Lack of genetic variation of an invasive clonal plant Eichhornia crassipes in China revealed by RAPD and ISSR markers

Random amplified polymorphic DNAs (RAPDs) and inter-simple sequence repeats (ISSRs) markers were used to analyze genetic structure of six populations of invasive plant Eichhornia crassipes that were sampled from its introduced regions in Southern China. Using 25 RAPD primers and 18 ISSR primers, 172 RAPD bands and 145 ISSR bands were produced respectively. But no polymorphic band was detected either within population or among populations by both markers, indicating the genetic diversity of E. crassipes in Southern China is extremely low, and all populations most likely consist of the same genotype. This study suggested that some other adaptability related factors, other than the genetic diversity, are responsible to the E. crassipes rapid expansion in China.     

我国特有植物青檀遗传结构的ISSR分析

青檀是我国特有的第三纪残遗植物,是宣纸纤维来源的重要原材料,现已被列入国家Ⅲ级保护植物。采用简单序列重复区间扩增多态性(ISSR)标记技术,对采自27个地理种群的628个青檀个体的遗传多样性和遗传结构进行了检测。8对引物共得到66个清晰的扩增位点,其中多态性位点63个,多态性位点百分率为95.45%。分析结果表明,青檀在物种水平上具有很高的遗传多样性(PPB=95.45%、Ao=1.9545、Ae=1.5729、He=0.3335、I=0.4980、Hb=0.3437)。在种群水平上的遗传多样性(PPB=69.98%、Ao=1.6998、Ae=1.4449、He=0.2561、I=0.3793、Hb=0.2656)和种群间遗传分化水平(Gst=0.23,Ф_ST=0.25)均处于中等水平。华北地区(30°-42°N)和华南地区(22°-30° N)青檀的遗传多样性和遗传结构的差异并不显著。古老的起源历史、较广的分布范围、异交的繁育系统、风媒种子、长命的生活史以及华南和华北地形和植被的差异可能是导致青檀目前遗传格局的主要原因。结合叶绿体序列(cpDNA)序列的遗传结构特征对青檀的保护策略进行了探讨。     

Fine-grained spatial genetic structure in the bivalve Gemma gemma from Maine and Virginia (USA), as revealed by Inter-Simple Sequence Repeat markers

Gemma gemma is a small ovoviviparous bivalve distributed in shallow sand flats along the North American Atlantic and Gulf of Mexico coasts. Genetic variation in G. gemma was analysed by means of Inter-Simple Sequence Repeats (ISSRs) at the following levels: (i) between localities (Maine and Virginia), (ii) among 10-m-diameter patches within localities, and (iii) within patches. Thirty individuals/patch and three patches/locality were analysed. Individuals were genotyped for 67 ISSR polymorphic loci from five primers. The portion of the genetic variation found between localities (2%) was small compared to that found either among patches within localities (37%) or within patches (61%). ISSRs in G. gemma allowed the detection of significant differentiation at individual and patch levels. By contrast, a low degree of genetic variability was found between localities. The small-scale genetic heterogeneity does not follow a simple, consistent pattern. Our results contrast with the generally accepted rule that aplanic species are locally homogeneous and globally heterogeneous and teleplanic species are the inverse.     

High genetic differentiation and low genetic diversity in Incarvillea younghusbandii, an endemic plant of Qinghai-Tibetan Plateau,revealed by AFLP markers

Incarvillea younghusbandii Sprague (Bignoniaceae) is a perennial herbaceous plant endemic to Qinghai-Tibetan Plateau. As a species of medical and horticulture importance, I. younghusbandii is threatened by over exploitation and habitat fragmentation. In this study, we analyze the genetic diversity and population structure of I. younghusbandii using amplified fragment length polymorphism (AFLP) markers. Our data reveal very low levels of genetic diversity in seven natural populations across Tibet. Specifically, at population level, the average Nei's genetic diversity index (H_E) and Shannon's diversity index (I) were 0.063 and 0.096, respectively. In contrast, high genetic differentiation among populations (Gst = 0.6238, Φ_ST = 0.614) is detected. The results of Neighbor-joining cluster, PCO, and STRUCTURE assignment reveal consistent pattern, suggesting seven well-defined genetic groups that are concordant with their geographical origins. The possible mechanisms and implications of these findings for conservation are discussed.     

