青鱼野生与养殖群体遗传变异的微卫星分析

研究利用自主开发的12个微卫星标记, 对来自于长江水系4个野生群体(湖北石首、湖南湘江、江苏邗江、浙江嘉兴)和1个养殖群体(江苏吴江)青鱼(Mylopharyngodon piceus)进行遗传多样性和遗传结构分析。遗传多样性分析结果显示这12个位点多态信息含量(PIC)介于0.660—0.923, 表明这12个位点均具有高度多态性(PIC>0.5)。5个群体的平均等位基因数(N_a)介于7.917—11.667, 平均有效等位基因数(N_e)介于4.837—6.035; 平均观测杂合度介于0.713—0.861; 平均期望杂合度介于0.749—0.819; 平均多态信息含量介于0.711—0.788, 表明这5个群体均具有较高的遗传多样性。遗传距离分析结果表明4个野生群体之间遗传距离较近, 养殖群体与这4个野生群体遗传距离均较远。UPGMA系统进化树显示, 湘江群体和石首群体首先聚为一支, 然后与邗江群体和嘉兴群体聚为一支, 最后与吴江养殖群体聚为一支。这12个微卫星位点具有较为丰富的遗传多样性特征, 可以用于青鱼不同群体的种质资源的评估和遗传多样性的分析。     

Characterising genetic diversity and effective population size in one reservoir and two riverine populations of the threatened Macquarie perch

Nine polymorphic microsatellite loci have been used to infer population genetic diversity and structure of the threatened Australian freshwater fish, Macquarie perch, across three tributaries of the Murrumbidgee River in south-eastern Australia. This investigation has revealed a high level of divergence among all three populations, along with contrasting patterns of genetic diversity. The Cotter Reservoir, which is a stronghold population for the species, has typically higher diversity and effective population size than nearby riverine populations. This suggests that the reservoir population is unlikely to have undergone a genetic bottleneck during and following dam construction. Genetic diversity estimates were comparable with one riverine site but were significantly higher than a population sampled from the Queanbeyan River. This comparison revealed significantly less heterozygotes in the Queanbeyan River and lower estimates of effective population size. Options and considerations for stock replenishment of this population are discussed.     

De novo development and characterization of polymorphic microsatellite markers in a schilbid catfish, <Emphasis Type="Italic">Silonia silondia</Emphasis> (Hamilton, 1822) and their validation for population genetic studies

The stock characterization of wild populations of Silonia silondia is important for its scientific management. At present, the information on genetic parameters of S. silondia is very limited. The species-specific microsatellite markers were developed in current study. The validated markers were used to genotype individuals from four distant rivers. To develop de novo microsatellite loci, an enriched genomic library was constructed for S. silondia using affinity–capture approach. The markers were validated for utility in population genetics. A total number of 76 individuals from four natural riverine populations were used to generate data for population analysis. The screening of isolated repeat sequences yielded eleven novel polymorphic microsatellite loci. The microsatellite loci exhibited high level of polymorphism, with 6–24 alleles per locus and the PIC value ranged from 0.604 to 0.927. The observed (Ho) and expected (He) heterozygosities ranged from 0.081 to 0.84 and 0.66 to 0.938, respectively. The AMOVA analysis indicated significant genetic differentiation among riverine populations (overall F_ST = 0.075; P < 0.0001) with maximum variation (92.5 %) within populations. Cross-priming assessment revealed successful amplification (35–38 %) of heterologous loci in four related species viz. Clupisoma garua, C. taakree, Ailia coila and Eutropiichthys vacha. The results demonstrated that these de novo polymorphic microsatellite loci are promising for population genetic variation and diversity studies in S. silondia. Cross-priming results indicated that these primers can help to get polymorphic microsatellite loci in the related catfish species of family Schilbidae.     

