厚壳贻贝养殖群体与野生群体线粒体DNA的遗传分析(英文)

采川线粒体DNA COI基因序列对厚壳贻贝2个养殖群体与2个野生群体的遗传多样性进行了研究.4个群体共获得30个单倍型.结果显示:在养殖群体中单倍型的数量和遗传多样性要比野生群体的低,可能是由于只有少量的有效父母本对养殖群体的遗传变异有贡献所致.养贿群体与当地野生群体之间也未发生显著的遗传分化,可能足因为它们之间存在基因流.在今后厚壳贻贝养殖过程中,本研究可以用在对养殖群体进行遗传监测,从而保证养殖群体的遗传多样性水平.     

光裸方格星虫野生与养殖群体线粒体控制区序列的遗传差异分析

基于线粒体控制区序列对光裸方格星虫（Sipunculus nudus Linnaeus，1766）的2个养殖群体（营盘YP、竹林ZL）和4个野生群体（防城港FC、钦州QZ、大冠沙DG和越南海防YN）的91个个体进行遗传差异分析，研究光裸方格星虫养殖和野生群体的遗传变异情况。结果显示:获得的514 bp DNA序列中，野生与养殖群体的多态性位点数分别为82和60，均显示出对AT的偏倚性。共定义85个单倍型，共享单倍型4个，其中共享单倍型Hap5为原始单倍型，营盘群体均为独享单倍型。各群体的单倍型多样性（H_d）相同，野生群体的平均核苷酸多样性（P_i）（0.01531）略高于养殖群体（0.01514），6个群体的遗传多样性水平依次为YN > YP > QZ > FC > ZL > DG。各群体间的遗传分化并不显著（P>0.05），光裸方格星虫的遗传变异主要来自群体内个体间（99.08%），同时未发现明显的地理谱系结构。研究表明，光裸方格星虫野生群体的遗传多样性水平总体略高于养殖群体；滩涂底播养殖方式较池塘养殖更利于维持光裸方格星虫遗传多样性；各群体间不存在显著的遗传分化，养殖群体正逐渐积累遗传变异，但尚未足够以形成其独立的遗传结构。     

草鱼野生与选育群体线粒体DNA控制区D-loop遗传变异分析

为探究经过2个选育世代后选育群体遗传多样性和遗传结构的变化, 研究对4个野生群体(邗江、九江、石首和吴江)和2个选育世代(F1和F2)进行了线粒体DNA控制区(D-loop)序列的遗传变异分析。实验结果表明, 4个野生群体在单倍型数目(H)、单倍型多样性(H_d)、核苷酸多样性(π)、平均核苷酸差异数(K)水平上均高于2个选育世代, 在2个选育世代内表现为F1代群体的核苷酸多样性(π)和平均核苷酸差异数(K)大于F2代群体, 但单倍型多样性(H_d)小于F2代群体; 单倍型分析结果表明, 6个群体间无共享单倍型, 4个野生群体间共发现2种共享单倍型(Hap1和Hap3), 石首群体和2个选育世代共享1种单倍型(Hap15); 遗传分化指数(F_st)分析结果表明, 邗江、九江、吴江3个野生群体和2个选育世代间存在较大的遗传分化(F_st范围为0.41475—0.55128), 石首群体与F1代群体之间存在较小的遗传分化, 与F2代群体之间存在中等水平的遗传分化, 同时F1代群体与F2代群体之间存在较小的遗传分化; 基于6个群体276个个体构建的邻接(Neighbor-Joining, NJ)进化树和基于27种单倍型构建的单倍型网络图也得到了相似的结论, 即邗江、九江、吴江3个野生群体和2个选育世代间的亲缘关系较远, 石首群体和2个选育世代两两之间的亲缘关系较近。以上结果表明, 经过2个世代的选择育种, 选育群体的遗传结构已发生了变化, 并且随着选育的进行, 选育世代的遗传多样性下降的较为明显, 这警示着我们在今后的育种工作中应适当改变现有的选育方案, 并实时监测选育群体的遗传多样性, 以便为今后进一步的选育工作打下坚实的基础。     