Genetic diversity of the endangered and endemic species Psathyrostachys huashanica natural populations using simple sequence repeats (SSRs) markers

Psathyrostachys huashanica Keng., a species endemic to China, is only distributed in Huashan Mountain in Shaanxi Province. It has been listed as “national first-class protected rare species.” In this study, the microsatellites of barley were used to analyze genetic diversity of P. huashanica populations sampled from three valleys (Huangpu, Xian and Huashan Valleys) in Mt. Huashan. A total of 33 alleles of 11 loci were detected from 266 individuals. The observed average number of alleles (A) is 2.75; the effective number of alleles (Ae) is 1.67. The percentage of polymorphic loci (PPB) is 58.33% in Huangpu Valley, 75% in Xian Valley, 83.33% in Huashan Valley, and the total PPB is 83.33%. About 77.6% of (F_ST = 0.324) genetic diversity was observed within the subpopulations. Genetic differentiation within each subpopulations was higher than that among the subpopulations. Mean genetic distance is 0.17 (range: 0.010–0.401). Correlation analysis detected significant correlation between genetic distance and vertical distance of altitude in Huashan Valley. Differentiation mainly occurred between the higher altitude subpopulations and the lower altitude subpopulations, suggesting that altitude might be the major factor that restricted the gene flow between different altitude subpopulations and resulted in differentiation of subpopulations.     

The extent of clonality and genetic diversity in the rare Caldesia grandis (Alismataceae): Comparative results for RAPD and ISSR markers

Genetic variation and clonal diversity of three natural populations of the rare, highly clonal marsh herb Caldesia grandis Samuelsson were investigated using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Both of the markers worked effectively in clone identification of C. grandis. RAPD markers detected more diversity than ISSR markers in the three populations examined. Of the 60 RAPD primers screened, seven produced highly reproducible bands. Using these primers, a total of 61 DNA fragments were generated with 52 (85.25%) being polymorphic indicating considerable genetic variation at the species level. Analysis of molecular variance (AMOVA) showed that a large proportion of genetic variation (81.5%) resided within populations, while only a small proportion (18.5%) resided among populations. With the use of 52 polymorphic RAPD markers, we were able to identify 127 genets among 342 samples from three populations. The proportion of distinguishable genets (PD: mean 0.37), Simpson's diversity index (D: mean 0.91), and evenness (E: mean 0.78) exhibited high levels of clonal diversity compared to other clonal plants. These results imply that sexual reproduction has played an important role at some time during the history of these populations. Nevertheless, the high level of diversity could have been also partially generated from somatic mutations, although this is unlikely to account for the high diversity generally found among C. grandis genets.     

Assessment of genetic diversity in Calamus thwaitesii BECC. (Arecaceae) using RAPD markers

Calamus thwaitesii Becc. is a potentially useful rattan found in the Western Ghats of India and Sri Lanka. The wild stock of this rattan species is greatly diminished due to overexploitation for the furniture industry and increasingly rare. Genetic diversity was estimated in 80 samples representing eight populations from the Western Ghats and Sri Lanka using Random Amplified Polymorphic DNA (RAPD) markers. RAPDs generated a total of 120 markers with 10 decamer primers, of which 85% were found to be polymorphic. The percentage of polymorphic loci varied from 40.00 to 60.83 and genetic distance between populations ranged from 0.0332 to 0.2777. Among the analysed populations, Goa was found to be genetically superior followed by Achenkovil, Sinharaja and Talakkaveri. Majority of the genetic diversity was distributed within populations (70.79%) and only (29.21%) among populations. Genetic relationships estimated by the unweighted pair-group method with arithmetic averaging (UPGMA) cluster analysis and principal co-ordinate analysis failed to separate Indian and Sri Lankan populations geographically into two distinct groups.     

Genetic diversity of wild populations of Rheum tanguticum endemic to China as revealed by ISSR analysis

Rheum tanguticum is an important but endangered traditional Chinese medicine endemic to China. The wild resources have been declining. Establishing the genetic diversity of the species would assist in its conservation and breeding program. Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population genetic structure in 13 wild populations of R. tanguticum from Qinghai Province. Thirteen selected primers produced 329 discernible bands, with 326 (92.94%) being polymorphic, indicating high genetic diversity at the species level. The Nei's gene diversity (He) was estimated to be 0.1724 within populations (range 0.1026–0.2104), and 0.2689 at the species level. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly within populations (71.02%), but variance among populations was only 28.98%. In addition, Nei's differentiation coefficients (G_st) was found to be high (0.3585), confirming the relatively high level of genetic differentiation among populations. Mantel test revealed a significant correlation between genetic and geographic distances (r = 0.573, P = 0.002), and the unweighted pair-group method using arithmetic average (UPGMA) clustering and Principal coordinates analysis (PCoA) demonstrated similar results. Meanwhile, the genetic diversity of R. tanguticum positively correlated with altitude and annual mean precipitation, but negatively correlated with latitude and annual mean temperature. This result might be an explanation that the natural distribution of R. tanguticum is limited to alpine cold areas. We propose conservation strategy and breeding program for this plant.     

