Genetic variation of wild and hatchery populations of the catla Indian major carp (Catla catla Hamilton 1822: Cypriniformes, Cyprinidae) revealed by RAPD markers

Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD) markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822) in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001) departure from homogeneity and the F(ST) values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA) dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.     

Population genetic structure of wild and hatchery black rockfish Sebastes inermis in Korea, assessed using cross-species microsatellite markers

The population structure of the black rockfish, Sebastes inermis (Sebastidae), was estimated using 10 microsatellite loci developed for S. schlegeli on samples of 174 individuals collected from three wild and three hatchery populations in Korea. Reduced genetic variation was detected in hatchery strains [overall number of alleles (N(A)) = 8.07; allelic richness (A(R)) = 7.37; observed heterozygosity (H(O)) = 0.641] compared with the wild samples (overall N(A) = 8.43; A(R) = 7.83; H(O) = 0.670), but the difference was not significant. Genetic differentiation among the populations was significant (overall F(ST) = 0.0237, P < 0.05). Pairwise F(ST) tests, neighbor-joining tree, and principal component analyses showed significant genetic heterogeneity among the hatchery strains and between wild and hatchery strains, but not among the wild populations, indicating high levels of gene flow along the southern coast of Korea, even though the black rockfish is a benthic, non-migratory marine species. Genetic differentiation among the hatchery strains could reflect genetic drift due to intensive breeding practices. Thus, in the interests of optimal resource management, genetic variation should be monitored and inbreeding controlled within stocks in commercial breeding programs. Information on genetic population structure based on cross-species microsatellite markers can aid in the proper management of S. inermis populations.     

太平洋牡蛎养殖与野生群体遗传变异的微卫星研究

应用微卫星标记技术研究5个中国太平洋牡蛎养殖群体和2个日本太平洋牡蛎野生群体的遗传变异。研究中所使用的7个微卫星位点在养殖和野生群体中都显示出了高多态性,平均等位基因数为19.1～29.9,平均期待杂合度为0.916～0.958。养殖群体和野生群体的平均等位基因丰度及观察杂合度没有显著性差异。遗传分化系数及等位基因杂合度分析显示所有的群体间都有显著性差异。构建的NJ树中,7个群体聚为3支,养殖群体和野生群体可以清楚地分开,在养殖群体中又分为南北两支。分配检验中,97%～100%的正确率证明了微卫星标记在群体识别分析中的可行性。本研究结果对太平洋牡蛎管理模式的设计和选择育种具有重要意义。     

Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei

Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (F(ST) = 0·09 - 0·49; P < 0·05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.     

Genetic differentiation between collections of hatchery and wild masu salmon (<Emphasis Type="Italic">Oncorhynchus masou</Emphasis>) inferred from mitochondrial and microsatellite DNA analyses

There has been very little effort to understand genetic divergence between wild and hatchery populations of masu salmon (Oncorhynchus masou). In this study, we used mitochondrial (mt) NADH dehydrogenase subunit 5 gene (ND5) and six polymorphic nuclear microsatellite DNA loci to compare the genetic variability in three hatchery broodstocks of masu salmon with the variability in eight putative wild masu populations sampled in five rivers including one known source river for the hatchery broodstocks. Both ND5 and microsatellites showed no significant genetic divergence (based on F_ST estimates) between four annual collections from the source river population, suggesting no change in genetic diversity over this time period. The F_ST estimates, an analysis of molecular variance (AMOVA), and a neighbor-joining tree using both DNA markers suggested significant differentiation between the three hatchery and all eight putative wild populations. We conclude that genetic diversity of hatchery populations are low relative to putative wild populations of masu salmon, and we discuss the implications for conservation and fisheries management in Hokkaido.     

凡纳滨对虾繁殖中不同亲本对子代遗传贡献率的差异

利用5个含有稀有等位基因的高度多态性微卫星位点比较了凡纳滨对虾繁殖中不同亲本对子代遗传贡献率的差异。通过稀有等位基因的5个微卫星位点能够对亲代和子代的谱系进行明确的鉴别。10个亲代个体中有8个个体对子代群体的基因库有贡献,不同个体之间的贡献率存在差别,最高为54.28%,最低为8.57%。在亲代和子代群体遗传结构的分析中,子代等位基因的数目与亲代相比降低了11.11%。子代的平均期望杂合度(He)、平均观测杂合度(Ho)和平均多态性信息含量(PIC)等指标均低于亲代。实验结果表明:亲本对子代基因库的贡献率的差异也是造成子代群体遗传变异水平降低的原因之一;微卫星标记可作为一种有效的工具用于对虾系谱的确认、人工繁育群体遗传多样性水平的监测等方面     

