中华稻蝗不同地理种群遗传多样性的AFLP分析

为研究中华稻蝗种群遗传多样性和遗传结构, 文章对我国7省市的7个中华稻蝗种群进行AFLP分析。选取7对引物扩增128个个体, 共产生336条带, 多态性条带292条, 占86.90%。结果表明: 中华稻蝗种群具有较高的遗传多样性水平, 其中海南万宁种群的遗传多样性高于其他各种群。Mantel检验(r=0.27, P=0.89)表明中华稻蝗各种群遗传距离与地理距离间没有显著相关性。种群间具有明显的遗传分化现象。UPGMA(Unweighted pair group method average)聚类分析显示, 7个中华稻蝗种群按地理距离分为3支: 北方北京昌平、山西太原和山东济宁为一支; 南方陕西汉中、湖南长沙和广西来宾为一支; 海南万宁单独为一支。上述结果以及PCA(Principal component analysis)分析均表明由于地理隔离中华稻蝗种群显示出明显的南北分化和岛屿大陆种群遗传分化现象。     

柴达木地区野生黑果枸杞种群遗传多样性的AFLP分析

采用扩增片段长度多态性(AFLP)分子标记技术对青海省柴达木地区5个野生黑果枸杞(Lycium ruthenicum)种群的120份样品的遗传多样性进行分析。结果表明: 柴达木地区野生黑果枸杞具有很高的遗传多样性, 9对选扩引物共得到1691条清晰条带, 其中多态性条带1678条, 多态性变异率为99.23%, 种群间的有效等位基因数为1.4712, Nei’s基因多样性为0.3245, Shannon信息指数为0.4367。分子方差分析(AMOVA)结果表明: 柴达木地区5个黑果枸杞种群的遗传变异主要存在于种群内部(92%), 种群间的遗传分化较小(8%, 遗传分化系数0.08)。黑果枸杞种群间的遗传相似系数介于0.9709-0.9922之间, 平均值为0.9835。种群间的聚类及Mantel检验(γ = 0.3368, p = 0.8064)均表明柴达木地区黑果枸杞种群地理距离与遗传距离之间的相关性不明显; 黑果枸杞个体间的聚类表明同一种群的个体不能完全聚在一起。对同一种源的遗传多样性分析发现, 诺木洪奥斯勒草场的种源内部的遗传变异更为丰富, 这或许可以推断诺木洪可能为柴达木地区野生黑果枸杞种质资源的中心产区。     

拟环纹豹蛛不同地理种群遗传多样性的AFLP标记研究

为查明拟环纹豹蛛Pardosa pseudoannulata不同地理种群的遗传多样性机制,应用AFLP技术对6个拟环纹豹蛛地理种群的遗传多样性进行了研究分析。8对引物组合扩增出1 038个AFLP条带,其中多态性条带占86.622%,全部个体显示了各自独特的AFLP图谱。AFLP标记的遗传多样性分析结果表明： 拟环纹豹蛛无论在物种水平(P=86.62%,H=0.2622,I=0.3101),还是在种群水平（P=73.0%,H=0.2155,I=0.2554）都表现出较高的遗传多样性。其中湖南长沙雷锋镇种群内遗传变异最大,云南高黎贡山福贡种群内遗传变异最小,华南北部（湖南、湖北、江西）地区拟环纹豹蛛遗传多样性明显高于华南南部（云南、海南）种群。据种群变异来源分析,有35.77%的遗传变异来自种群间,64.23%的变异来源于种群内（N_m=0.898）,不同地理种群显示出一定的遗传分化。分析认为海拔是影响拟环纹豹蛛遗传分化的重要因素,这为进一步明确我国稻田狼蛛优势种群在农药胁迫下的遗传适应性机制提供了实验依据。     

中国二化螟不同地理种群的AFLP遗传分析

利用AFLP标记对中国11省13个二化螟Chilo suppressalis(Walker)地理种群进行遗传多态性分析,以揭示不同区域种群间遗传分化,为建立较准确的二化螟发生区划及区域治理对策提供新的依据。选取3对引物,共扩增出445个位点,其中多态性位点数为386,多态性比率为86.8%。种群间分化系数(Gst)为0.74,基因流仅为0.176;13个地理种群间遗传一致度较高,均大于0.67。遗传距离聚类分析表明,二化螟13个地理种群可区分为4类,其中淮北平原类(赣榆、阜宁、阜南)、东南山区类(鄞县、闽侯)、荆湘川类(荆州、邵阳、德阳)三类种群分别具有较一致的地理气候特征或相对较近的距离。研究还表明,与其他测试种群的遗传距离普遍较大、相对孤立的地理种群,其聚类结果有一定的随机性,因此,取样点较多、且样点分布较均匀的聚类分析结果才有较高可信度。     