High genetic differentiation and variation as revealed by ISSR marker in Pseudotaxus chienii (Taxaceae), an old rare conifer endemic to China

Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China, with a historically disjunct distribution pattern. Eleven populations sampled throughout its range were examined using inter-simple sequence repeats (ISSR) markers. Twenty primers generated 242 bands, and each detected polymorphic loci, with 73.14% of polymorphic loci overall. The estimate for θ^B was 0.5306, whereas G_ST and Φ_ST values were 0.6146 and 0.6401, respectively. 50.62% of the total diversity based on Shannon's index of phenetic diversity was attributed to among populations, which was consistent with the θ^B estimation. Compared with other conifers, remarkable genetic differentiation occurred among P. chienii populations. A Mantel test indicated that pairwise values of θ^B were significantly related with geographical distances between populations (r = 0.676, P = 0.001). In terms of the above results, conservation strategies and maintenance plans of P. chienii were recommended.     

四川西部濒危植物桃儿七遗传多样性的RAPD分析

桃儿七是一种具有重要药用价值的珍稀濒危植物。采用RAPD分子标记技术,对在四川西部地区的桃儿七7个自然种群的遗传多样性水平和遗传结构进行了分析。用12个RAPD引物对7个种群共140个样品进行了扩增,共得到111条清晰带,其中32条具有多态性,在物种水平上多态位点百分率(PPB)为28.83%,在种群内的多态位点百分率变动幅度为4.50%至16.22%。同其它一些濒危植物相比,桃儿七种群具有较低的遗传多样性(He=0.0622,Ho=0.0987)。7个自然种群间出现了很强的遗传分化,分化指数接近70%。种群间的基因流低(Nm=0.2240)。造成上述结果的可能原因是与桃儿七的繁育方式和有限的基因流等因素有关。应将遗传多样性相对较高的松潘县牟尼沟种群作为原位保护的核心种群进行保护,尽量保护所有现有种群。     

Genetic diversity of Sinojackia dolichocarpa (Styracaceae), a species endangered and endemic to China,detected by inter-simple sequence repeat (ISSR)

Sinojackia dolichocarpa, a species endangered and endemic to China, is distributed only in the regional area of Shimen and Sangzhi in Hunan Province. Inter-simple sequence repeat (ISSR) markers were used to investigate the genetic diversity within and among the four natural populations of S. dolichocarpa. Leaf samples were collected from 84 individuals. Thirteen ISSR primers selected from 80 primers gave rise to 137 discernible DNA bands of which 100 (72.99%) were polymorphic. On average each primer gave rise to 10.5 bands including 7.7 bands with polymorphic profile. At the species level, high genetic diversity was detected (PPB: 72.99%; H_E: 0.2255; Ho: 0.3453). However, relatively low genetic diversity existed within populations. Population in Maozhuhe (MZH) exhibits the greatest level of variability (PPB: 40.38%, H_E: 0.1566, Ho: 0.2330), whereas the population in Jingguanmen (JGM) finds its own variability at the lowest level (PPB: 30.66%; H_E: 0.1078; Ho: 0.1601). A high level of genetic differentiation among populations was revealed by Nei's gene diversity statistics (45.30%), Shannon's information measure (45.24%) and analysis of molecular variance (AMOVA) (52.88%). The main factors responsible for the high level of differentiation among populations are probably related to the selfing reproductive system and the isolation of populations. The strong genetic differentiation among populations indicates that the management for the conservation of genetic variability in S. dolichocarpa should aim to preserve every population.     

Highly differentiated populations of the narrow endemic and endangered species Primula cicutariifolia in China,revealed by ISSR and SSR

The perennial herb Primula cicutariifolia Pax is an endangered and endemic species with narrow distribution in eastern Anhui and Zhejiang provinces of China. In this study, the levels of genetic variation and the pattern of genetic structure in five natural populations of P. cicutariifolia were assessed by inter-simple sequence repeats (ISSR) and simple sequence repeat (SSR) markers. Both markers revealed that there was remarkably low genetic variation within populations (e.g., H_e = 0.19 and 0.18, for ISSR and SSR respectively) and high differentiation among populations (G_ST = 0.714 and 0.611; Φ_ST = 0.698 and 0.599, for ISSR and SSR respectively). The level of population genetic diversity was correlated to population size only detected by ISSR markers. The genetic structure of P. cicutariifolia may be explained by limited gene flow that was caused by habitat fragmentation and limited seeds and pollen dispersal ability, self breeding system and biennial life form. To protect and avoid disappearance of P. cicutariifolia, much more attentions should be paid to protect all the remnant populations and their habitats, and three management units, i.e. Tianmushan, Damodao, and Panan units, were proposed.     