New polymorphic microsatellite markers in Pacific abalone Haliotis discus hannai and their application to genetic characterization of wild and aquaculture populations

Seven new microsatellite markers were developed for the Pacific abalone (Haliotis discus hannai, Haliotidae), and allelic variability was compared between a wild population and a hatchery population in Yeosu, Korea. All loci amplified readily and demonstrated allelic variability, with the number of alleles ranging from 6 to 15 in the wild population and from 3 to 12 in farmed populations. Average observed and expected heterozygosities were estimated at 0.65 and 0.77 in the hatchery samples, and 0.79 and 0.87 in the wild samples. These results indicated lower genetic variability in the hatchery population, as compared with the wild population and significant genetic differentiation between the wild population and the hatchery samples (F _ST=0.055, p<0.001). These microsatellite loci may be valuable for future population genetic studies and for tracking hatchery samples used in stock enhancement programs.     

Gene diversity analysis of mitochondrial DNA, microsatellites and allozymes in landlocked Atlantic salmon

This study investigates the patterns of genetic diversity detected in allozymes, mtDNA, and microsatellites, in order to assess their relative efficacy to differentiate sympatric landlocked salmon populations and to estimate changes in genetic diversity between wild and first-generation hatchery fish. Overall, the three genetic markers indicated a genetic differentiation between two sympatric populations of Lake Saint-Jean, Québec. MtDNA and microsatellites also showed significant differences between wild and first-generation hatchery fish originating from the same river. Allozyme analysis was the most limited approach due to the low genetic diversity detected and the necessity to kill specimens. Although low polymorphism was found in mtDNA, it was the most discriminant marker between wild populations. Microsatellite analysis appears to be a promising approach due to its high sensitivity in differentiating wild populations, in detecting changes in allele composition between wild and first-generation hatchery fish and its potential for increased resolution by augmenting the number of polymorphic loci. Given the benefits and disadvantages of the three methods, the combination of mtDNA and microsatellite analyses will best address our research objectives.     

Comparative genetic diversity of wild and hatchery-produced Pacific oyster (Crassostrea gigas) populations in Korea using multiplex PCR assays with nine polymorphic microsatellite markers

The Pacific oyster, Crassostrea gigas, is the most important and valuable commercial fishery species in Korea. Its farming started 20 years ago and is still rapid expansion in Korea. In this study, to maintain the genetic diversity of this valuable marine resource, possible genetic similarity and differences between the wild population and hatchery population in Tongyeong, Korea were accessed using multiplex assays with nine highly polymorphic microsatellite loci. A total of 250 different alleles were found over all loci. Despite a long history of hatchery practices, very high levels of polymorphism (mean alleles = 22.89 and mean heterozygosity = 0.92) were detected between the two populations. No statistically significant reductions were found in heterozygosity or allelic diversity in the hatchery population compared with the wild population. However, significant genetic heterogeneity was found between two populations. These results provide no evidence to show that hatchery practice of Pacific oyster in Korea has significantly affected the genetic variability of the hatchery stock. Although further studies are needed for comprehensive determinations of the hatchery and wild populations with increased number of Pacific oyster sample collections, information on the genetic variation and differentiation obtained in this study can be applied for genetic monitoring of aquaculture stocks, genetic improvement by selective breeding and designing of more efficient conservation management guidelines for these valuable genetic materials.     

Comparative Assessment of Genetic Variability in the Populations of Endemic and Endangered Yellow Catfish, Horabagrus brachysoma (Teleostei: Horabagridae), Based on Allozyme, RAPD, and Microsatellite Markers

The comparative assessment of genetic diversity using allozymes, random amplified polymorphic DNA (RAPD), and microsatellite markers was conducted in endemic and endangered yellow catfish (Horabagrus brachysoma) sampled from three locations in Western Ghats river systems of India. Among the three markers, microsatellites show more polymorphism, having 100% polymorphic loci, whereas allozymes show the least (56%). In RAPD, 60.5% of fragments were polymorphic. Observed heterozygosity and F(ST) values were very high in microsatellites, compared with the other markers. Microsatellite and RAPD markers reported a higher degree of genetic differentiation than allozymes among the populations depicted by pairwise F(ST)/G(ST), AMOVA, Nei's genetic distance, and UPGMA dendrogram. The three classes of markers demonstrated striking genetic differentiation between pairs of H. brachysoma populations. The data emphasize the need for fishery management, conservation, and rehabilitation of this species.     

