元江鲤种群遗传多样性

选择12对微卫星标记检测了于2011年采集自元江(红河上游中国江段)5个样点192尾鲤的群体遗传多样性.共检测到201个等位基因,每个位点等位基因2-27个.各群体各位点平均等位基因(NA)12.25-14.67个,平均有效等位基因(NE)8.28-9.73个,平均观察杂合度(Ho)o.7765-0.8037,平均期望杂合度(HE)0.7761-0.8080,平均多态信息含量(PIC)0.7534-0.7843.元江鲤种群192个个体各位点NA、NE、Ho、HE、PIC分别为16.50、11.26、0.7927、0.8049、0.7966,种群遗传多样性水平高.元江鲤群体之间遗传分化小,可作为一个种群管理单元进行管理.增殖放流要防止遗传多样性丧失.     

Microsatellite diversity and population genetic structure of redfin culter ( Culter erythropterus ) in fragmented lakes of the Yangtze River

Redfin culter (Culter erythropterus) is a small lethic freshwater fish and widely distributed in the adjacent lakes of the Yangtze River of China. Five microsatellite loci were applied to investigate the genetic variation and population structure of redfin culter from seven lakes in the middle-and-lower reaches of the Yangtze River. The gene diversity was high among the populations (H > 0.9), the average number of alleles among seven populations was low with a range from 2.00 to 3.87. The mean observed (H _O) and expected (H _E) heterozygosity ranged from 0.111 to 0.419 and from 0.162 to 0.750, respectively. Significant deviations from Hardy-Weinberg Equilibrium expectation were found in 50% of the total locus-population combination tests in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percentage of variance among and within these populations were 6.18 and 93.82, respectively. The Fst values (0.062, P < 0.001) among studied populations indicated that there were significant genetic differentiations among redfin culture populations from the scattered lakes with different connections to the Yangtze River. These results are useful for the evaluation and conservation of small freshwater fishes. The factors that may be involved in low intra-population polymorphism and the pattern of the population genetic structure of redfin culter from the Yangtze River were discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: C. Sturmbauer     

Genetic Variation Analysis within and among Six Varieties of Common Carp (Cyprinus carpio L.) in China Using Microsatellite Markers

Five microsatellites were used to study the genetic diversity and genetic structure of one wild and five domestic varieties of common carp in China (the Yangtze River wild common carp, Xingguo red carp, purse red carp, Qingtian carp, Russian scattered scaled mirror carp and Japanese decorative carp). All loci in this study showed marked polymorphism with the number of alleles ranging from 4 to 13. Domestic varieties (except Xingguo red carp) showed less genetic diversity than the Yangtze River wild common carp in terms of allelic diversity. Population differentiation was assessed and each combination of populations displayed significant differentiation (P < 0.05) with the exception of that between the Yangtze River wild common carp and Xingguo red carp. Genetic distance analysis (Nei's standard genetic distance and pairwise F _st distance) showed that the largest distance was between Russian scattered scaled mirror carp and the Yangtze River wild common carp and the smallest distance was between the Yangtze River wild common carp and Xingguo red carp. However, among six populations Japanese decorative carp displayed the highest level of variability in terms of heterozygosity.     

长江水系草鱼遗传多样性的微卫星DNA分析

利用已发表的鲤微卫星引物在草鱼中进行PCR扩增,结果有5对引物(6个座位)能成功扩增并且有较高多态性,等位基因数在3-7个之间。这些异种扩增的草鱼微卫星符合孟德尔遗传规律。测序证明草鱼中的微卫星核心重复序列部分与鲤中的原始核心序列相似,也有一些变化。随后用这6个多态微卫星座位研究了来自长江水系的四个草鱼群体的遗传结构,结果显示每个群体的平均等位基因数在38与48之间,平均观测杂合度(Ho)在04000与05741之间,平均期望杂合度(HE)在04773与06489之间,有多个座位在不同的群体中偏离哈代-温伯格平衡。遗传距离分析表明四川群体与洞庭湖群体遗传距离最远,而嘉鱼群体与鄱阳湖群体遗传距离较近。分子变异分析(AMOVA)表明,群体内遗传变异与群体间遗传变异分别占总遗传变异的9560%与440%,固定系数(FST)为0044,这表明长江水系草鱼目前的群体分化很微弱。       

