Isolation and characterization of microsatellite loci in the threatened wild toad lily Tricyrtis flava (Liliaceae)

Twelve polymorphic microsatellite loci were isolated and characterized from the threatened toad lily Tricyrtis flava. The number of alleles ranged from three to 17, and the observed and expected heterozygosities ranged from 0.35 to 0.96 and from 0.50 to 0.93, respectively, in a population of T. flava. We also tested cross‐species amplifications of the markers in three other species of Trycyrtis sect. Flavae. Most of 12 markers developed for T. flava were successfully amplified in the species of sect. Flavae and will be useful for population genetic studies of these species.     

The effect of geographic range and dichogamy on genetic variability and population genetic structure in Tricyrtis section Flavae

Populations of each of the four species of Tricyrtis sect. Flavae were sampled using enzyme electrophoresis to examine the effect of geographic range and dichogamy on the genetic diversity of the species. The most widespread species, T. nana, had the lowest level of genetic diversity at both the population and the species level. The depauperate genetic diversity at the population level of T. nana appears to result from the high self-fertilization of the species. The low genetic diversity at the species level of T. nana probably resulted from the bottleneck effect during the speciation process in which this species diverged from the progenitor species, T. flava. Genetic differentiation among populations was high in both adichogamous T. nana and protandrous T. flava. High self-fertilization in T. nana and the colonizing nature of T. flava are likely the main factors causing the differentiated population genetic structure. In contrast to a previous study on chloroplast DNA (cpDNA) variation in Tricyrtis sect. Flavae, T. nana was most closely related to T. flava, which corresponds to the morphological resemblance of both species.     

The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by （δμ）^2 and DA distances, and the divergence times between populations were estimated by （δμ）^2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles （10）, whereas Bohai black and Buffalo had the smallest number of private alleles （2）. Chinese Holstein showed the highest genetic variability. Its observed number of alleles （Na）, mean effective number of alleles （MNA）, and mean heterozygosity （He） were 7.7500, 4.9722, and 0.7719, respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first, followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations. Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago （MYA）, however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600 MYA, respectively.     

Low gene flow but high genetic diversity in the threatened Mallorcan midwife toad Alytes muletensis

We investigated fine-scale genetic structuring in the rare and vulnerable Mallorcan midwife toad Alytes muletensis using eight polymorphic microsatellite markers. The current range of this amphibian is restricted to some 19 sites of which six are derived from reintroductions, all located in the mountain ranges of Mallorca. We sampled tadpoles from 14 pools covering 10 natural sites and two reintroduction sites for microsatellite DNA analyses. Relatively high levels of genetic variation were found in most pools (H(E) = 0.38-0.71, allelic richness = 2.6-6.2). Only at one pool has the population recently gone through a bottleneck. Dispersal between pools in different torrents does not occur whereas downstream dispersal between pools within the same torrent does happen at low frequencies. This occasional exchange of individuals does not lead to neighbouring pools in the same torrent being panmictic. This can be concluded because all F(ST) values (0.12-0.53) differ significantly from zero and STRUCTURE analyses identified neighbouring pools as separate populations. Furthermore, assignment and migration tests showed little exchange between neighbouring pools. If upstream locations or complete torrents go extinct, they are unlikely to be recolonized naturally. For conservation purposes, reintroductions of tadpoles to sites where local extinctions have occurred may therefore be advisable.     

采用微卫星标记分析13个中外牛品种的遗传变异和品种间的遗传关系

本研究应用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)推荐的10对微卫星引物,结合荧光–多重PCR技术,检测了10个中国地方黄牛品种和3个外来牛品种的基因型。通过计算基因频率、多态信息含量和遗传杂合度,以Nei’s遗传距离和Nei’s标准遗传距离为基础,采用非加权组对算术平均聚类法构建了聚类图,分析了13个牛品种的群体内遗传变异和群体间遗传关系。并以聚类分析和群体结构分析为基础,将13个中外黄牛品种分为三类:Ⅰ类属于普通黄牛品种,包括延边牛、沿江牛、长白地方牛、蒙古牛、阿勒泰白头牛、哈萨克牛、复州牛和西藏牛;Ⅱ类属于含有瘤牛血统的黄牛品种,包括日喀则驼峰牛和阿沛甲咂牛;Ⅲ类属于外来牛品种,包括德国黄牛、西门塔尔牛和夏洛来牛。研究结果为加强我国地方黄牛品种种质特性研究以及地方牛品种资源的保护与利用提供了科学的依据。     