野生和养殖大鲵群体遗传多样性的微卫星分析

中国大鲵是世界上最大的两栖动物并且为我国特有，现在该物种野生种群急剧下降, 而人工养殖种群逐渐增多。为了对大鲵(Andrias davidianus)群体进行遗传多样性的本底调查, 本文用10对微卫星引物对28尾野生大鲵和16尾人工养殖的大鲵样本进行了遗传多样性分析。结果表明, 在10对引物中有7对检测到多态位点, 野生群体和养殖群体的观察等位基因数分别为5–8和4–6, 期望杂合度分别为0.81和0.75, 说明本实验中研究的大鲵的遗传多样性水平较高。通过人工养殖群体和野生群体的比较发现, 人工养殖群体存在较大的等位基因丢失现象, 并且遗传多样性水平低于野生群体。以上结果将为大鲵的人工繁育和遗传多样性的保护、利用提供一定的理论依据。     

基于线粒体DNA控制区序列的重庆岩原鲤人工养殖群体遗传多样性分析

为研究重庆市长寿和涪陵地区岩原鲤(Procypris rabaudi)人工养殖群体的遗传多样性, 采用PCR扩增获得175尾岩原鲤个体的线粒体DNA控制区(mtDNA D-loop)部分序列片段。对其中692 bp序列分析共发现11个单倍型, 其中Hap1为主要单倍型, 占总样本的76.57%。单倍型Hap10演化速率较快, 并且与单倍型Hap6遗传距离最远。长寿及涪陵地区岩原鲤人工群体的单倍型多样性分别为0.4100±0.0550和0.3970±0.0820, 核苷酸多样性分别为0.0013±0.0003和0.0013±0.0004。通过与长江上游江段野生群体(苍溪江段、合江江段、木洞江段、通江江段、万州江段、武隆江段、习水河和唐河)及北碚区人工养殖群体的遗传多样性进行比较, 发现岩原鲤长寿及涪陵地区人工养殖群体遗传多样性明显低于野生群体, 但略高于北碚人工养殖群体。为保持岩原鲤人工养殖群体的遗传多样性, 应尽量选择遗传距离较远的亲本进行配对, 并定期补充不同遗传背景的个体作为后备亲鱼。     

长吻(鱼危)养殖群体与野生群体遗传多样性分析

长吻(鱼危)(Leiocassis longirostris)是中国土著珍稀鱼类。近年来, 由于江河水利工程、环境污染及人类生产活动已经对江河的渔业资源造成了难以逆转的破坏, 长吻(鱼危)的渔业资源已逐渐枯竭。目前, 长吻(鱼危)在四川、广东等地实现适度规模养殖。以四川眉山、湖北石首和安徽淮南3个人工养殖长吻(鱼危)群体及4个长江野生长吻(鱼危)群体(重庆段、武汉段、安庆段和南京段)为实验材料, 利用线粒体DNA (mtDNA)控制区序列作为分子标记对135个个体的遗传结构进行了分析。结果表明, 在790 bp 的同源序列中, 长吻(鱼危) 3个养殖种群共检测到变异位点27个, 占全部序列的3.42%, 66个个体共检测到18种单倍型; 在野生群体中, 69个个体共检测到35个变异位点和36个单倍型, 长吻(鱼危)野生群体平均单倍型多样性和平均核苷酸多样性(Hd=0.9736±0.0070, Pi=0.0087±0.0015)高于长吻(鱼危)养殖群体(Hd=0.8867±0.0013, Pi=0.0056±0.0013); 群体间的遗传分化水平较低(F_st值为0.0014—0.1125)。采用邻接法(NJ法)和统计简约原理对所有单倍型进行系统发育树和统计简约网状图的构建, 结果表明: 各群体内的个体均不能分别构成独立的分支, 而是相互交叉聚在一起。分析结果表明, 长吻(鱼危)养殖群体与野生群体之间的基因交流充分, 未出现遗传分化, 但相对长吻(鱼危)野生群体, 长吻(鱼危)养殖种群多态性偏低。     

