Genetic diversity of threeAristichthys nobilis populations and one inbreeding stock

Genetic diversity of threeAristichthys nobilis populations and one inbreeding stock was studied using random amplified polymorphic DNA (RAPD) method. Materials of natural populations were collected from two counties of Guangxi Province, Hengxian (NH) and Shanglin (NS) and one city of Hubei Province, Wuhan city. (NW). Shanglin and Hengxian's river system respectively belongs to Qianjiang and Yujiang River, two tributaries confluencing to Xunjiang River, main tributary of Xijiang River, which is the biggest tributary of the Zhujiang River system, and Wuhan's water system belongs to the Yangtse River system. The inbreeding stock (RS) was the more than 10 generation descendant by brother-sister mating system whose parents were collected from Shanglin. The results showed that the genetic variety of individuals of RS was very low (0.105 4), whereas that of natural populations was relatively high, which from high to low was 0.158 1 (NW), 0.132 0 (NH) and 0.110 5 (NS). As an index for genetic distance pair-wise populations, the genetic variety between populations was studied, which characterized the genetic distance between populations. The genetic distance of NW and NH, NW and NS, NW and RS were respectively high, whereas that of NH and NS, NS and RS, NH and RS was low. Chi-test (χ ²) and the analysis of the genetic variety pair-wise populations was taken as efficient approach for studying population difference. Foundation item: Supported by the National Ninth-Five Research Program (No. 96-08010301), and Species Resource and Biotech of Freshwater Fish Pivot Laboratory of Agriculture Ministry Biography: Wang He(1978-), male, Master, research direction: molecular genetic markers in fish     

长江上游鲢群体遗传多样性和遗传分化

为了解三峡大坝、向家坝等水电工程建设后长江上游鲢群体的遗传多样性和遗传分化，利用线粒体细胞色素b（Cyt b）基因分析了长江上游向家坝库区（邵女坪）、三峡库区干流（巴南、丰都、万州、太平溪）及支流（箭滩河、嘉陵江、小江）等8个鲢群体的遗传多样性、历史动态及群体之间的遗传分化．结果表明:长江上游鲢群体的遗传多样性较高，单倍型多样性为0.770~0.876，核苷酸多样性为0.687%~1.967%；8个群体的错配分析图都呈双峰分布，中性检验Tajima’s D和Fu’s Fs值均为正值或统计上不显著的负值，表明长江上游鲢群体在历史上较为稳定；分子方差变异分析（AMOVA）显示，长江上游鲢群体的遗传变异主要来自群体内部（95.87%），仅有4.13%的变异来自群体之间；群体之间的遗传分化指数F_ST显示，箭滩河群体与太平溪、小江群体之间存在显著的遗传分化，其他群体之间遗传分化不显著；Mantel检验显示，群体之间的遗传分化程度与地理距离远近无相关性；单倍型网络图显示，长江上游鲢群体没有形成明显的系统地理格局．建议加强长江上游鲢遗传资源保护，将产生分化的群体作为不同的管理单元进行保护．      

Genetic diversity in the Yangtze finless porpoise by RAPD analysis

To estimate the genetic diversity in the Yangtze finless porpoise ( Neophocaena phocaenoides asiaeorientalis), the randomly amplified polymorphie DNA technique was applied to examine ten animals captured from the Yangtze River. Out of 20 arbitrary primers used in the experiment, seventeen produced clearly reproducible bands. Calculated by Nei‘s formula d = 1-NAB/NT, the genetic distances ranged from O. 0986 to O. 5634. Compared with other cetacean populations, this genetic distance is quite low.Such a low genetic diversity suggests that this population may be suffering from reduced genetic variation,and be very fragile. More studies are needed for understanding the basis for this apparent low genetic diversity and to help protect this endangered, unique population.     