基于微卫星标记的中国枣食芽象甲地理种群遗传多样性分析

【目的】枣食芽象甲Scythropus yasumatsui是我国北方枣树Zizyphus jujuba上的一种重要的灾害性害虫,在陕西、山西、河北、河南等枣树主产区普遍发生。本研究旨在揭示我国枣食芽象甲不同种群间的遗传分化和基因交流规律。【方法】利用枣食芽象甲转录组测序的SSR序列,使用荧光标记PCR及毛细管电泳分型方法,筛选出8个微卫星位点,对我国5个省份(山西、陕西、宁夏、河北和河南)10个地理种群共308头枣食芽象甲样本进行种群遗传多样性分析。【结果】8个SSR位点均存在无效等位基因且偏离哈迪 温伯格平衡。各位点的有效等位基因数(Ne)为2.113~8.016,多态信息含量(PIC)为0.561~0.908,期望杂合度(He)为0.476~0.865;种群间遗传分化系数(Fst)平均值为0.151;基因流(Nm)平均值为1.594。枣食芽象甲种群间遗传分化系数与地理距离之间显著正相关(r=0.596, P=0.0035),基于Nei’s遗传距离和Cavalli-Sforza & Edwards余弦遗传距离的系统进化树将10个地理种群均聚为3个相同的分支。【结论】结果说明,枣食芽象甲种群遗传多样性较高,不同地理种群间存在高度的遗传分化,且有一定的基因交流;地理隔离是影响枣食芽象甲地理种群遗传分化和基因交流的重要因素。     

Analysis of genetic diversity and population structure of Chinese yak breeds （Bos grunniens） using microsatellite markers

Nine Chinese yak breeds (Maiwa,Tianzhu White,Qinghai Plateau,Sibu,Zhongdian,Pall,Tibetan High Mountain,Jiulong,and Xin-jiang) and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations,genetic relationship between populations,and population structure for each breed.A total of 206 microsatellite alleles were observed.Mean F-statistics (0.056) for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds.The Neighbor-Joining phylogenetic free was constructed based on Nei's standard genetic dis-tances and two clusters were obtained.The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together.The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one clus-ter includes yaks from Tibet Autonomous Region and Qinghai Province,one cluster combines Zhongdian,Maiwa,and Tianzhu White,and Jiulong and Xinjiang come into the third cluster.Pali was mainly in the first cluster (90%),Jiulong was mainly in the second cluster (87.1%),Zhongdian was primarily in the third cluster (83%),and the other yak breeds were distributed in two to three clusters.The Gayal was positively left in the fourth cluster (99.3%).     

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。     

Allozymic variation and divergence in three species of Antirrhinum L. (Scrophulariaceae-Antirrhineae)

An allozymic study of three wild species of Antirrhinum L. A. lopesiamum Rothm., A. mollissimum Roihni. and A. microphyllum Rothm. is described. All are members of subsection Kickiella Rothm., and are narrow-range endemics of the Iberian Peninsula. The variability of the different loci, as well as the number and mobility of the alleles, differ among the three species, a demonstration of the usefulness of allozymes for the systematics of the genus. The finding of alleles unique to each species indicates high divergence among species suggesting ancient diversification, and supports the hypothesis of a geographical model of speciation. All three species show high levels of within-species variability, mainly partitioned within populations, while between populations genetic differentiation is low. Correlations between population size, sample size and genetic variability, and the usefulness of allozymic data for conservation purposes, are discussed.     