企鹅珍珠贝养殖群体与涠洲岛野生群体的微卫星分析和形态分析

本研究应用19对马氏珠母贝(Pinctada martensii)微卫星引物,分析企鹅珍珠贝(Pteria penguin)涠洲岛野生群体和养殖群体的遗传多样性。结果显示,19个微卫星位点在野生和养殖群体中的平均等位基因数(Na)分别为4.0和3.0,平均有效等位基因数(Ne)分别为3.255 5和2.803 5,群体平均多态信息含量(PIC)为0.548 5,说明企鹅珍珠贝群体的多态性水平较高。野生群体的平均观测杂合度(Ho)为0.679 8,平均期望杂合度(He)为0.674 9,平均Shannon's多样性信息指数(I*)为1.197 9;养殖群体的Ho、He和I*则分别为0.554 8、0.551 1和0.900 1,说明涠洲岛野生群体的遗传多样性要高于养殖群体。各座位平均遗传分化系数(Fst)为0.038 9,平均基因流(Nm)为6.177 5,说明涠洲岛野生群体和养殖群体间基因交流较频繁,群体遗传分化很小。采用通径分析法探讨涠洲岛野生和养殖群体的壳长、腹缘壳高和垂直壳高对壳宽的决定效应,以探索形态性状与分子标记的关联。结果显示野生群体壳长对壳宽的直接影响最大,养殖群体垂直壳高对壳宽性状的直接作用最大。将三个指标与腹缘壳高的比值进行比较,以消除两个群体年龄差异造成的误差,结果显示涠洲岛野生群体的壳长/腹缘壳高值(0.701 6)明显低于养殖群体(1.077 9),可作为SSR分子标记的有力补充用于快速鉴别企鹅珍珠贝野生群体和养殖群体。     

鲮鱼的微卫星位点筛选和群体遗传多样性初步分析

利用鲤科鱼类微卫星引物在鲮鱼中进行扩增,结果在24对引物中，13对引物能成功扩增，且在鲮鱼中的扩增产物表现稳定，其中11对有较高多态性,等位基因数在2—7个之间，扩增的条带符合孟德尔遗传规律。随后利用筛选的微卫星座位对鲮鱼野生和养殖群体遗传多样性进行了初步分析。分析结果显示：鲮鱼野生群体的平均等位基因数5.2个；观测杂合度在0.25与0.8之间，平均观测杂合度(Ho)是0.61±0.2，平均期望杂合度(He)是0.8±0.09；群体座位平均多态信息含量(PIC)为0.72±0.1。相比之下，养殖群体的平均观测杂合度(Ho)和平均期望杂合度(He)都低于野生群体，分别是0.59±0.2、0.75±0.1。两群体间的遗传相似度为0.7774、遗传距离为0.2518。研究表明：用其他鱼类分离出的微卫星引物可以快速筛选到适用于鲮鱼遗传分析的微卫星座位。     

秦岭细鳞鲑人工繁育群体与野生群体遗传变异分析

研究利用线粒体DNA(细胞色素b基因序列和D-loop区序列)序列对秦岭细鳞鲑(Brachymystax lenok tsinlingensis)野生群体和人工繁育群体的种群遗传结构进行了分析。结果表明,在86个个体扩增出的线粒体D-loop区730 bp片段中,A+T含量(63.5%)明显高于G+C含量(36.5%)。Cyt b基因序列扩增1141 bp,A+T含量(52.8%)明显高于G+C含量(47.2%)。野生群体43个个体共检测到18个单倍型,繁育群体43个个体中共检测到24个单倍型,两个群体共享8个单倍型;秦岭细鳞鲑野生群体的单倍型多样性和核苷酸多样性(h=0.907±0.026;π=0.00287±0.00074)低于繁育群体(h=0.917±0.035;π=0.00349±0.00083),AMOVA分析显示,98.37%的分子差异位于群体内,1.63%的分子差异位于群体间,两群体之间的遗传分化水平较低(Fst=0.01631,P=0.1075;Nm=30.16)。采用邻接法构建的系统发育树和单倍型网络图分析表明,各群体内的个体不形成单系群,两者之间互有交叉。总之,秦岭细鳞鲑野生群体与繁育群体之间基因交流充分,未出现遗传分化。     