草鱼EST-SSR标记及5个不同地域群体的遗传结构分析

以草鱼(Ctenopharyngodon idella)脑、肌肉、肝等组织构建cDNA文库,经测序获得unigenes序列45 318个,从中筛选微卫星序列共5 556个,据此设计EST-SSR引物118对,其中19对引物能够扩增出带型清晰且多态性较高的谱带。用这19个EST-SSR标记研究3个长江水系群体(石首、监利和长沙)和2个珠江水系群体(清远和肇庆)草鱼的遗传结构。结果表明,5个群体的平均多态信息含量(PIC)为0.415 4～0.460 4,显示草鱼群体的遗传多样性偏低;平均观测杂合度(Ho)为0.415 8～0.501 3,平均期望杂合度为(He)0.450 6～0.502 8,其中,长沙群体平均期望杂合度最高,为0.502 8,监利群体的平均观察杂合度和平均期望杂合度均最低,分别为0.415 8和0.450 6,即长沙群体的遗传多样性最高,监利群体的遗传多样性最低;对数据进行F-检验,结果表明,群体间的遗传分化程度低。Hardy-Weinberg平衡的卡方检验结果表明,5个群体均一定程度上偏离了平衡;聚类分析显示长沙群体、石首群体与监利群体聚成一支;肇庆群体与清远群体聚成一支,这与草鱼群体的流域分布一致。     

利用30个微卫星标记分析长江中下游鲢群体的遗传多样性

摘要: 利用30对微卫星分子标记对长江中下游5个鲢群体进行了遗传多样性分析。结果表明: 在30个基因座中, 共检测到144个等位基因, 每个座位检测到的等位基因数为1～10个, 其中有25个座位具有多态性, 多态位点百分率为83.33,5个群体的平均等位基因数A为4.0/4.1, 平均有效等位基因数Ne为2.4445～2.6332, 平均观察杂合度Ho为0.3233～0.3511, 平均期望杂合度He为0.4421～0.4704, 平均多态信息含量PIC为0.4068～0.4286。对数据进行F-检验, Fst值表明群体间的遗传分化程度中等, 并对基因型进行了基于Hardy-Weinberg平衡的卡方检验, 所得P值说明5个群体均一定程度上偏离了平衡。5个群体间的遗传相似系数为0.8466～0.9146,遗传距离为0.0893～0.1665, 并根据Nei氏标准遗传距离用UPGMA方法对5个鲢群体进行亲缘关系聚类。     

Genetic diversity and differentiation of Acanthoscelides obtectus Say (Coleoptera: Bruchidae) populations in China

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Microsatellite diversity and population genetic structure of yellowcheek, Elopichthys bambusa (Cyprinidae) in the Yangtze River

Yellowcheek carp (Elopichthys bambusa) is the only species of genus Elopichthys. It is widely distributed in Chinese freshwaters but currently its populations have declined to threatening level. We examined the genetic diversity and population structure of E. bambusa in the Yangtze River basin. A total of nine polymorphic microsatellite markers were employed to study five populations occurring in middle and lower reaches of the river. The results revealed low-to-moderate genetic diversity. The number of alleles per locus varied between 3 and 8 with an average of 4.8. Observed heterozygosity ranged from 0.15 to a maximum of 1.00. Significant deviations (P < 0.01) from Hardy–Weinberg equilibrium were observed for all the tested locus-population combinations with clear heterozygosity deficits. AMOVA indicated that majority of the variance lies within populations (93.81%) than among the populations (7.05%). Pairwise F_ST and unbiased genetic distance pointed out significant differentiation among the samples from populations with different connections to the Yangtze River. In the UPGMA dendrogram, clustering pattern of populations indicated that most of the populations are reproductively isolated due to anthropogenic interventions. Clustering of PYL and DTL populations shows ongoing gene flow through the mainstream. The recent hydrological alterations and overfishing are major factors shaping the current genetic structure. These results can be helpful for effective management and sustainable conservation of E. bambusa populations.     