微卫星标记对12个中外牛品种群体遗传结构的研究

选用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)推荐的12对微卫星引物, 采用荧光标记–多重PCR技术, 检测了9个中国地方黄牛品种和3个外来牛品种的遗传多样性。利用等位基因频率计算出各群体的平均遗传杂合度(H)、多态信息含量(PIC)和群体间的DA及DS遗传距离。基于DA遗传距离, 用UPGMA法进行聚类分析, 结果12个中外牛品种被聚为4类: Ⅰ类属于南方黄牛品种, 包括恩施牛、黎平牛、昭通牛和川南山地牛; Ⅱ类属于中原黄牛品种, 包括郏县红牛、早胜牛和平陆山地牛; Ⅲ类属于北方黄牛, 包括延边牛和长白地方牛; Ⅳ类属于外来牛品种, 包括西门塔尔牛、夏洛来牛和德国黄牛。研究结果为中国地方牛品种的保护和利用提供了理论依据。     

微卫星标记分析中国梨木虱种群的遗传多样性

中国梨木虱Cacopsylla chinensis (Yang et Li)是梨树主要害虫之一。为了从分子水平评估中国梨木虱种群内的遗传变异和种群间的遗传分化, 本文应用7对微卫星DNA引物对中国16个地区中国梨木虱种群进行遗传多样性分析。结果表明： 各位点有效等位基因为2.2927～10.0610, 多态信息含量(PIC)值在0.5073～0.8735之间。16个种群的平均期望杂合度为0.7876, 遗传距离在0.0951～1.0139之间, Nei氏期望杂合度为0.4771～0.7892, Shannon信息指数在0.8396～1.9989之间, 群体分化率F_ST为11.61%, 基因流平均值为2.2236。结果表明, 7个微卫星位点均具有较高的多态性, 各种群间的遗传分化水平较低, 基因交流程度较高, 遗传变异主要存在于种群内的个体间。研究结果为制定针对中国梨木虱的有效防治策略提供部分分子生物学的基础资料。     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is regarded as one of the domestication cen-ters for chickens and archaeological studies provided evidence of chicken domestication in northern Chinaas early as 6000 BC[1]. At present, China has the larg-est chicken population in the world, represen…     

应用微卫星标记分析不同桔小实蝇种群的遗传多样性

为探究不同桔小实蝇Bactrocera dorsalis (Hendel)地理种群的遗传变异、入侵来源和扩散情况,利用13对引物对中国南方10省区、泰国、夏威夷、菲律宾和老挝的30个桔小实蝇种群共180个个体的遗传多样性水平进行了研究。 Popgene32和NTSYS-pc2.10e软件分析结果表明：30个不同桔小实蝇种群的遗传相似度在0.3599~0.9153范围内。种群的Nei氏基因多样性指数平均为0.6464±0.1026,Shannon信息指数I平均为1.2845±0.2632, 提示桔小实蝇种群具有较丰富的遗传多样性。UPGMA聚类分析显示,福建地区和海南地区分别独立一支,广东地区和台湾地区种群聚成一支,而广西、泰国、湖南、云南、老挝、四川、 重庆和贵州地区聚为一大支系。据此提出泰国种群和老挝种群是最早入侵我国的种群,云南地区是最早的入侵地,广西地区可能为又一较早入侵地。     

Phylogeography of the natterjack toad Bufo calamita in Britain: genetic differentiation of native and translocated populations

The natterjack toad Bufo calamita is rare in Britain, which is at the northwestern edge of its biogeographical range. We investigated the level of genetic differentiation amongst almost all (34 out of 38) of the surviving British populations of this species, and among six new populations established by translocations during the 1980s. For eight microsatellite loci, allele sizes and frequencies were analysed using samples from each of these populations. The populations clustered into three robustly differentiated groups, each of which corresponded with a geographical region (east/southeast England, Merseyside and Cumbria). The Cumbrian populations showed a further weak geographical substructuring into northern and southern clades. The populations in south Cumbria were genetically more diverse than those in any of the other regions, as judged by the mean numbers of alleles per locus and the mean heterozygosity estimates. The translocated populations clustered close to their founders and, with one exception, did not differ significantly with respect to mean allele numbers, heterozygosity or polymorphism level. However, significant genetic differentiation (as measured by unbiased R _ST) was found between all but one of the founder-translocation pairs. The implications of this phylogeographic study for the future conservation of B. calamita in Britain are discussed.     