用微卫星技术研究珠江流域三个野生大眼鳜群体的遗传多样性

采用微卫星标记技术,探讨了广西右江、左江及红水河三江段野生大眼鳜群体的遗传多样性。采用生物信息学方法,自主开发了4对大眼鳜微卫星DNA引物,此外,还从28对鳜属微卫星通用引物中筛选出15对,19对标记均表现为高度多态性。对32尾右江(YJ)、35尾左江(ZJ)及36尾红水河(HSH)三地理群体野生大眼鳜进行遗传多样性分析,总群体的固定指数Fix范围为0.001 4~1.000,表明19个位点在总群体内表现为杂合子缺失,其对环境的应对能力有所下降。遗传参数统计结果表明,总群体观测等位基因数(Na=19.4737)、香农指数(I=2.399 8)、平均杂合度(Ave Het=0.720 6)、多态信息含量(0.447PIC0.947)均显示:在哈温平衡下,大眼鳜3群体遗传多样性丰富;但3群体遗传多样性存在差异,红水河群体的遗传多样性比左江群体、右江群体的遗传多样性丰富,左江和右江群体的遗传多样性水平较为接近。群体间遗传分化水平较大(0.15群体间近交系数Fst=0.153 90.25),15.39%的遗传变异来自于群体间,84.61%的遗传变异来自于群体内,群体内近交系数Fis为0.576 1,各座位的基因流Nm分布范围较广(0.147 4~8.909 1),平均Nm值为1.374 5,表明3群体间属于中等遗传分化水平,基因流基本顺畅,群体内的近交系数较高,容易引起遗传结构的变化。基于Nei's遗传距离的聚类分析显示左江群体与右江群体首先聚为一支,再与红水河聚为一支,符合其在地理位置上的关系。     

基于微卫星的喀斯特地区长梗吊石苣苔和吊石苣苔的遗传多样性研究

长梗吊石苣苔Lysionotus longipedunculatus (W.T. Wang) W.T. Wang是我国吊石苣苔属中的一个比较罕见的物种,目前濒危等级被评估为极危CR Blac (ⅰ,ⅱ,ⅴ),而同属的吊石苣苔L. pauciflorus Maxim.分布范围非常广泛、生境变化多样,濒危等级为无危LC。本研究通过筛选出16个微卫星位点对长梗吊石苣苔的两个居群进行遗传多样性研究,并对比相近地区的吊石苣苔居群,比较研究导致长梗吊石苣苔濒危的原因。结果显示二者的遗传多样性都比较低,有较高自交现象,但吊石苣苔具有明显的走茎,可以有效地克隆繁殖,相较之下,长梗吊石苣苔较弱的克隆繁殖能力可能是导致其濒危的原因之一。     

The genetic diversity of central and peripheral populations of ratlike hamster (<Emphasis Type="Italic">Cricetulus triton</Emphasis>)

The impact of habitat fragmentation and isolation on the genetic diversity of populations has attracted much attention in studies of meta-population and conservation biology. In this work, using the randomly amplified polymorphic DNA (RAPD) technique, we studied the genetic diversity of central, peripheral and peninsular populations of ratlike hamster, which were collected in five locations of the North China Plain and its surrounding areas, in 1999. The study revealed that, i) the genetic diversity of central population of Raoyang County>the sub-central populations of Gu’an County and Taikang County > the peripheral population of Shunyi District>the peninsular population of Mentougou District; ii) the genetic diversities of the five populations were positively correlated to the nearest distances to the peripheral line of population distribution; iii) there were significant differences of gene frequencies of some RAPD fragments among the five populations. More RAPD fragments disappeared in peripheral populations than in central or sub-central populations. The frequencies of two RAPD fragments were correlated to the latitude. This study clearly indicated that the variation of the genetic diversities of the five populations was caused by edge effect and fragmentation through the enhanced inbreeding and genetic drift, and thus supported the view that habitat fragmentation and related edge effect reduce the population genetic diversity.     