利用COI基因序列分析长江与澜沧江水系日本沼虾群体的遗传结构

测定了我国长江水系和澜沧江水系的日本沼虾9个群体，共79个个体的线粒体COI基因序列片段（约450 bp），结果发现有89个变异位点，共计有46个单倍型。其中云南昆明（KM）群体具有较丰富的遗传多样性（h=1.000，π=0.028），而重庆（CQ）群体的遗传多样性最小（h=0.700，π=0.008）。AMOVA分析表明，群体间的遗传变异占总遗传变异的9.66%，而90.34%的遗传变异源于群体内。采用邻接法（NJ）构建的分子系统树显示，46个单倍型明显地聚为长江中下游和长江上游与澜沧江两个族群。其结果可以为合理开发和利用日本沼虾自然野生资源，以及建立和保护日本沼虾种质资源库及基因库提供必要的参考。     

Genetic variation of Mytilus coruscus Gould (Bivalvia: Mytilidae) populations in the East China Sea inferred from mtDNA COI gene Sequence

In order to characterize the genetic relationship of six populations of Mytilus coruscus Gould in the East China Sea, a 681 bp region of mtDNA COI gene was sequenced and analyzed. Eighty four individuals in total were collected from three cultured populations and three wild populations from three localities of the coast of East China Sea. The sequences from these different populations identified 62 polymorphic sites, which included 41 singleton variable sites and 21 parsimony informative sites that defined 45 distinct haplotypes. Phylogenetic analysis showed that most haplotypes were highly interconnected with each other. Thirty seven of the 45 haplotypes were only found in their own populations, seven were found at two-four localities and only haplotype NO.2 was found in all six populations, indicating that most haplotypes were locally restricted. All haplotypes had shaped two similar branches, each including individuals from all six strains. The results of F_ST values indicated that the genetic distances between populations are not closely associated with their geographic distances.     

不同地理种群银杏大蚕蛾COI基因序列变异与遗传分化

银杏大蚕蛾Caligula japonica是亚洲东部的特有种, 既是一种重要的林业害虫, 也是一种珍贵的野生蚕类资源。为了揭示银杏大蚕蛾地理种群间的内在联系, 测定了我国分布的12个地理种群的线粒体细胞色素氧化酶C亚基I（COI）基因部分序列（GenBank登录号: FJ358506-FJ358517）, 对地理种群间的序列变异和遗传分化进行了分析。结果表明: 银杏大蚕蛾地理种群间的COI序列同源性高达99%~100%, 显示出比较小的遗传差异。序列对准后从供试COI序列中仅鉴定出9个变异位点和6个单元型, 其中3种是共享单元型。系统发育分析结果表明种群间已经按地理位置形成了一定的地理格局, AMOVA分析显示北方组和南方组之间已经具有明显的遗传分化（FST=0.478, P<0.001）。综合分析, 我们认为北方组和南方组之间的遗传分化可能与差异巨大的生态条件有关。研究结果为银杏大蚕蛾的种群遗传学和生态学研究提供了一个基本的分子生物学线索。     

陕西省林麝mtDNA D-loop区序列结构和种群遗传多样性

林麝(Moschus berezovskii)曾广泛分布于中国,由于盗猎和栖息地缩小,秦岭地区野生种群数量迅速下降,圈养繁殖种群已成立了几十年,但大多数圈养种群的遗传背景不清,种群规模增长非常缓慢。为了给这一物种的保护和管理提供有用的信息,调查了陕西省林麝1个圈养种群3个野生种群线粒体DNA(mt DNA)D-Loop 632 bp片段的遗传多样性和种群结构。在69个个体中其碱基组成为A+T的平均含量63.2%高于G+C含量36.8%,共检测到变异位点171个(约占总位点数的27.05%)。核苷酸多样性(Pi)为0.04424,平均核苷酸差异数(K)为19.908。69个个体分属32个单倍型,单倍型间的平均遗传距离(P)为0.070。32个单倍型构建的NJ系统树聚为3个分支,4个林麝群体中的单倍型是随机分布的。4个群体的平均遗传距离为0.043(标准误SE为0.005),凤县养殖场群体与留坝和陇县群体的亲缘关系较远。单倍型间的平均遗传距离为0.043,可见其遗传分化尚未达到种群分化的水平。结果表明,陕西省林麝群体mt DNA D-loop区序列存在着较丰富的变异和遗传多样性,凤县野生群体和凤县养殖场群体的核苷酸多样性和单倍型多样较高,养殖场种群没有出现近亲繁殖及遗传多样性下降的情况。凤县野生群体和凤县养殖场群体两者遗传分化较小,存在着较高的基因流水平。     