Comparative genetic diversity of wild and hachery populations of Korean threadsail filefish Stephanolepis cirrhifer using cross-species microsatellite markers

The threadsail filefish Stephanolepis cirrhifer is a highly commercial fisheries resource in Korea that suffers intensive anthropogenic pressure across much of its range. For basic information about its current genetic status in relation to stock enhancement, the level and distribution of genetic variation between a wild and a hatchery-bred population were investigated using 10 microsatellite markers developed for Thamnaconus modestus. High levels of polymorphism were observed between the two populations. A total of 95 different alleles were found at all loci, with some alleles being unique. The allelic variability ranged from six to 13 in the wild population and from five to 13 in the hatchery one. The average observed and expected heterozygosities were estimated to be 0.72 and 0.80 in the wild sample and 0.70 and 0.79 in the hatchery one, respectively. These results showed similar genetic variability in the hatchery population, as compared with the wild population and significant genetic differentiation between the wild population and the hatchery samples (F _ST = 0.016, P < 0.05). Genetic drift in the intensive breeding practices for stock enhancement has probably promoted differentiation between populations. Significant deviations from Hardy-Weinberg equilibrium were detected in both populations. Our results indicate that further studies using species-specific microsatellite markers will be necessary for a more reliable assessment of genetic diversity of the species.     

Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations

Admixture between wild and captive populations is an increasing concern in conservation biology. Understanding the extent of admixture and the processes involved requires identification of admixed and non-admixed individuals. This can be achieved by statistical methods employing Bayesian clustering, but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943–1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pairwise F_ST of 0.047 and 0.053). By analysing a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor rescuing a part of the indigenous population from introgression.     

Intra-specific genetic diversity in wild olives (Olea europaea ssp cuspidata) in Hormozgan Province, Iran

Wild olive (O. europaea ssp cuspidata) plants grow in various regions of Iran and are expected to have considerable genetic diversity due to adaptation to the various environmental conditions. We examined the genetic diversity of four populations of wild olive growing in Hormozgan Province located in southern Iran by using 30 RAPDs and 10 ISSR markers. The mean value of polymorphism for RAPD loci was 73.71%, while the value for ISSR loci was 81.74%. The Keshar population had the highest value of intra-population polymorphism for both RAPD and ISSR loci (66.86 and 62.71%, respectively), while the Tudar population had the lowest values (20.35 and 28.81%, respectively). Similarly, the highest and lowest number of effective alleles, Shannon index and Nei's genetic diversity were also found for these two populations. The highest value of H(pop)/H(sp) within population genetic diversity for RAPD and ISSR loci was found for the Keshar population (H(pop) = 0.85 and H(sp) = 0.90). OPA04-750, OPA13-650 and OPA02-350 RAPD bands were specific for Tudar, Bondon and Keshar populations, respectively, while no specific ISSR bands were observed. Analysis of molecular variance as well as the pairwise F(ST) test showed significant differences for RAPD and ISSR markers among the populations. The NJ and UPGMA trees also separated the wild olive populations from each other, indicating their genetic distinctness. UPGMA clustering of the four wild olive populations placed the Tudar population far from the other populations; Keshar and Bokhoon population samples revealed more similarity and were grouped together. We conclude that there is high genetic diversity among O. europaea ssp cuspidata populations located in southern Iran. We also found RAPD and ISSR markers to be useful molecular tools to discriminate and evaluate genetic variations in wild olive trees.     

A population genetics study of Anopheles darlingi (Diptera: Culicidae) from Colombia based on random amplified polymorphic DNA-polymerase chain reaction and amplified fragment lenght polymorphism markers

The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymorphism markers (AFLPs). Six RAPD primers produced 46 polymorphic fragments, while two AFLP primer combinations produced 197 polymorphic fragments from 71 DNA samples. Both of the evaluated genetic markers showed the presence of gene flow, suggesting that Colombian An. darlingi populations are in panmixia. Average genetic diversity, estimated from observed heterozygosity, was 0.374 (RAPD) and 0.309 (AFLP). RAPD and AFLP markers showed little evidence of geographic separation between eastern and western populations; however, the F ST values showed high gene flow between the two western populations (RAPD: F ST = 0.029; Nm: 8.5; AFLP: F ST = 0.051; Nm: 4.7). According to molecular variance analysis (AMOVA), the genetic distance between populations was significant (RAPD:phiST = 0.084; AFLP:phiST = 0.229, P < 0.001). The F ST distances and AMOVAs using AFLP loci support the differentiation of the Guyana biogeographic province population from those of the Chocó-Magdalena. In this last region, Chocó and Córdoba populations showed the highest genetic flow.     