Genetic variation analysis within and among six varieties of common carp (Cyprinus carpio L.) in China using microsatellite markers

Five microsatellites were used to study the genetic diversity and genetic structure of one wild and five domestic varieties of common carp in China (the Yangtze River wild common carp, Xingguo red carp, purse red carp, Qingtian carp, Russian scattered scaled mirror carp and Japanese decorative carp). All loci in this study showed marked polymorphism with the number of alleles from 4 to 13. Domestic varieties (except Xingguo red carp) showed less genetic diversity than the Yangtze River wild common carp in terms of allelic diversity. Population differentiation was assessed and each combination of populations displayed significant differentiation (p < 0.05) with the exception of that between the Yangtze River wild common carp and Xingguo red carp. Genetic distance analysis (Nei's standard genetic distance and pairwise F(st) distance) showed that the largest distance was between Russian scattered scaled mirror carp and the Yangtze River wild common carp and the smallest distance was between the Yangtze River wild common carp and Xingguo red carp. However, among six populations Japanese decorative carp displayed the highest level of variability in terms of heterozygosity.     

基于SSR标记的大明松天然群体遗传多样性分析

大明松是广西和贵州特有的高山松类,具有很高的经济价值和生态价值,其自然种群长期没有得到充分的保护和利用,不利于该树种长期稳定发展。为了合理保护和开发利用大明松天然遗传资源,该文利用12个SSR分子标记对大明松3个天然群体进行遗传多样性研究,分析其群体间的遗传分化和基因流,为该物种的保护策略提供参考。研究结果表明:(1)12对引物共检测到37 个等位基因,多态位点百分率为100%。每个位点平均观察等位基因数(Na)为3.08,平均有效等位基因数(Ne)为1.68, 不同位点间有效等位基因数差异较大; 每个位点平均观察杂合度(Ho)为0.35,平均期望杂合度(He)为0.40,平均多态信息含量(PIC)为0.31。(2)3 个群体的Shannon''s多样性指数变化范围为0.48～0.65,Nei''s基因多样度的变化范围为0.27～0.39,与其他近缘种松类相比遗传多样性偏低。群体平均观察杂合度为0.40,平均期望杂合度为0.33,平均有效等位基因数为1.58。群体间基因分化系数(Gst)为0.10,群体间的遗传分化水平较低,大部分变异均存在群体内。群体间的基因流(Nm)为2.74,说明大明松群体间的基因交流比较充分。该研究可为大明松生物多样性保护提供重要参考依据,为科学利用大明松资源打下基础。     

Analysis of genetic diversity in Glyptosternum maculatum (Sisoridae, Siluriformes) populations with AFLP markers

We determined the genetic diversity of geographic populations from three spawning grounds (Nyang River, Lhasa River, Shetongmon Reach of Yarlung Zangbo River) of Glyptosternum maculatum with amplified fragment length polymorphism (AFLP) markers. Five primer combinations detected 332 products, 51 of them (15.4%) were polymorphic in at least one population. The Shetongmon population was found to be the richest in genetic diversity as was indicated by the percentage of polymorphic loci and heterozygosity, followed by the Nyang population and the Lhasa population. The pair-wise genetic distance between populations were all very close, ranging from 0.0015 to 0.0042 with an average of 0.0024. The genetic distance was not proportional to the geographic distance. The analysis of molecular variance demonstrated that all variation occurred within populations. The average estimated fixation index (F _st) of three populations across all polymorphic loci was −0.0184, indicating the absence of genetic differences among the three sampled populations. The differentiation among populations was not significant, and population structure was weak. Our observations will help identify the genetic relationship among populations as the first approach to understand the genetic diversity of Glyptosternum maculatum.     

基于SSR标记探讨三种金花茶植物的遗传多样性和遗传结构

薄叶金花茶、小花金花茶和小瓣金花茶是三种濒危金花茶植物,为了解珍稀濒危植物遗传多样性和遗传结构,该研究利用微卫星标记对他们的7个种群共184个个体进行了遗传多样性和遗传结构分析。结果表明:11个位点共检测到等位基因92个。在物种水平上,小瓣金花茶平均等位基因数(N_A)为3.9、有效等位基因数(N_E)为2.328、观测杂合度(H_o)为0.520、期望杂合度(H_e)为0.501,高于薄叶金花茶和小花金花茶。在种群水平上,有效等位基因数(N_E)在1.788～2.466之间,期望杂合度(H_e)在0.379～0.543之间;种群间遗传分化系数(FST)在0.143 7～0.453 3之间,种群间基因流(N_m)在0.301 5～1.488 9之间。AMOVA分子变异分析显示65.72%的变异存在于种群内。三种金花茶具有较低水平的遗传多样性和高水平的种群间遗传分化。STRUCTURE和PCoA种群遗传结构分析结果将取样种群分为2组,即薄叶金花茶和小花金花茶大部分个体分为一组,小瓣金花茶大部分个体分为一组。现存所有种群应根据实际情况尽快采取就地保护或迁地保护措施。     