Genetic structure in Orchesella cincta (Collembola): strong subdivision of European populations inferred from mtDNA and AFLP markers

Population genetic structure is determined both by current processes and historical events. Current processes include gene flow, which is largely influenced by the migration capacity of a species. Historical events are, for example, glaciation periods, which have had a major impact on the distribution of many species. Species with a low capacity or tendency to move about or disperse often exhibit clear spatial genetic structures, whereas mobile species mostly show less spatial genetic differentiation. In this paper we report on the genetic structure of a small, wingless arthropod species (Orchesella cincta: Collembola) in Europe. For this purpose we used mtDNA COII sequences and AFLP markers. We show that large genetic differences exist between populations of O. cincta, as expected from O. cincta's winglessness and sedentary lifestyle. Despite the fact that most variability was observed within populations (59%), a highly significant amount of AFLP variation (25%) was observed between populations from northwestern Europe, central Europe and Italy. This suggests that gene flow among regions is extremely low, which is additionally supported by the lack of shared mtDNA alleles between regions. Based on the genetic variation and sequence differences observed we conclude that the subdivision occurred long before the last glaciation periods. Although the populations still interbreed in the lab, we assume that in the long term the genetic isolation of these regions may lead to speciation processes.     

资源昆虫角倍蚜遗传多样性及遗传分化的AFLP分析

本研究采用AFLP分子标记技术对资源昆虫角倍蚜Schlechtendalia chinensis 6个种群共102个个体的样本进行遗传多样性分析, 探讨角倍蚜主要分布区不同种群之间的遗传分化及其变异程度, 为合理利用和保护该经济昆虫提供分子方面的证据。结果表明: 经过摸索实验筛选出的4对选择性扩增引物共扩增条带126条, 多态性条带比例为100%, 种群多态性位点比例介于23.81%～66.67%之间; Nei's基因多样性指数介于0.0942～0.1980之间; Shannon's多样性数介于0.1381～0.3027之间; AMOVA分析显示57.99%的变异来源于种群内, 42.41%的变异来源于种群间（P<0.01）; 总群体的Fst值为0.4242; NJ聚类树显示角倍蚜6个种群共形成两个大的聚类簇, 阳雀、丹寨和汉中种群聚为一支, 安县、竹山和龙胜3个种群聚为另一支。总体上, 角倍蚜种内的遗传多样性较低, 而种群间的遗传分化较大, 遗传距离与地理距离之间没有显著的相关关系（P>0.05）。     

野生扁蓿豆种质资源AFLP遗传多样性的分析

本研究采用AFLP标记对河北省、辽宁省、吉林省、山西省、内蒙古自治区和西藏自治区的10份野生扁蓿豆居群进行遗传多样性分析。从64对AFLP引物组合中,筛选出8对扩增条带清晰、多态性高的引物组合,8对引物共扩增出640个条带,其中多态性条带有472个,多态性位点百分率为73.8%;Nei's基因多样性指数平均为0.157,Shannon's多态性信息指数平均为0.099;居群间遗传相似系数(GS)平均值为0.827。聚类和主成分分析可将10个扁蓿豆居群聚为3大类,结果与居群的地理分布大致相符,呈一定的地域性分布规律。由此可见,AFLP分子标记研究结果能较好地揭示扁蓿豆居群间的遗传多样性。对我国各地的野生扁蓿豆资源的广泛收集、评价和基因资源的保护有重要的意义。     

Clonal diversity in a Rhododendron ferrugineum L. (Ericaceae) population inferred from AFLP markers

In the European Alps, Rhododendron ferrugineum can constitute dense populations with almost 100% of cover. The developmental pattern by layering and the resulting complexity of population structure make it difficult to identify distinct clones even by excavation. Therefore genotypic structure of a R. ferrugineum population, in the French Alps, was inferred from AFLP markers. In a first step, we analysed 400 samples using AFLP profiles generated by one selective primer pair. Seventeen bands out of 25 were polymorphic (68%). We identified a total of 32 multilocus genotypes. In a second step, the 32 genotypes were verified by applying two additional primer pairs to the two most distant samples from each genotype. The mean similarity (proportion of band sharing) between pairs of clones was 0.85 (range from 0.52 to 0.94). The spatial distribution of clones showed that vegetative spreading mainly occurred down a slope. Based on an annual shoot mean growth of 2.6 cm/year and the size of the widest clone, we estimated the age of the oldest individual to be at least 300 years. A single genotype can occupy a large surface and sometimes form a dense patch, suggesting that this species adopts a phalanx growth form with limited intermingling of some genets.     

