = 0.107; F_ST = 0.082, respectively). Moderated genetic differences (F_ST = 0.067; D_C = 0.080) were observed between the EKA and ACU. Clustering analysis revealed a well‐defined group between EKA and TPA (El Tiron Parejo). In the Bayesian analysis three groups were defined. The first group was formed by EKA and TPA, the second group included ACU, LAJ (La Lajilla), and PRO (Prodatec). In the third group was the commercial strain. In the assignment of individuals, EKA and ACU were represented by exclusive genotypes. Identification of two genetic stocks, one located in the EKA and the other in the ACU population, will be relevant for future management of these hatcheries. Additionally, the information from microsatellites and the statistical procedures presented will be important tools for genetic monitoring of these farm populations.