台湾海峡鲐鱼种群遗传结构

以往研究表明,台湾海峡的鲐鱼分属2个地理种群,即东海种群和闽南——粤东地方种群.为研究这2个种群的遗传结构,对鲐鱼闽东(30尾)和闽南(30尾)种群进行了AFLP分析,8对选择性引物在2个种群60个个体中,共扩增出497个位点,其中多态位点343个.闽东和闽南种群的多态位点比例、Nei遗传多样性指数和Shannon遗传多样性指数分别为57.75％、64.59％,0.1779、0.2123,0.2725和0.3228,2个种群的遗传多样性处于同一水平.与其他鱼类对比显示,台湾海峡鲐鱼种群的遗传多样性水平高.生境广及生命周期短被认为是台湾海峡鲐鱼具有较高遗传变异水平的原因;基因分化系数Gst、Shannon遗传多样性指数和AMOVA分析均显示鲐鱼的遗传变异主要来源于种群内,而种群间无明显的遗传分化.Nm显示2个种群间基因交流频繁.种群的显性基因型频率分布显示2个种群有基本相同的种群遗传结构.结果表明,鲐鱼闽东和闽南种群间无明显的遗传差异.幼体较强的扩散能力、海洋环流及洄游特性可能是造成台湾海峡鲐鱼种群间遗传同质性较高的原因.     

舟山群岛四个养殖獐种群遗传多样性和遗传结构

基于ISSR分子标记技术,对来自舟山群岛4个獐(Hydropotes inermis)养殖种群的遗传多样性和遗传结构进行了分析.26条ISSR引物共扩增出286个可分析位点,多态位点百分比(PPL)为64.34％.獐物种水平上的Nei's遗传多样性指数(H)为0.210,Shannon's多态信息指数(Ⅰ)为0.318,各种群的H介于0.157-0.190之间,I在0.228-0.278之间,与已报道的ISSR标记在其它动物物种中的应用结果相比,其遗传多样性较为丰富.Structure软件分析结果显示,所有个体根据遗传信息的不同可以被分为4个组群,每个养殖场内的个体基本上都在各自独立的组群中,这与地理区域的划分相似.另外发现各养殖场獐种群间已表现出了较大的遗传分化(Gst=0.163).同时,为了解各种群间的遗传关系,计算了各种群间的Nei's遗传距离,结果显示舟山种群(ZS)和秀山种群(XS)之间的遗传距离最近,为0.045,而岱山种群(DS)和朱家尖种群(ZJJ)间的遗传距离最大,为0.066.基于以上结果,建议加强不同岛屿种群间的个体交流,特别是朱家尖种群(ZJJ)与其它种群间的交流.     

Relationships between Bambusa species (Poaceae,Bambusoideae) revealed by random amplified polymorphic DNA

RAPD (random amplified polymorphic DNA) molecular markers were used to investigate relationships between a sample of Bambusa species from South Eastern China that have been placed in Bambusa or in several segregate genera, Dendrocalamopsis, Leleba, Lingnania, Neosinocalamus and Sinocalamus by different authors. On the resultant neighbor-joining tree, a thorny core Bambusa cluster was distinguished, as was a Lingnania group, and a cluster of Dendrocalamus species with more capitate inflorescences. However, Leleba was found to be a polyphyletic group in the present study.     

Spatial and temporal population genetic variation and structure of Nothotsuga longibracteata (Pinaceae), a relic conifer species endemic to subtropical China

Nothotsuga longibracteata, a relic and endangered conifer species endemic to subtropical China, was studied for examining the spatial-temporal population genetic variation and structure to understand the historical biogeographical processes underlying the present geographical distribution. Ten populations were sampled over the entire natural range of the species for spatial analysis, while three key populations with large population sizes and varied age structure were selected for temporal analyses using both nuclear microsatellites (nSSR) and chloroplast microsatellites (cpSSR). A recent bottleneck was detected in the natural populations of N. longibracteata. The spatial genetic analysis showed significant population genetic differentiation across its total geographical range. Notwithstanding, the temporal genetic analysis revealed that the level of genetic diversity between different age class subpopulations remained constant over time. Eleven refugia of the Last Glacial Maximum were identified, which deserve particular attention for conservation management.     