基于ISSR数据探讨节茎曲柄藓(Campylopus umbellatus(Arn.) Paris)遗传多样性和居群遗传结构

选用简单序列重复区间扩增多态性(ISSR)分子标记,对分布于浙江清凉峰国家级自然保护区顺溪坞和凉源、浙江台州临海天台山、浙江舟山嵊泗列岛、江苏苏州天平山、广西上思十万大山、台湾宜兰县马告生态公园和云南西双版纳纳板河流域国家自然保护区8个自然居群的40份节茎曲柄藓(Campylopus umbellatus(Arn.) Par.)的遗传多样性进行了研究.应用筛选出的12条引物,共扩增出172条清晰、重复性高的条带.使用POPGENE 3.2分析发现:其中158条条带的多态性位点百分率(PPB)为91.86%,根井正利基因多样性指数(H)为0.292 2,香农-维纳多样性指数(I)为0.445 9,说明节茎曲柄藓居群遗传多样性水平较高.8个居群的遗传分化系数(G_(st))为0.634 6,居群间的基因流(N_m)为0.287 9,63.33%的遗传变异存在于居群间,36.67%的遗传变异存在于居群内,说明节茎曲柄藓居群间的遗传分化明显.基于ISSR数据的聚类分析表明:以遗传距离65为分组阈值,8个居群可被分为6组,节茎曲柄藓居群间的遗传分化主要由地理因素造成,居群内的遗传分化可能与生境的异质性有关.     

基于线粒体Cytb基因序列的褐石斑鱼种群遗传多样性分析

为评估种质资源状况被世界自然保护联盟(International Union for Conservation of Nature, IUCN)评定为易危物种的褐石斑鱼(Epinephelus bruneus)野生种群的遗传多样性和遗传分化水平，采用PCR方法测定褐石斑鱼西太平洋海区的中国海南岛(HN)、福建厦门(XM)和韩国济州岛(HG)3个地理群体的线粒体细胞色素b(Cytb)基因的部分序列，并对其基因序列遗传变异、谱系结构和群体扩张历史特征进行分析。结果显示，褐石斑鱼3个地理种群(88个个体)共检测出18个多态位点，共有7种单倍型；各地理群体遗传多样性水平较低，而且单倍型在群体间分布不均，韩国群体遗传多样性最高，中国海南和厦门群体遗传多样性较低。地理距离最远的韩国群体和中国海南群体遗传分化最高(F_ST=0.177 5),地理距离最近的中国海南群体和厦门群体的遗传分化最低(F_ST=0.013 4)。Mantel检验结果显示，3个褐石斑鱼群体间遗传距离和地理距离间存在显著相关，距离隔离(Isolation by Distance, IBD)...     

Genetic structure and diversity of Oryza sativa L. in Guizhou, China

Preserving many kinds of rice resources and rich variations, Guizhou Province is one of the districts with the highest genetic diversity of cultivated rice （Oryza sativa L.） in China. In the current research, genetic diversity and structure of 537 accessions of cultivated rice from Guizhou were studied using 36 microsetellite markers and 39 phenotypic characters. The results showed that the model-based genetic structure was the same as genetic-distance-based one using SSRs but somewhat different from the documented classification （mainly based on phenotype） of two subspecies. The accessions being classified into indica by phenotype but japonica by genetic structure were much more than that being classified into japonica by phenotype but indica by genetic structure. Like Ding Ying＇s taxonomic system of cultivated rice, the subspecific differentiation was the most distinct differentiation within cultivated rice. But the differentiation within indica or japonica population was different： japonica presented clearer differentiation between soil-watery ecotypes than indica, and indica presented clearer differentiation between seasonal ecotypes than japonica. Cultivated rices in Guizhou revealed high genetic diversity at both DNA and phenotypic levels. Possessing the highest genetic diversity and all the necessary conditions as a center of genetic diversity, region Southwestern of Guizhou was suggested as the center of genetic diversity of O. sativa L. from Guizhou.     