Isolation and characterization of microsatellite DNA loci in sea bass,Lates calcarifer Bloch

Polymerase chain reaction (PCR)‐based isolation of microsatellite arrays (PIMA) technique was used to isolate seven polymorphic microsatellite loci in sea bass, Lates calcarifer Bloch. A total of 62 samples of wild and cultivated sea bass collected from a few populations within Peninsular Malaysia were used in the study. For seven polymorphic loci, the number of alleles ranged from four to nine and locus heterozygosities ranged from 0.710 to 1.000. The loci will be useful for studying population structure, genetic variability of wild and hatchery stocks of L. calcarifer and broodstock management purposes.     

Polymorphic microsatellite loci for population studies of the razor clam, <Emphasis Type="Italic">Sinonovacula constricta</Emphasis>

The razor clam (Sinonovacula constricta) is an important aquacultured bivalve in China. The natural populations of this species are decreasing quickly. To facilitate studies on genetic diversity and population structure of wild populations, microsatellites were isolated from a CA enriched genomic library. Eight microsatellite loci were polymorphic in 30 individuals from Chongming in Shanghai, China. The number of alleles per polymorphic locus varied from 6 to 13 and the values of observed heterozygosity and expected heterozygosity ranged from 0.350 to 1.000 and from 0.602 to 0.902, respectively. These microsatellites are being used in studying population differentiation and genetic diversity for effective conservation and management genetic resources of S. constricta.     

长筒石蒜居群遗传多样性RAPD分析

利用RAPD标记对长筒石蒜3个居群的遗传多样性及分化程度进行了研究。12条随机引物扩增出94个可分析位点,多态位点比率(PPB)为65.96%,表明长筒石蒜具有比较高的遗传多样性。经POP-GENE32分析表明:Nei’s基因多样性指数(h)为0.1897,香农多样性指数(Ⅰ)为0.2945,基因分化系数(GST)为0.1191,基因流(Nm)为3.6980。经WINAMOVA分析表明:居群内遗传变异占71.75%,而居群间只占28.25%。遗传多样性分析表明,各居群的遗传多样性水平由高到低为琅琊山居群>宝华山居群>盱眙居群。遗传分化表明:长筒石蒜各居群间遗传分化程度较低;大部分遗传变异存在于居群内部,表明其具有较强的进化潜力,自然情况下不会处于濒危状态,野生种质资源的破坏,主要来自于人为干扰。     

Population genetic structure of wild and farmed rusa deer (<Emphasis Type="Italic">Cervus timorensis russa</Emphasis>) in New-Caledonia inferred from polymorphic microsatellite loci

Historical records indicate that 12 rusa deer (Cervus timorensis russa) were introduced in New-Caledonia during the 1870s. We used eight polymorphic microsatellite DNA loci to assess the genetic differentiation and diversity of farmed and wild deer populations. Past genetic bottlenecks were detected in both sub-populations, although higher genetic diversity was maintained in farmed populations, probably due to the regular introduction of reproducers from wild populations and from other farms. The genetic structure of farmed and wild populations differed significantly. There was a significant isolation by distance for wild populations, whereas farmed populations were significantly differentiated between farms independently from their geographical proximity. Wild rusa deer consisted of small populations (with effective population sizes ranging between 7 and 19 individuals depending on the methods used), with a low parent–offspring dispersion range (0.20–2.02 km). Genetic tools and direct observations provided congruent estimates of dispersion and population sizes. We discuss the relevance of our results for management purposes.     

西昌华吸鳅的微卫星引物筛选及赤水河四个地理种群的遗传多样性分析

采用高通量测序法对西昌华吸鳅(Sinogastromyzon sichangensis)基因组进行随机测序并筛选出符合条件的微卫星位点, 设计可用于PCR扩增的引物, 筛选出29对具有多态性的引物, 平均等位基因数为14.5, 观测杂合度(H_o)和期望杂合度(H_e)分别为0.620和0.882, 多态信息含量(PIC)为0.859。选取其中多态性较高的20对引物在赤水河及其支流的4个地理种群中进行扩增, 分析不同地理种群的遗传多样性和种群分化情况。结果表明, 赤水镇种群观测杂合度最高(0.669), 茅台镇种群观测杂合度最低(0.520); 习水河多态信息含量最高(0.868), 茅台镇种群多态信息含量最低(0.841)。赤水河干流的几个种群未出现显著分化, 而习水河种群与其他3个种群的遗传分化程度较高。AMOVA分析显示遗传变异主要发生在群体内, 群体间遗传变异仅占3.33%, 群体内遗传变异占96.67%。种群遗传结构分析表明, 赤水河干流整体遗传背景趋于一致, 而习水河种群则单独聚为一个亚类群。研究为西昌华吸鳅的资源保护和种群遗传学研究提供了基础资料。     