Identification and characterization of microsatellite markers for the population genetic structure in endemic red-tailed barb,Gonoproktopterus curmuca

Gonoproktopterus curmuca is an endangered red tailed barb found in Southern part of Western Ghat, India. As a part of stock-specific, propagation assisted rehabilitation and management program, polymorphic microsatellites markers were used to study the genetic diversity and population structure of this species from the three River systems of Southern Western Ghats, such as Periyar River, the Chalakkudy River, and the Chaliyar River. From selected eight polymorphic microsatellite markers, the number of alleles per locus ranged from 2 to 8, and the average number of alleles among 3 populations ranged from 5.0 to 5.75. The mean observed (H_ob) and expected (H_ex) heterozygosity ranged from 0.5148 to 0.5360 and from 0.5996 to 0.6067, respectively. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at majority of the loci (except Gcur MFW72 and Gcur MFW19) and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance indicates that the percent of variance among populations and within populations were 6.73 and 93.27, respectively. The pairwise F_ST values between populations indicate that there were significant deviations in genetic differentiations for the red-tailed barb populations from these three Rivers of the Western Ghats, India. The microsatellites methods reported a low degree of gene diversity and lack of genetic heterogeneity in the population of G. curmuca, which strongly emphasize the need of fishery management, conservation and rehabilitation of G. curmuca.     

三峡库区5 个鲢群体遗传变异的微卫星分析

研究利用10 个高度多态的微卫星标记对三峡水库秭归、巫山、云阳、忠县、木洞等5 个库区鲢(Hypophthalmichthys molitrix)的野生群体进行了遗传多样性分析。检测到161 个等位基因, 群体共有等位基因84 个, 每个微卫星位点的等位基因数729 不等。平均观测杂合度Ho 为0.7840.846, 平均期望杂合度He 为0.8280.847, 平均多态信息含量PIC 为0.7970.817。Fst 值为-0.0010.009, 表明5 个鲢群体间没有遗传分化。Hardy-Weinberg 平衡检验表明巫山、云阳、木洞群体在一些位点上偏离遗传平衡。Bottleneck 分析显示长江三峡库区江段的鲢群体可能在历史上经历了遗传瓶颈。5 个群体间的遗传相似系数为0.8910.950, 遗传距离为 0.0500.115, 根据 Nei's 遗传距离所绘制的聚类图, 表明鲢群体间的遗传距离与其地理距离基本一致。贝叶斯分析结果也证实三峡库区5 个鲢群体可视为一个类群。尽管没有检测到遗传分化, 数据清晰地表明三峡库区的鲢群体仍有很高的遗传多样性, 研究结果为三峡地区和长江上游的鲢种质资源保护和种群评估提供了参考。       

Genetic Structure of Wild Rice Oryza Glumaepatula Populations in Three Brazilian Biomes Using Microsatellite Markers

The existence of Oryza glumaepatula is threatened by devastation and, thus, the implementation of conservation strategies is extremely relevant. This study aimed to characterize the genetic variability and estimate population parameters of 30 O. glumaepatula populations from three Brazilian biomes using 10 microsatellite markers. The levels of allelic variability for the SSR loci presented a mean of 10.3 alleles per locus and a value of 0.10 for the average allelic frequency value. The expected total heterozygosity (H_e) ranged from 0.63 to 0.86. For the 30 populations tested, the mean observed (H_o) and expected heterozygosities (H_e) were 0.03 and 0.11within population, respectively, indicating an excess of homozygotes resulting from the preferentially self-pollinating reproduction habit. The estimated fixation index ( _IS ) was 0.79 that differed significantly from zero, indicating high inbreeding within each O. glumaepatula population. The total inbreeding of the species (_IT ) was 0.98 and the genetic diversity indexes among populations, _ST and _ST, were 0.85 and 0.90, respectively, indicating high genetic variability among them. Thus, especially for populations located in regions threatened with devastation, it is urgent that in situ preservation conditions should be created or that collections be made for ex situ preservation to prevent loss of the species genetic variability.     