Genetic diversity among Chinese sika deer （Cerrus nippon） populations and relationships between Chinese and Japanese sika deer

Sika deer （Cervus nippon） is a cervid endemic to mainland and insular Asia and endangered. We analyzed variation in the mitochondrial DNA （mtDNA） control region for four subspecies to understand the genetic diversity, population structure and evolutionary history in China. 335 bp were sequenced and eight haplotypes were identified based on 25 variable sites among the populations. Sika deer in China showed lower genetic diversity, sug- gesting a small effective population size due to habitat fragmentation, a low number of founder individuals, or the narrow breeding program. AMOVA analysis indicated that there was significant genetic subdivision among the four populations, but no correlation between the genetic and geographic distance. PhyIogenetic analyses also revealed that Chinese sika deer may be divided into three genetic clades, but the genetic structure among Chinese populations was inconsistent with subspecies designations and present geographic distribution. Including the sequence data of Japanese sika deer, the results indicated that Chinese populations were more closely related to Southern Japanese populations than to the Northern Japanese one, and the Taiwan population was closer to populations of Northeastern China and Sichuan than to those of Southern China.     

Genetic analysis of gynogenetic and common populations of Verasper moseri using SSR markers

The genetic structure and variation of the artificial meio- gynogenetic population and common population of barfin flounder (Verasper moseri) were analyzed using eight microsatellite markers. A total of 29 alleles were detected, of which 23 alleles were in the artificial gynogenetic population while 29 alleles were in the control group. The average observed heterozygosity (H _O) of eight loci in the control group (0.526 8) was several times higher than that (0.185 8) in the gynogenetic population. The results indicate that the genetic diversity of the control group was much higher than that of the gynogenetic population of barfin flounder (Verasper moseri). Most loci significantly deviated from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction (p < 0.005 56) in the gynogenetic population, while four loci deviated from HWE in the control group. The coefficient of gene differentiation (G _ST) was 0.131 0, and the genetic distance was 0.171 8 between the two populations, suggesting a significant genetic differentiation between the two populations. Biography: MA Hongyu (1979–), male, Ph. D. candidate, research direction: marine biotechnology and molecular genetics.     

基于CR及Cytb基因序列的大泷六线鱼野生群体遗传多样性分析

为进一步了解山东省内大泷六线鱼(Hexagrammos otakii)群体遗传背景和分化情况,合理保护与开发利用渔业资源,选取线粒体控制区(CR)和细胞色素b基因(Cytb)对分布于山东省近海沿岸的3个大泷六线鱼野生群体以及北黄海1个离岸大泷六线鱼野生群体的线粒体基因序列进行对比,分析它们的序列特征、遗传多样性和种群历史动态情况。经PCR扩增得到大泷六线鱼野生群体的CR和Cytb基因序列,全长分别为485bp和651bp。基于CR基因序列共检测到40个多态位点,单倍型多样性平均值为0.908,核苷酸多样性平均值为0.006,定义了53种单倍型。基于Cytb基因序列检测到56个多态位点,转换颠换比值为19.04,种内单倍型多样性平均值为0.934,核苷酸多样性平均值为0.005,定义了38种单倍型。对比分析表明,4个大泷六线鱼野生群体均具有高单倍型多样性和低核苷酸多样性。NJ系统进化树、群体间/内平均遗传距离、Fst值、基因流及AMOVA分析结果显示:山东省内近海沿岸大泷六线鱼野生群体和北黄海离岸野生群体遗传差异不显著,群体间存在频繁的基因交流,未形成显著的遗传分化。种群动态结果表明大泷六线鱼于更新世晚期经历了快速扩张,并形成了现有遗传格局。山东省内近海沿岸大泷六线鱼野生群体和北黄海离岸野生群体遗传结构之间不存在显著的地理隔离,这可能与人为增殖放流和秋冬季节黄海沿岸流及暖流有关,从而使得群体之间基因交流广泛。     