Conservation Genetics of Jacquemontia reclinata (Convolvulaceae), an Endangered Species from Southern Florida: Implications for Restoration Management

Guidelines designed to aid in the restoration of rare species have been previously proposed using two primary strategies to select individuals for augmentation and reintroduction: mixing progeny from different populations or separating individuals from different populations. Understanding the genetic structure and diversity of an endangered species can offer insights into conservation management strategies. We used random amplified polymorphic DNA markers to assess the genetic structure and diversity of Jacquemontia reclinata , a federally endangered species endemic to Southeastern Florida. We sampled 20 percent of total number of individuals from eight of the ten known wild populations. Across individuals high levels of polymorphic loci (94.7%) were found and larger populations had greater genetic diversity. Cluster and ordination analyses found that one population was genetically differentiated from all the others; this population grows in a unique habitat. Most genetic variation (77.5%) was found within populations, and genetic distances between populations were not explained by their geographic distances. We recommend the use of two management units in restoration programs for J. reclinata , one consisting of the genetically differentiated population and the second consisting of the other seven populations sampled.     

Isolation and characterization of polymorphic microsatellite markers in the blowflies Lucilia illustris and Lucilia sericata

Thirteen polymorphic microsatellite loci were developed for blowflies for use in studies of genetic differentiation in wild populations of Lucilia illustris, to detect the possible occurrence of bottlenecks and to study changes in genetic variation in laboratory populations of Lucilia sericata following artificial bottlenecks. In this preliminary study it was revealed that heterozygosity was lower than expected in wild populations and genetic variation had been lost in the laboratory population despite being kept at a large size.     

Genetic assessment of captive Chinese water deer populations in Zhoushan Archipelago,China

Chinese water deer is a rare and vulnerable animal in China because of the poaching for medical use and the habitat loss. In this study, the genetic diversity and population genetic structure of 40 Chinese water deer from three populations in Zhoushan Archipelago were investigated with ten highly polymorphic microsatellite loci, including 4 screened from the nuclear DNA in the study, and 6 selected from the literature. According to the results, these captive populations had a higher genetic diversity than other rare cervid species, such as forest musk deer. No signs of inbreeding were detected. Low genetic differentiation among these populations was found. The probable reasons included the isolation by distance, the exchange among islands, or the supplement of the wild Chinese water deer. We proposed the deer raisers to strengthen the exchanges from different islands or mainland, and if possible, some deer would be returned to the wild to expand the wild population.     

The genetic population structure and temporal genetic stability of gilthead sea bream Sparus aurata populations in the Aegean and Ionian Seas,using microsatellite DNA markers

We examined 662 gilthead sea bream Sparus aurata from wild samples of the species in the Aegean and Ionian Seas, using 20 EST-linked microsatellite markers, in three multiplex panels, as well as seven anonymous loci. Most of the markers were revealed to be highly polymorphic. We found low genetic differentiation between the sampling stations/areas with total F_ST 0.002 (P < 0.05). Based on comparison of five temporal samples, our results indicate genetic data consistency over time for all tested samples, pointing to stable populations, despite reported repeated escape events. Our results confirm the genetic population structure previously observed in these specific areas, using by far more markers than in previous studies in both coding and non-coding DNA loci. The limited genetic structure and the temporal genetic stability indicate neither major genetic differentiation of local populations by geographic isolation nor influence from anthropogenic factors. These results provide a baseline for future reference in any management programme of both wild and farmed population of S. aurata as well as of other aquaculture species with a potential introgression among farmed and wild populations.     