唐鱼养殖种群与广州附近4个野生种群的遗传关系

唐鱼(Tanichthys albonubes)是为数不多的几种原产中国的世界性观赏鱼类之一。自2003年以来, 多个唐鱼野生种群相继被发现, 其濒危状态和等级由野外灭绝降为极危。为研究唐鱼养殖种群与广州附近野生种群之间的遗传关系, 本文分析了唐鱼3个代表性养殖种群和4个野生种群, 共计186个样本的Cyt b基因、2个核基因(ENC1和RAG1)以及13个微卫星位点数据。基于K2P模型的遗传距离结果显示, 唐鱼野生种群间的遗传距离在0.005-0.015之间, 养殖种群间的遗传距离为0.001-0.009。系统发育分析表明, 唐鱼养殖种群包含4个单倍型谱系分支, 其中2个分别与广州附近2个野生种群聚在一起, 另外2个分别独立成支。单倍型网络亲缘关系分析显示, 清远种群只有1个单倍型且与芳村养殖种群共享, 芳村养殖种群拥有最多的单倍型。基于微卫星数据的STRUCTURE分析表明, 所有种群最佳分簇数为2, 清远种群与养殖种群聚为一簇, 良口和石门种群聚为另一簇。主成分分析结果显示, 养殖种群高度重叠并能与野生种群分开, 清远种群与养殖种群存在部分重叠。利用IMa3的基因流分析表明, 存在清远种群至芳村养殖种群的单向基因流。综合本文结果, 作者认为唐鱼养殖种群应起源于广州附近多个野生种群。清远种群来源于养殖种群中的芳村养殖种群。建议在未来唐鱼的保护策略中, 应禁止不规范的放流活动并且禁止将不同野生种群补充至养殖种群, 同时加强唐鱼养殖种群和野生种群的遗传资源管理和持续监测。     

Genetic diversity of cultured populations of giant freshwater prawn (Macrobrachium rosenbergii) in China using mtDNA COI and 16S rDNA markers

Partial sequences of mitochondrial DNA 16S rDNA and COI genes (395 bp and 498 bp respectively) were sequenced from samples of ten cultured populations of Macrobrachium rosenbergii (Giant Freshwater Prawn – GFP) in Zhejiang, Guangdong and Guangxi Provinces in China and two wild populations of GFP from Mekong River and Dongnai River in Viet Nam. Five haplotypes of 16S rDNA were identified in the 360 samples. The wild populations displayed nucleotide diversity (π) of 0.0008 and 0.0003, and genetic diversity (h) of 0.3030 and 0.1310 in the Mekong River and Dongnai River respectively. The cultured populations displayed no significant genetic diversity. COI sequences identified 17 haplotypes based on 21 polymorphic sites. At this marker, the 12 populations showed a range of h from 0.1290 to 0.6940 and π from 0.0003 to 0.0073. The largest genetic distance (Da) among the 12 populations was 0.0065 (between ZJB and BT/DN populations) and the lowest Da was 0.0003 (between GDD and GDA populations). The wild populations had higher genetic diversity than the cultured populations, but three of cultured populations from Zhejiang (ZJA, ZJB and ZJC) had π higher than wild populations, because they originated from Thailand, Bangladesh and the Mekong River in Viet Nam.     