珍稀濒危植物石山苏铁的SSR引物设计和遗传多样性分析

揭示珍稀濒危植物石山苏铁(Cycas sexseminifera)种群的遗传多样性水平和遗传分化大小,确定优先保护种群,对石山苏铁的有效保护和管理策略的制定具有重要意义。本研究基于简化基因组序列分析设计Simple Sequence Repeats (SSR)引物,并利用SSR引物进行遗传多样性检测。实验共获得6对SSR引物,6对引物共检测出37个观测等位基因(Na),其中最小观测等位基因数目为3,最大观测等位基因数目为12,平均每个位点等位基因数目为6.167。位点GZST002、GZST055、GZST065、GZST088是高度多态性位点(PIC>0.5)。石山苏铁各种群期望杂合度(He)为0.330-0.533,平均值为0.444,表明石山苏铁遗传多样性处于中等水平;7个种群的He值大小顺序为广西植物研究所引种(ZWS)>崇左广河(GH)>崇左排汝(PR)>隆安陇怀(LH)>崇左中干(ZG)>百色作登(ZD)>隆安新会(XH)。固定系数(F)为-0.161-0.480,平均值为0.074,其中LH、PR、XH 3个野生种群为负值,GH、ZD、ZG 3个野生种群的固定系数则大于0;7个种群的F值大小顺序为百色作登(ZD)>广西植物研究所引种(ZWS)>崇左中干(ZG)>崇左广河(GH)>隆安陇怀(LH)>隆安新会(XH)>崇左排汝(PR)。因此,综合各个遗传指标,石山苏铁需要重点保护和引种的野生种群是遗传多样性相对较高的崇左广河(GH)种群。同时建议开发更多的SSR引物和采集更广范围的石山苏铁野生种群,精准筛选遗传多样性高的优良种群,以利于更全面和准确地评估石山苏铁的遗传多样性水平和濒危机制。     

特有种四合木种群遗传结构分析

对四合木种群的遗传结构进行了研究．结果表明，四合木在种群水平上维持较高的遗传多样性．大部分遗传多样性存在于种群内，种群间的遗传分化很低．四合木的较高的遗传多样性是在长期进化过程中适应生境条件变化形成的．其基因组DNA存在较高的变异性，各种群之间存在一定的基因流，四合木各种群可看成是meta-种群，应注意保护四合木中具有丰富的遗传多样性的meta-种群．     

生境片断化对植物的遗传影响

生境片断化指大片连续的生境被分割成空间隔离的小生境的现象。通常认为，生境片断化使植物残遗种群由于经历随机遗传漂变和高水平的近交以及基因流的下降，而发生遗传侵蚀，遗传多样性下降，遗传结构改变，变得更加分化。但近期的研究证明，并不是所有的片断化事件都导致植物种群遗传变异丧失，且种群问的基因流甚至有可能增加了。片断化对植物种群的遗传作用还受到诸如世代长短的种间差异、片断化前的丰富度、有性和无性繁殖系统的多样性、种子库以及和传粉媒介及种子传播者的相互作用等的影响。     

基于SSR分子标记的广西极小种群野生植物长叶苏铁遗传多样性分析

了解广西区内的国家一级重点保护植物长叶苏铁（Cycas dolichophylla K.D.Hill）的遗传多样性和变异特征对广西长叶苏铁的保护和管理有着重要意义。本研究利用筛选出的6对稳定性好的SSR引物对分别来自广西百色市田阳县梅茶镇（PL）、德保县那甲镇（NL）和德保县城关镇（QH）的3个长叶苏铁种群的遗传多样性和变异特征进行分析。结果表明：6对引物中,高度多态性引物（GZST055、GZST065、GZST088）和低度多态性引物（GZST002、GZST013、GZST019）各占50%。广西长叶苏铁3个种群的平均观测等位基因为2.833,平均有效等位基因为2.005,平均Shannon信息指数为0.657,平均观测杂合度为0.259,平均期望杂合度为0.359。群体的遗传分化系数为0.049,说明群体间遗传分化小,且群体内遗传变异占所有遗传变异的97%,3个种群的基因交流频繁且遗传背景相互混杂。总体来看,广西长叶苏铁遗传多样性水平较低,而德保县那甲镇（NL）种群的遗传多样性相对最高,应将该种群作为重点保护单元进行保护。本研究还对广西长叶苏铁资源保护工作提出了建议和对策。     