Isolation and characterization of thirteen polymorphic microsatellite loci for Lithocarpus glaber

We isolated and characterized polymorphic microsatellite loci in Lithocarpus glaber (Fagaceae), an evergreen broadleaved monoecious tree, to provide tool for analyzing genetic structure and diversity. Thirteen polymorphic microsatellite loci were developed and tested in two L. glaber populations. The number of alleles per locus varied from 2 to 19. The observed and expected heterozygosities within populations were 0.037–0.833 and 0.316–0.931, respectively. Four loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction in each population and no significant linkage disequilibrium between pairs of loci was found. These polymorphic loci showed high levels of polymorphism within tested populations and will be useful in further population genetic studies.     

Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae)

Domestication occurs as humans select and cultivate wild plants in agricultural habitats. The amount and structure of variation in contemporary cultivated populations has been shaped, in part, by how genetic material was transferred from one cultivated generation to the next. In some cultivated tree species, domestication involved a shift from sexually reproducing wild populations to vegetatively propagated cultivated populations; however, little is known about how domestication has impacted variation in these species. We employed AFLP data to explore the amount, structure, and distribution of variation in clonally propagated domesticated populations and sexually reproducing wild populations of the Neotropical fruit tree, Spondias purpurea (Anacardiaceae). Cultivated populations from three different agricultural habitats were included: living fences, backyards, and orchards. AFLP data were analysed using measures of genetic diversity (% polymorphic loci, Shannon's diversity index, Nei's gene diversity, panmictic heterozygosity), population structure (F(ST) analogues), and principal components analyses. Levels of genetic variation in cultivated S. purpurea populations are significantly less than variation found in wild populations, although the amount of diversity varies in different agricultural habitats. Cultivated populations have a greater proportion of their genetic variability distributed among populations than wild populations. The genetic structure of backyard populations resembles that of wild populations, but living fence and orchard populations have 1/3 more variability distributed among populations, most likely a reflection of relative levels of vegetative reproduction. Finally, these results suggest that S. purpurea was domesticated in two distinct regions within Mesoamerica.     

栖息条件对中华蜜蜂遗传多样性的影响

为了评估不同栖息条件对中华蜜蜂(简称中蜂)种群遗传多样性的影响,本研究运用微卫星标记的方法,对皖南山区4个不同采样点120个中华蜜蜂群体的2400只工蜂样本进行了分析.结果表明:与天然林野生中蜂群相比,单一茶树种植结构下,皖南中蜂群的等位基因数、平均期望杂合度和多态信息含量的差异均不显著;人工驯养中蜂群的等位基因数、多态信息含量差异显著,平均期望杂合度差异不显著;2006年采集的野生中蜂群与天然林野生中蜂群的等位基因数、平均期望杂合度和多态信息含量均差异显著.各种群间存在极显著的遗传分化,平均分化系数为0.32.说明皖南地区茶树单一化种植不会影响中蜂的遗传结构与资源保护.     

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.     

野生与人工驯养长爪沙鼠群体遗传结构比较分析

目的探索野生与人工驯养的长爪沙鼠群体遗传状况。方法采用12个微卫星引物,对银川与呼和浩特地区捕获的野生长爪沙鼠群体和首都医科大学人工驯养20余年的长爪沙鼠群体的遗传结构进行比较分析。结果12个微卫星位点中有等位基因29个,3个群体的平均等位基因数分别为2.4167、2.2500、2.2500,平均有效等位基因数分别为1.7505、1.7195、1.6968;有11个微卫星位点呈现多态,多态位点百分率分别为91.67%、83.33%、83.33%,香隆指数分别为0.6239、0.5962、0.5591;平均观测杂合度分别为0.5231、0.5051、0.4825,平均期望杂合度分别为0.4008、0.3882、0.3655;银川和首医群体之间的遗传距离最大,为0.1033;呼和浩特和首医群体之间的距离最小,为0.0592。结论3个群体处于Hardy-Weinberg平衡状态,3个群体之间及与总体之间的遗传结构差异无显著性（P〉0.05）。     