Isolation and characterization of microsatellite markers for Araucaria angustifolia (Araucariaceae)

Araucaria angustifolia is a dioecious tree species that occurs in the southern part of Brazil. Because of the intense exploitation of the species due to its valuable wood, only 2% of the original population still remains. Twenty‐nine species‐specific and highly polymorphic microsatellite loci were developed from a genomic library enriched for AG/TC repeats. Levels of polymorphism were evaluated using a total of 16 adult trees from a natural population. An average of 8.1 alleles per locus was detected, and expected heterozygosity ranged from 0.63 to 0.72.     

Evaluation of the genetic diversity and population structure of Chinese indigenous horse breeds using 27 microsatellite markers

We determined the genetic diversity and evolutionary relationships among 26 Chinese indigenous horse breeds and two introduced horse breeds by genotyping these animals for 27 microsatellite loci. The 26 Chinese horse breeds come from 12 different provinces. Two introduced horse breeds were the Mongolia B Horse from Mongolia and the Thoroughbred Horse from the UK. A total of 330 alleles were detected, and the expected heterozygosity ranged from 0.719 (Elenchuns) to 0.780 (Dali). The mean number of alleles among the horse breeds ranged from 6.74 (Hequ) to 8.81 (Debao). Although there were abundant genetic variations found, the genetic differentiation was low between the Chinese horses, which displayed only 2.4% of the total genetic variance among the different breeds. However, genetic differentiation (pairwise FST) among Chinese horses, although moderate, was still apparent and varied from 0.001 for the Guizou–Luoping pair to 0.064 for the Jingjiang–Elenchuns pair. The genetic differentiation patterns and genetic relationships among Chinese horse breeds were also consistent with their geographical distribution. The Thoroughbred and Mongolia B breeds could be discerned as two distinct breeds, but the Mongolia B horse in particular suffered genetic admixture with Chinese horses. The Chinese breeds could be divided into five major groups, i.e. the south or along the Yangtze river group (Bose, Debao, Wenshan, Lichuan, Jianchang, Guizhou, Luoping, Jinjiang and Dali), the Qinghai‐Tibet Plateau group (Chaidamu, Hequ, Datong, Yushu, Tibet Grassland and Tibet Valley), the Northeast of China group (Elenchuns, Jilin and Heihe), the Northwest of China group (Kazakh, Yili and Yanqi) and the Inner Mongolia group (Mongolia A, Sanhe, Xinihe,Wuzhumuqin and Sengeng). This grouping pattern was further supported by principal component analysis and structure analysis.     

中国龙虾微卫星标记的筛选及遗传多样性分析

文章以M13通用引物和重复序列(CT)₁₅、(AT)₁₅引物, 利用PCR法对中国龙虾(Panulirus stimpsoni Hoehuis)部分基因组DNA文库进行筛选。共获得78个微卫星序列, 分别分布于55个阳性重组克隆中, 其中完美型(perfect)共50个, 占64%; 非完美型(imperfect)3个, 占3.8%; 混合完美型(compound perfect)6个, 占7.7%; 混合非完美型(compound imperfect)19个, 占24.5%。根据微卫星序列, 设计并筛选出15对微卫星多态性引物, 对中国龙虾的群体进行了遗传多样性分析。获得3~12个等位基因, 等位基因大小在78~425 bp之间, 基本符合引物设计的理论长度。期望杂合度范围为0.48~0.87, 平均值为0.71, 表明中国龙虾基因组微卫星具有较高的杂合度与遗传多样性。15个微卫星位点的PIC值从0.44到0.84, 平均值为0.60, 说明这些微卫星位点在中国龙虾基因组中包含丰富的遗传信息, 合适用于中国龙虾的各种分子标记及遗传学分析和应用。     