Population genetic structure in wild and hatchery populations of white cloud mountain minnow (Tanichthys albonubes): Recommendations for conservation

We used mitochondrial (mt) cytochrome b gene (cyt b) to compare the genetic variability in three hatchery broodstocks of white cloud mountain minnow with the variability in six wild populations sampled in two river drainages. A total of 43 haplotypes in 102 specimens were observed, with no haplotype shared between wild and hatchery populations. The nucleotide diversity of the wild samples (0.048) was significantly higher than that of the hatchery ones (0.007), but the haplotype diversity was almost similar between them. Two major phylogenetic haplotype groups were revealed and estimated to diverge about 6.531 myr (million years) ago. Significant genetic differentiation was revealed between wild and hatchery populations as well as among nine sampled populations, suggesting at chance effect during the founding process for the hatchery population and a subsequent genetic drift. According to the network, the connection between wild and hatchery populations indicates that present hatchery populations originated from single wild population. We suggested that two regions (Pearl River system and Lu River) identified by reciprocal mtDNA monophyly and SAMOVA should be regarded as three different ESUs and two different MUs in South China, respectively.     

The marine indo-west pacific break: contrasting the resolving power of mitochondrial and nuclear genes

Simultaneous studies of both nuclear and mitochondrial markerswere undertaken in two widespread Indo-West Pacific (IWP) marineinvertebrates to compare and contrast the ability of these markersto resolve genetic structure. In particular, we were interestedin the resolution of a genetic break between the Indian andPacific Oceans due to historical isolation. Sequence variationfrom the nuclear gene encoding myosin heavy chain (MyHC) andthe mitochondrial gene cytochrome oxidase I (COI) were examinedfor the snapping shrimp Alpheus lottini from wide-ranging populationsthroughout the Indian and Pacific Oceans. A previously identifiedgenetic break between oceans based on COI sequences appearsto have been an artifact caused by the inadvertent inclusionof pseudogene sequences; our new COI data provide evidence onlyof a break between IWP and East Pacific populations. Distributionof a single nucleotide polymorphism in MyHC, on the other hand,shows evidence of a cline between Indian and Pacific Oceans.New allozyme and mtDNA sequence data were also obtained forthe starfish Linckia laevigata. Allozyme data show a clear geneticbreak between Indian Ocean populations and Pacific (includingwestern Australian) populations, whereas the distribution ofmtDNA haplotypes shows a region of overlap in the central IWP.Comparisons of our data for both Alpheus and Linckia with datafrom other population genetic studies in the IWP suggest thatnuclear markers (allozymes, sequence data and morphologicalcharacters) may in some instances reveal historical patternsof genetic population structure whereas mtDNA variation betterreflects present day patterns of gene flow.     

PATTERNS OF GENETIC DIFFERENTIATION AND CONSERVATION OF THE SLABSIDE PEARLYMUSSEL, LEXINGTONIA DOLABELLOIDES (LEA, 1840) IN THE TENNESSEE RIVER DRAINAGE

The restoration and recovery of imperiled mussel species willrequire the re-establishment of populations into historicallyoccupied habitats. The possible existence of genetic differentiationamong populations should be considered before inter-basin transfersare made. Eighty individuals of the federal candidate speciesLexingtonia dolabelloides were sampled from populations in theNorth Fork Holston, Middle Fork Holston, Clinch, Paint Rockand Duck rivers of the Tennessee River basin in the southeasternUnited States. We sequenced 603 base-pairs of a mitochondrialDNA gene (ND-1) and 512 base-pairs of a nuclear DNA gene (ITS-1).Analyses of molecular variation (AMOVA) values for both genesindicated that the majority of variation in L. dolabelloidesresided within populations (82.9–88.3%), with 11.7–17.1%of variation among populations. Haplotype frequencies differedsignificantly among populations for both genes sequenced. Clusteringof haplotypes in minimum-spanning networks did not conform stringentlyto population boundaries, reflecting high within-populationand low between-population variability. Maximum parsimony analysisdid not identify any population as a monophyletic lineage. AMantel test showed no significant correlation between geographicalstream distance and genetic distance, thus not supporting apattern of isolation-by-distance. Overall, results providedsupport to manage fragmented populations of L. dolabelloidesin the Tennessee River drainage as two management units (MUs),but did not provide evidence for the existence of ESUs followingpublished molecular criteria. (Received 26 October 2004; accepted 29 April 2005)