Microsatellite polymorphisms of Sichuan golden monkeys

Previous study using protein electrophoresis shows no polymorphism in 44 nuclear loci of Sichuan golden monkey （Rhinopithecus roxellana）, which limits our understandings of its population genetic patterns in the nuclear genome. In order to obtain sufficient information, we scanned 14 microsatellite loci in a sample of 32 individuals from its three major habitats （Minshan, Qinling and Shennongjia）. A considerable amount of polymorphisms were detected. The average heterozygosities in the local populations were all above 0.5. The differentiations among local populations were significant. There was evidence of geneflow among subpopulations, but geneflow between Qinling and Shennongjia local populations was the weakest. Minshan and Qinling populations might have gone through recent bottlenecks. The estimation of the ratio of the effective population sizes among local populations was close to that from census sizes. Comparisons to available mitochondria data suggested that R. roxellana＇s social structures played an important role in shaping its population genetic patterns. Our study showed that the polymorphism level of R. roxellana was no higher than other endangered species; therefore, measures should be taken to preserve genetic diversity of this species.     

Genetic relationships among Chinese and American isolates of Phytophthora sojae assessed by RAPD markers

The genetic diversity of three geographic populations of Phytophthora sojae from China and the United States was determined using random amplified polymorphic DNA （RAPD）. The purpose was to explore genetic relationships among Chinese and American isolates of the organism. 21 random primers were selected among 200 random primers screened. A total of 223 reproducible RAPD fragments were scored among 111 individuals, of which 199 （89.23%） were polymorphic. Analysis of genetic variation showed that there existed higher genetic variation in the United States population in comparison to the Chinese populations. Nei＇s genetic identity and principal component analysis indicated that the populations of Fujian and United States are closer to each other than to Heilongjiang populations. Shannon-Wiener diversity index revealed that the United States populations have a higher genetic di- versity than that of Chinese populations. These data are in support of the hypothesis that P. sojae in the United States might not have been introduced from China.     

基于SSR的广西同色兜兰和带叶兜兰遗传多样性分析

评估四季开花型同色兜兰（Paphiopedilum concolor）和春季开花型带叶兜兰（P.hirsutissimum）的遗传多样性和种群结构,探究不同开花习性兜兰属物种间的遗传分化,为兜兰的可持续利用和野生资源保护提供理论依据。本研究利用10个多态性EST-SSR位点对12个同色兜兰和带叶兜兰种群的231个个体分型,开展遗传多样性、瓶颈效应、系统发育、遗传结构、遗传分化、距离隔离和环境隔离分析。结果表明,同色兜兰种群的大多数遗传多样性指标都显著（P<0.05）低于带叶兜兰;分子方差分析（AMOVA）结果显示,两者来自种群间的变异都较少,且带叶兜兰来自个体内的遗传变异高于同色兜兰。在同色兜兰的两个种群中检测到显著（P<0.05）瓶颈效应,而在带叶兜兰全部种群中均未检测到。群体水平的非加权平均（UPGMA）树和个体水平的邻接（NJ）树均显示同色兜兰和带叶兜兰间系统发育关系相对较近,并各自聚为一支。主坐标分析（PCoA）和Structure分析结果均支持系统发育分析结果。此外,遗传分化系数（F_ST）证实两个物种间的种群分化已达到较高水平。狭窄的自然分布和过去的种群瓶颈可能导致了同色兜兰的部分遗传多样性丧失。地理隔离是驱动同色兜兰和带叶兜兰种群遗传分化的主要因素,而环境隔离的作用较小。     

Genetic diversity of reared N.miichthioides population

The genetic diversity of 30 rearedNibea miichthioides individuals was analyzed by random amplified polymorphic DNA (RAPD) with 20 random primers. The result showed that the genetic diversity of reared individuals was relatively low with 15.31% polymorphism and 0.031 9 of the average difference (AD). The result also indicated that RAPD is a useful way in genetic diversity analysis of fish population.