基于微卫星标记的印度中部Madhya Pradesh地区疟疾强化控制和非强化控制区的斯氏按蚊基因流和种群遗传结构分析

[目的]斯氏按蚊Anopheles stephensi是亚洲东南部城市人体疟疾的主要媒介,印度12％的疟疾病例由其引起.本实验研究了印度中部Madhya Pradesh地区东北部的疟疾强化控制(EMCP)区和非强化控制(非EMCP)区斯氏按蚊的基因流.在EMCP区,由于采用了各种疟疾防控措施因而疟疾病例首先降低,但是很快回升,说明总的疟疾风险维持稳定.[方法]应用7个微卫星位点,对印度中部Madhya Pradesh地区东北部的4个EMCP区和非EMCP区采集的斯氏按蚊进行基因分型,以分析各种群参数.[结果]发现各标记在所有种群中表现出高度的多态性.在两区间未发现很大的遗传多样性.观察到EMCP区的东部种群(FST=0.0485,RST =0.1112)比非EMCP区的北部种群(FST=0.020,RST =0.0145)具有较高的遗传分化,在EMCP区和非EMCP区之间观察到较高的基因流(12.90,6.16,5.06和2.38).RST的灵敏度高于FST,说明分化可能是由于突变而非遗传漂变引起的.[结论]本研究表明,在EMCP区和非EMCP区内以及EMCP区和非EMCP区之间存在很高的基因流.基因流水平高以及抗虫性的发展似乎是EMCP区和非EMCP区疟疾病例发生增加的重要原因.     

Random amplified polymorphic DNA (RAPD) markers reveal less genetic variation in the endangered plant Cerastiumfischerianum var. molle than in the widespread conspecific C. fischerianum var. fischerianum (Caryophyllaceae)

Random amplified polymorphic DNA (RAPD) analysis was used to assess the level of genetic diversity in an endangered plant Cerastiumfischerianum var. molle and the widespread conspecific C. fischerianum var. fischerianum. At both the variety and the population level, C. fischerianum var. molle had a lower level of RAPD variation than var. fischerianum. Analysis of molecular variance ( AMOVA ) showed that most of the genetic diversity exists among populations for both varieties. Genetic differentiation among populations probably resulted from the highly selfing habits of both varieties. To conserve C. fischerianum var. molle genetically, preservation of only a part of the population is insufficient.     

Prominent genetic structure across native and introduced ranges of Pluchea indica,a mangrove associate,as revealed by microsatellite markers

阔苞菊(Pluchea indica)是一种红树林伴生植物,以其在原产地的药用特性和部分引入地的入侵性而闻名。本研究旨在评估阔苞菊在其分布范围内遗传变异的地理分布,确定影响其遗传结构的因素,并利用这些信息对阔苞菊在原产地和引入地的保护和管理策略提出建议。 我们以来自阔苞菊原产地(亚洲)和引入地(美国)的31个种群共348个个体的15个核微卫星位点数据对阔苞菊的遗传多样性和种群结构进行了评估。在大尺度范围以及局部区域两种空间尺度上对阔苞菊遗传变异的空间格局进行了探讨,并验证了以下假说：地理距离和自然地理屏障将影响种群结构并在空间尺度上产生不同程度的分化。研究结果表明,与所研究区域内的其它红树林物种的遗传多样性参数相比, 我们发现阔苞菊在种群水平上具有相对较高的遗传多样性以及在物种水平上具有明显的遗传分化。大多数阔苞菊种群显示杂合子缺失, 这主要是由于近交和有限的基因流所导致。在较大空间尺度上进行的种群结构分析显示,该物种自然分布范围内存在两个主要遗传谱系,中国的种群与印度尼西亚、马来西亚、新加坡、泰国、柬埔寨和菲律宾的种群分别属于不同的谱系,而美国的种群可能来自于中国的谱系。 此外,在局部区域范围内也同样检测到种群之间的遗传分化。大部分阔苞菊种群所表现出的遗传瓶颈效应强调了其具有本地灭绝的风险。基于上述研究结果,我们建议采用原位保护策略对阔苞菊进行管理,并开展对优先保护种群的保护行动以维持遗传多样性。