Genetic diversity and variance of Stentor coeruleus (Ciliophora: Heterotrichea) inferred from inter-simple sequence repeat (ISSR) fingerprinting

We used inter-simple sequence repeat fingerprinting to analyze the genetic structure of 16 populations of Stentor coeruleus from three lakes and three ponds in China. Using 14 polymorphic primers, a total of 99 discernible DNA fragments were detected, among which 76 (76.77%) were polymorphic, indicating median genetic diversity in these populations. Further, both Nei's gene diversity (h) and Shannon's information index (I) between the different populations revealed a median genetic diversity. At the same time, gene flow was interpreted to be low. The main factors responsible for the median level of diversity and low gene flow within populations are probably due to a low frequency of sexual recombinations. Analysis of molecular variance showed that there was high genetic differentiation among the five water bodies. Both cluster analysis and a nonmetric multidimensional scaling analysis suggested that genotypes isolated from the same locations displayed a higher genetic similarity than those from different ones, separating populations into subgroups according to their geographical locations. However, there is a weak positive correlation between the genetic distance and geographical distance.     

基于AFLP标记的山东省5个野核桃群体的遗传多样性分析

利用AFLP分子标记,对分布于山东省内5个样地(泰山鹁鸽崖、鲁山核心区边缘、崂山北九水、昆嵛山南天门和泰山佛爷寺)的46个野核桃(Juglans cathayensis Dode)单株的遗传多样性进行了分析,并采用聚类分析方法探讨了它们的遗传关系.结果表明:用8对PstI/ MseI系列引物组合从46个单株中共扩增出1 034条带,其中多态性条带1 005条,多态性条带百分率达97.20％;每对引物可扩增出113 ～ 154条多态性条带,平均每对引物可扩增出125.6条多态性条带.在这些条带中包含174条特异性条带(其中有19条缺失条带),通过特异性条带可鉴别出91.3％的野核桃单株.5个野核桃群体的多态性条带百分率(PPB)、观测等位基因数(Na)、有效等位基因数(Ⅳe)、Nei,s基因多样度(H)和Shannon's信息指数(I)分别为50.57％ ～ 63.51％、1.505 7～1.635 1、1.273 5 ～ 1.300 4、0.163 2～0.181 9和0.249 1 ～0.281 3,PPB、Na、Ne、H和I的平均值分别为55.23％、1.552 3、1.284 3、0.169 6和0.259 4,表明野核桃群体遗传多样性较高、遗传变异较为丰富.46个单株的遗传相似性系数为0.536 8 ～0.8645,平均值为0.624 9.聚类分析结果显示:在遗传相似性系数0.66处,可将46个单株分成7组,其中部分来源于同一产地的单株没有聚在同一组中,表明这些野核桃单株的遗传关系与其地理分布不完全一致.     

Genetic diversity and structure of natural Pinus tabulaeformis populations in North China using amplified fragment length polymorphism (AFLP)

Chinese pine (Pinus tabulaeformis carr.), endemic to China, is a conifer species with extensive and fragmented distribution in North China. In this study, the genetic diversity and structure of 20 natural populations of this species were investigated using amplified fragment length polymorphism (AFLP) markers. A total of 445 fragments were revealed with 8 pairs of primers, 379 (85.17%) of which were polymorphic. A moderate level of genetic diversity was detected at the species level (Shannon's information index I = 0.356, Nei's gene diversity H_E = 0.271) and at the population level (I = 0.219, H_E = 0.206). Most of genetic variation was within populations while a considerable level of genetic differentiation was detected (G_ST = 0.352, Ф_ST = 0.304). The high differentiation could be attributed to the complex and fragmented habitats, and a limited gene flow among populations (N_m = 0.572). The Mantel test indicated that there was significant correlation (r = 0.455, P < 0.001) between Nei's genetic distance and geographical distance among all the populations. The results suggested that proper countermeasures should be taken to prevent the habitat further deterioration and maintain the genetic diversity of this species.     

福寿螺3个地理群体遗传多样性的AFLP分析

应用AFLP分子标记技术对我国江苏苏州、福建漳州和广东珠海3个地理群体福寿螺进行了遗传多样性分析.8对选择性引物在3个群体的90个个体中,共扩增出382个位点,多态位点369个.江苏、福建和广东3个福寿螺群体的多态位点比率和Shannon's指数分别为84.82%、85.08%、79.06%,0.4259、0.4308、0.4079;表明3个群体遗传多样性在同一水平上.不同地理来源的福寿螺个体归群分析聚成3类,与地理分布一致,表明3个地理群体间已出现遗传分化,广东群体和福建群体首先聚在一起,再与江苏群体聚类.Shannon's指数和AMOVA分析估算均显示福寿螺的遗传变异主要来自于群体内个体间.综上所述,3个福寿螺群体具有丰富的遗传多样性而且已形成相对独立的遗传结构;并找到了3个群体间遗传特异性AFLP标记,可用于群体间分子鉴定和辅助分类.     