Utility of EST-derived SSRs as population genetics markers in a beetle

Microsatellite, or simple sequence repeat (SSR), loci can be identified by mining expressed sequence tag (EST) databases, and where these are available, marker development time and expense can be decreased considerably over conventional strategies of probing the entire genome. However, it is unclear whether they provide information on population structure similar to that generated by anonymous genomic SSRs. We performed comparative population genetic analyses between EST-derived SSRs (EST-SSRs) and anonymous SSRs developed from genomic DNA for the same set of populations of the insect Diabrotica virgifera, a beetle in the family Chrysomelidae. Compared with noncoding, nontranscribed regions, EST-SSRs were generally less polymorphic but had reduced occurrence of null alleles and greater cross-species amplification. Neutrality tests suggested the loci were not under positive selection. Across all populations and all loci, the genomic and EST-SSRs performed similarly in estimating genetic diversity, F(IS), F(ST), population assignment and exclusion tests, and detection of distinct populations. These findings, therefore, indicate that the EST-SSRs examined can be used with confidence in future genetic studies of Diabrotica populations and suggest that EST libraries can be added as a valuable source of markers for population genetics studies in insects and other animals.     

Genetic evidence for male-biased dispersal in the Siberian jay (Perisoreus infaustus) based on autosomal and Z-chromosomal markers

Sex-bias in natal dispersal patterns can have important genetic and evolutionary consequences; however, reliable information about sex-biased dispersal can be difficult to obtain with observational methods. We analysed the sex-specific patterns of genetic differentiation among three Siberian jay (Perisoreus infaustus) populations, using 11 autosomal and six Z-chromosomal microsatellite markers. Irrespective of marker-type and indices used (viz. F(ST), average pairwise relatedness and effective number of immigrants), all analyses provided strong evidence for male-biased dispersal. Population structuring at autosomal loci (F(ST) =0.046, P<0.05) exceeded that at Z-chromosomal loci (F(ST) =0.033, P<0.05), and levels of introgression were inferred to be significantly higher for Z-chromosomal when compared to autosomal loci. Of the three populations studied, levels of genetic variability were the lowest in the southernmost fringe population, despite the fact that it harboured a group of divergent Z-chromosomal haplotypes that were not found in the other two populations. In general, the results provide strong genetic evidence for male-biased dispersal in Siberian jays, where observational data have previously suggested male philopatry. The results also highlight the utility of Z-chromosomal markers for gaining insights into the genetic diversity and structuring of populations.     

用微卫星标记分析皱纹盘鲍群体的遗传变异

利用微卫星标记技术, 对皱纹盘鲍山东长岛和辽宁獐子岛的两个野生群体以及山东崆峒岛一个养殖群体的遗传变异进行了分析。对6个微卫星基因座的多态性进行了评估, 各基因座的多态信息含量(PIC)值均大于0.5, 适合对鲍群体遗传结构的分析。结果表明, 这6个基因座在3个皱纹盘鲍群体中共获得57个等位基因, 等位基因数(A)平均为9.50, 有效等位基因数(N_e)平均为5.8572, 平均杂合度观测值(H_o)和期望值(^H_e)分别为0.6925和0.7966; 两个野生群体的杂合度观测值(H_o)和期望值(H_e)均高于养殖群体。上述结果为保护和利用皱纹盘鲍的遗传多样性提供了依据。     

Population structure of the olive flounder (Paralichthys olivaceus) in Korea inferred from microsatellite marker analysis

The population structure of olive flounder Paralichthys olivaceus was estimated using nine polymorphic microsatellite (MS) loci in 459 individuals collected from eight populations, including five wild and three hatchery populations in Korea. Genetic variation in hatchery (mean number of alleles per locus, A = 10·2–12·1; allelic richness, A_R = 9·3–10·1; observed heterozygosity, H_O = 0·766–0·805) and wild (mean number of alleles per locus, A = 11·8–19·6; allelic richness, A_R = 10·9–16·1; observed heterozygosity, H_O = 0·820–0·888) samples did not differ significantly, suggesting a sufficient level of genetic variation in these well‐managed hatchery populations, which have not lost a substantial amount of genetic diversity. Neighbour‐joining tree and principal component analyses showed that genetic separation between eastern and pooled western and southern wild populations in Korea was probably influenced by restricted gene flow between regional populations due to the barrier effects of sea currents. The pooled western and southern populations are genetically close, perhaps because larval dispersal may depend on warm currents. One wild population (sample from Wando) was genetically divergent from the main distribution, but it was genetically close to hatchery populations, indicating that the genetic composition of the studied populations may be affected by hydrographic conditions and the release of fish stocks. The estimated genetic population structure and potential applications of MS markers may aid in the proper management of P. olivaceus populations.     

Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.