Genetic analysis of four wild chum salmon<Emphasis Type="Italic">Oncorhynchus keta</Emphasis> populations in China based on microsatellite markers

Synopsis To assess the genetic variation and population structure of wild chum salmon in China, we analyzed microsatellite loci for populations in the Amur, Wusuli, Suifen Current and the Tumen rivers. We evaluated expected heterozygosity with two estimators of genetic differentiation (F_ST and G_ST) and Nei’s standard genetic distance. The average expected heterozygosity across the 10 loci was 0.65 in the Wusuli River and the Suifen Current River, 0.64 in the Amur River and 0.66 in the Tumen River, The results of this study show that the recent declines in chum salmon have not led to low levels of genetic variability in China. The proportion of inter-population subdivision among chum salmon was between 5.7 and 6.8%. According to the estimator used, the NJ tree based on Nei’s standard genetic distance indicated that there were two different branches (the Sea of Okhotsk branch and the Sea of Japan branch), the Amur River and the Wusuli River populations were closer, while the Suifen Current River and the Tumen River clustered together. The genetic test for population bottlenecks provided no evidence for a significant genetic signature of population decline, which is consistent with the record of the four populations we have in the last few years.     

Allozyme Variation and Phylogenetic Relationships in Picea jezoensis (Pinaceae) Populations of the Russian Far East

Genetic variation and differentiation of 12 populations of Picea jezoensis from the Russian Far East were studied using 20 allozyme loci. The mean number of alleles per locus was 2.63, the percent of polymorphic loci was 88.1%, the observed heterozygosity was 0.181, and the mean value of expected heterozygosity amounted to 0.189. The values of expected heterozygosity of the northern and central mainland populations were higher than in the southern part of the natural range. A significant bias of Hardy–Weinberg heterozygosity to equilibrium heterozygosity (H_eq) suggests that most of the mainland populations have recently experienced a severe expansion in population size while populations from Kamchatka Peninsula have undergone a reduction in population size. Unbiased Nei’s genetic distance values were low within and between the mainland and Sakhalin Island populations (D_N=0.008). The largest values (D_N=0.063) were found between the mainland/Sakhalin and Kamchatka Peninsula populations. Based on genetic distance, P. jezoensis and P. kamtschatkensis could be considered as distinct taxa, but P. ajanensis, P. microsperma, and P. komarovii do not warrant taxonomic recognition.     

Genetic variation and population structure of endemic yellow catfish, <Emphasis Type="Italic">Horabagrus</Emphasis><Emphasis Type="Italic">brachysoma</Emphasis> (Bagridae) among three populations of Western Ghat region using RAPD and microsatellite markers

Random amplified polymorphic DNA (RAPD) and microsatellite markers were applied to evaluate the genetic variation in endemic and endangered yellow catfish, Horabagrus brachysoma sampled from three geographic locations of Western Ghat, South India river systems. In RAPD, of 32 10-mer RAPD primers screened initially, 10 were chosen and used in a comparative analysis of H. brachysoma collected from Meenachil, Chalakkudy and Nethravathi River systems. Of the 124 total RAPD fragments amplified, 49 (39.51%) were found to be shared by individuals of all 3 populations. The remaining 75 fragments were found to be polymorphic (60.48%). In microsatellites, six polymorphic microsatellite loci were identified by using primers developed for Pangasius hypophthalmus, Clarias macrocephalus and Clarias gariepinus. The identified loci were confirmed as microsatellite by sequencing after making a clone. The nucleotide sequences of 6 loci were published in NCBI genbank. The number of alleles across the six loci ranged from 4 to 7 and heterozygosities ranged from 0.07 to 0.93. The mean number of alleles and effective number of alleles per locus were 5.00 and 3.314, respectively. The average heterozygosity across all investigated samples was 0.72, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods reported a high degree of gene diversity and genetic distances depicted by UPGMA dendrograms among the populations of H. brachysoma.     

Isolation and characterization of polymorphic microsatellites in a Yangtze River fish,brass gudgeon (Coreius heterodon Bleeker)

The brass gudgeon (Coreius heterodon) is a fish of economic importance in the Yangtze River. From a (GATA)_n‐enriched genomic library, 25 microsatellites were developed by employing the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. Nine loci exhibited polymorphism with two to 12 alleles (mean 3.9 alleles/locus) in a test population, and observed heterozygosity ranged from 0.1111 to 0.9630 (mean 0.4426). Three of the nine loci showed polymorphism in a congeneric species, the largemouth bronze gudgeon Coreius guichenoti. These loci should provide sufficient level of genetic diversity to evaluate the fine‐scale population structure of C. heterodon.     

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。