用AFLP技术分析紫茎泽兰的遗传多样性

利用AFLP技术,选择EcoRI/MesI这一酶切组合,应用6对E 3/M 3引物组合进行选择性扩增,检测了24个地区的紫茎泽兰种群的基因组DNA多态性。共扩增出509个遗传位点,其中392个多态位点,多态率为77.01%。有效等位基因数(Ne)为1.50,Nei’s基因多样性指数(H)为0.29,Shannon信息指数(I)为0.42。并通过Jaccard的方法将电泳带矩阵转化为遗传相似性系数矩阵,进行了UPGMA聚类分析。结果表明:被检测的24个紫茎泽兰种群遗传多样性丰富;丰富程度与入侵定植时间有关,最早受紫茎泽兰入侵的云南省遗传多样性最丰富,变异最大,大致分为9个类群,紫茎泽兰的遗传基因可能对该省多样的气候条件或生境产生了明显的适应性变化;新入侵地区的则遗传多样性相对较低,并与云南省临近地区具有明显的种源地的地源性亲缘关系。子实的风媒传播是紫茎泽兰入侵的主要途径,样点间均具有明显的地源性亲缘关系;水媒也可能是该草传播的途径之一。紫茎泽兰可能首先从缅甸、越南、老挝经风媒入侵我国云南南部,逐渐扩散入侵中北部,又从云南北部和东部传入四川、贵州、广西、湖北等省。     

AFLP fingerprinting and genotypic characterization of some serovars of Bacillus thuringiensis

Amplified fragment length polymorphism (AFLP)-based fingerprinting of 24 serovars of Bacillus thuringiensis (Bt) representing different serotypes was performed using 13 EcoR1 (+2) and Mse1 (+3) primer combinations for genotypic characterization. A high degree of polymorphism was established among the Bt serovars. A total of 1107 fragments ranging from 30–850 bp were generated out of which 1106 were polymorphic. Discrimination rates of different primer combinations at various band levels (1–5) among different Bt serovars were more than 90%. Cluster analysis revealed very low similarity values, ranging from 7–50%, among the Bt serovars indicating their remarkable genetic diversity. AFLP analysis establishes the molecular relatedness between the serovars and serotypes. This revised version was published online in July 2006 with corrections to the Cover Date.     

Assessment of DNA fingerprinting for determining genetic diversity in sheep populations

Genomic DNA, prepared from 12 animals from four sheep flocks, was digested with either HaeIII or Hin fI and probed with three DNA fingerprinting probes. Mean DNA fingerprint band sharing and band frequency calculated for each flock were used to estimate genetic diversity. Each of the DNA fingerprinting systems showed the same trend in diversity within the sampled flocks, and greater diversity between the flocks than within the flocks. DNA fingerprinting therefore provides a useful measure of genetic diversity in sheep.     

Genetic diversity of Ranunculus acris L. (Ranunculaceae) populations in relation to species diversity and habitat type in grassland communities

Correlates between genetic diversity at intra- and interpopulation levels and the species diversity in plant communities are rarely investigated. Such correlates may give insights into the effect of local selective forces across different communities on the genetic diversity of local plant populations. This study has employed amplified fragment length polymorphism to assess the genetic diversity within and between 10 populations of Ranunculus acris in relation to the species diversity (richness and evenness) of grassland communities of two different habitat types, 'seminatural' and 'agriculturally improved', located in central Germany. Within-population genetic diversity estimated by Nei's unbiased gene diversity (HE) was high (0.258-0.334), and was not correlated with species richness (Pearson's r = -0.17; P = 0.64) or species evenness (Pearson's r = 0.15; P = 0.68) of the plant communities. However, the genetic differentiation between R. acris populations was significantly correlated with the difference in species evenness (Mantel's r = 0.62, P = 0.02), but not with difference in species richness of plant communities (r = -0.17, P = 0.22). Moreover, we also found that populations of R. acris from the 'seminatural' habitat were genetically different (amova, P < 0.05) from those in 'agriculturally improved' habitats, suggesting that gene flow between these habitat types is limited. The results reported in this study may indicate that habitat characteristics influence the genetic diversity of plant species.     