Genetic differences between wild and hatchery populations ofDiplodus sargus andD. vulgaris inferred from RAPD markers: implications for production and restocking programs design

Restocking and stock enhancement programs are now recognized as an important tool for the management of fishery resources. It is important, however, to have an adequate knowledge on the genetic population structure of both the released stock and the wild population before carrying out such programs. In this study, random amplified polymorphic DNA (RAPD) markers were applied to assess genetic diversity and population structure of wild and hatchery populations of the white seabreamDiplodus sargus and the common two-banded seabreamD. vulgaris (Sparidae). The estimated values for intrapopulation genetic variation, measured using the percentage of polymorphic loci (%P), Shannon indexH’, and Nei’s gene diversity (h), showed high values for all populations. The percentage of genetic variation withinD. sargus andD. vulgaris populations, based on coefficient of gene differentiation, reached 82.5% and 90% of the total genetic variation, respectively. An undeniable decrease in genetic variation was found in both hatchery populations, particularly inD. sargus, compared to the wild ones. However, the high values of variation within all populations and the low levels of genetic variation among populations did not indicate inbreeding or depression effects, thus indicating a fairly proper hatchery management. Nevertheless, the results of this study highlight the importance of monitoring the genetic variation of hatchery populations, particularly those to be used in restocking programs. The creation of a genetic baseline database will contribute to a more efficient conservation management and to the design of genetically sustainable restocking programs.     

Protein variation in wild Atlantic salmon, with particular reference to southern Ireland

The extent of genetic variation in wild Atlantic salmon parr, Sulmo salur L., from river systems in Ireland, Iceland and eastern Canada, was investigated using starch gel electrophoresis. Within Ireland, seven polymorphic enzyme loci ( sAAT-4 *, GPI-1 *, IDDH-1 *, IDDH-2 *, IDHP-3 *, MDH-3 * and mMEP-2 *) were screened in nine different rivers and nine tributaries from the River Blackwater. Significant heterogeneity in gene frequencies occurred between riverine samples and between samples from tributaries of the River Blackwater. Variation between tributaries was as great as between rivers elsewhere in the country. Levels of population differentiation were comparable to those found in other regions throughout the range of the species, and temporal stability in gene frequencies was apparent when the results were compared with previously published data. Screening of riverine samples from Iceland and eastern Canada (Newfoundland and New Brunswick) allowed the Irish results to be considered in a broader context. Irish salmon cluster in the western European group, to which may be added Icelandic populations. Salmon from eastern Canada show a high level of genetic distinctiveness from the European group.     

Differentiation between natural and cultivated populations of Medicago sativa (Leguminosae) from Spain: analysis with random amplified polymorphic DNA (RAPD) markers and comparison to allozymes

The conservation of a crop's wild relatives as genetic resources requires an understanding of the way genetic diversity is maintained in their populations, notably the effect of crop-to-wild gene flow. In this study, the amount of differentiation between natural and cultivated populations of Medicago sativa was analysed using random amplified polymorphic DNA (RAPD) markers and an extension of the AMOVA procedure adapted to autotetraploid organisms. Simulations of structured populations were performed to test whether AMOVA provides estimates of population structure in autotetraploids that can be directly compared to those obtained for allozyme data. Simulations showed that straight phi-statistics allow a good estimation of population differentiation when unbiased allelic frequencies are used to correct the conditional expectations of squared genetic distances. But such unbiased estimates can not be practically guaranteed, and population structure is notably overestimated when some populations are fixed for the presence of amplified fragments. However, removing fixed loci from the data set improves the statistical power of the test for population structure. The genetic variation of 15 natural and six cultivated populations of M. sativa was analysed at 25 RAPD loci and compared to estimates computed with allozymes on the same set of populations. Although RAPD markers revealed less within-population genetic diversity than allozymes, the quantitative and qualitative patterns of population structure were in full agreement with allozymes. This confirmed the conclusions drawn from the allozymic survey: crop-to-wild gene flow occurred in many locations, but some other mechanisms opposed cultivated traits to be maintained into natural populations.