利用RAPD标记分析濒危植物白豆杉种群的遗传结构

以我国特有的濒危裸子植物白豆杉为材料,采用RAPD标记对其分布于浙江、江西、湖南和广西的11个天然种群予以检测,通过贝叶斯法估测了种群的遗传分化程度,并和由其他算法得出的结果进行了比较.求出的θ^B（Hickory）、GST（Nei）及φST（AMOVA）值分别为0.5018、0.5865和0.5436;而经由Shannon指数计算出的种群间遗传多样性所占比例为0.4839,同贝叶斯法估计出的结果最为接近.和其他松杉类植物相比,白豆杉种群间发生了极其显著的遗传分化,这可能是因为：（1）种群长期处于星散分布状态;（2）雌雄异株,而生于林下的雌株经常不能正常受粉;（3）种群取样跨越的地理范围宽广.Mantel检验表明,种群间的遗传分化程度和地理距离之间显著相关（r=0.719,P=0.003）.此外还发现白豆杉的遗传变异水平偏低,推测瓶颈效应和遗传漂变对小种群的作用是造成这一后果的重要因素.对白豆杉种群的保育和管理提出了建议.     

Genetic structure of Pyrenophora teres net and spot populations as revealed by microsatellite analysis

The population structure of the fungal pathogen Pyrenophora teres, collected mainly from different regions of the Czech and Slovak Republics, was examined using a microsatellite analyses (SSR). Among 305 P. teres f. teres (PTT) and 82 P. teres f. maculata (PTM) isolates that were collected, the overall gene diversity was similar (? = 0.12 and ? = 0.13, respectively). A high level of genetic differentiation (F_ST = 0.46; P < 0.001) indicated the existence of population structure. Nine clusters that were found using a Bayesian approach represent the genetic structure of the studied P. teres populations. Two clusters consisted of PTM populations; PTT populations formed another seven clusters. An exact test of population differentiation confirmed the results that were generated by Structure. There was no difference between naturally infected populations over time, and genetic distance did not correlate with geographical distance. The facts that all individuals had unique multilocus genotypes and that the hypothesis of random mating could not be rejected in several populations or subpopulations serve as evidence that a mixed mating system plays a role in the P. teres life cycle. Despite the fact that the genetic differentiation value between PTT and PTM (F_ST = 0.30; P < 0.001) is lower than it is between the populations within each form (F_ST = 0.40 (PTT); F_ST = 0.35 (PTM); P < 0.001) and that individuals with mixed PTT and PTM genomes were found, the two forms of P. teres form genetically separate populations. Therefore, it can be assumed that these populations have most likely undergone speciation.     

Mating system and population genetic structure of Bruguiera gymnorrhiza (Rhizophoraceae), a viviparous mangrove species in China

In order to explain the diversity patterns and develop the conservation strategies, the population genetic structures and the mating systems of Bruguiera gymnorrhiza from the coastlines of south China were investigated in this study. The mating system parameters were analyzed using progeny arrays for allozyme markers. The multilocus outcrossing rates (tm) ranged from 0.845 (Fugong) to 0.267 (Dongzhai harbor). High allozyme variations within the five collected populations were determined and compared with the published data of other plant species with the mixed mating systems. At species level, the percentage of polymorphic loci (P) was 80%, the average number of alleles per locus (A) was 2.440, and the heterozygosity (He) was 0.293. The total gene diversity within each population (H_S = 0.2782) and the coefficient of genetic differentiation (G_ST = 0.0579) among the populations were estimated. On the basis of this population genetic structure, it is suggested that the gene flow (Nm = 3.85) is quite high, which is possibly related to its water-dispersed hypocotyls. It is also suggested that the mating system of this species is of mixed mating.     

Genetic variations among mulberry genotypes (Morus alba) as revealed by Random Amplified Polymorphic DNA (RAPD) markers

Turkey is one of the most important mulberry fruit producers in the world. In particular, in Eastern and Inner part of Turkey, mulberry fruits are processed into several products such as `Mulberry Pekmez', `Mulberry Pestil', `Mulberry Kome' etc. Therefore, mulberry fruits give higher economic returns thus have greater employment potentials in Turkey. In order to improve the yield and fruit quality through breeding, the genetic variations and relationships among 15 selected white mulberry genotypes (Morus alba L.) were evaluated using Random Amplified Polymorphic DNA (RAPD). A total of 101 DNA markers were generated by 16 random primers, with an average of 6.3 easily detectable markers per primer. Several RAPD markers showed unique patterns of mean frequency that differed among the white mulberry genotypes. The distance matrix showed that the highest genetic distance (0.902) was between EMS13 and EMS8 and the least (0.413) was between EMS12 and EMS15. According to the results, RAPD analysis can be used for the characterization and grouping of mulberry genotypes. The genetically divergent genotypes identified from this study would be of much use in the future breeding program.