Genetic diversity of Hibiscus tiliaceus (Malvaceae) in China assessed using AFLP markers

Amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic variations within and among nine natural populations of Hibiscus tiliaceus in China. DNA from 145 individuals was amplified with eight primer pairs. No polymorphisms were found among the 20 samples of a marginal population of recent origin probably due to a founder effect. Across the other 125 individuals, 501 of 566 bands (88.5%) were polymorphic, and 125 unique AFLP phenotypes were observed. Estimates of genetic diversity agreed with life history traits of H. tiliaceus and geographical distribution. AMOVA analysis revealed that most genetic diversity resided within populations (84.8%), which corresponded to results reported for outcrossing plants. The indirect estimate of gene flow based on phiST was moderate (Nm=1.395). Long-distance dispersal of floating seeds and local environments may play an important role in shaping the genetic diversity of the population and the genetic structure of this species.     

Genetic diversity and population structure of the red stingray,Dasyatis akajei inferred by AFLP marker

To examine population genetic diversity and variation of the red stingray Dasyatis akajei, samples from 1 freshwater region and 6 coastal localities within its distribution range were analyzed by using amplified fragment length polymorphism (AFLP) technology. A total of 207 loci were identified by 4 primer combinations from 87 individuals, 174 of which were polymorphic (84.1%). A high level of Nei's gene diversity was observed with the overall value of 0.230 ± 0.179. No significant genealogical clusters associated with sampling sites were revealed on the UPGMA tree. Both analysis of molecular variance (AMOVA, Φ_ST = 0.085, P = 0.00) and pairwise F_ST indicated significant genetic differentiation among four marine samples. However, no particular genetic differentiation was detected between marine and the limited sampling freshwater populations (AMOVA, Φ_CT = 0.056, P > 0.05). Except for the TZ vs. WZ (5.193), the gene flow estimates (N_m) demonstrated the effective immigrants were 1.918-2.976, suggesting low level dispersal between pairwise marine populations. Species-specific habits (demersal and sluggish habits) are probably responsible for the population structuring.     

Genetic diversity and species-specific PCR-based markers from AFLP analyses of Thai bananas

A large amount of banana genetic resource has been found in Thailand which is believed to be one of the centers of its origins. To assess genetic diversity and determine genetic relationships of edible bananas in Thailand, 110 accessions of banana species and cultivars collected from villages and natural locations were investigated. UPGMA clustering of numerical data from Amplified Fragment Length Polymorphism (AFLP) patterns showed two large groups which corresponded to genome designations of Musa acuminata (AA) and Musa balbisiana (BB), the known ancestors of most edible cultivars. The AFLP data suggested that among Thai bananas, AA and AAA cultivars were closely related to M. acuminata subsp. malaccensis, while some of ‘B’ genome contained ones closely related to wild M. balbisiana in Thailand and some may have been imported. Eight species-specific PCR-based primer pairs, generated from the AFLP results clearly identify ‘A’ and ‘B’ genomes within cultivars and hybrids. The analyses were useful to readily and easily infer progenitors of these cultivars and pronounce wide genetic diversity of the bananas in Thailand.     

光皮桦6个南方天然群体的遗传多样性

为揭示中国特有珍贵用材树种光皮桦(Betula luminifera)天然群体的遗传多样性和遗传结构, 采用AFLP分子标记, 分析了采自浙江、福建、江西、广西和贵州5个省区6个天然群体的120份样品。9对引物获得了355个位点, 其中多态性位点323个。分析结果表明光皮桦天然群体具有较高的遗传多样性, 多态位点百分率(PPL)达90.99%, 各群体的PPL和Nei’s基因多样性(h_j)分别为93.20-98.60%和0.3143-0.3645; 总群体遗传多样性指数(H_t)为0.3616, 群体间遗传分化系数(F_st)为0.0650, 群体间总的基因流较高(N_m= 3.5962)。AMOVA分析表明群体间的遗传变异占总变异的11.49%, 浙江临安群体和贵州修文群体间的遗传距离最大(0.0665), 江西龙南群体和广西龙胜群体间的遗传距离最小(0.0173), 且遗传结构分析显示这两个群体的部分个体可能来自同一近祖。Mantel检测发现, 群体间的遗传距离与地理距离没有显著相关性(r = 0.423, P = 0.113), 而与两两群体所在地的均温差呈显著相关(r = 0.449, P = 0.017)。结合群体实地调查, 可以得出光皮桦天然群体的遗传多样性和遗传结构的形成不仅与其广域分布、自然杂交、种子特性以及生活史有关, 而且与群体被人为砍伐、生境片断化等因素有重要关系。基于上述结果我们提出了光皮桦天然种群的保护策略。