High Genetic Differentiation of Hippophae rhamnoides ssp. yunnanensis (Elaeagnaceae), a Plant Endemic to the Qinghai-Tibet Plateau

RAPD markers were used to detect genetic diversity and population genetic differentiation of Hippophae rhamnoides ssp. yunnanensis, a sea buckthorn endemic to the Qinghai-Tibet plateau. The genetic parameters of percentage of polymorphic bands (92.86%), Nei’s gene diversity (h, 0.255), and Shannon’s index (I, 0.397) indicated high genetic diversity in this subspecies. The subpopulation differentiation suggested that 45.9% of genetic variation was among populations. High genetic differentiation among populations was also detected using AMOVA (47.02%). The main factors responsible for high genetic differentiation are probably related to natural geographic barriers among populations, gene drift, and limited gene flow caused by restricted pollen flow and seed flow. A Mantel test indicated that geographic distances were significantly correlated with genetic distances. The UPGMA phenogram based on Nei’s unbiased genetic distances and the result of three-dimensional model plots performed by principal coordinate analysis also supported the correlation. Altitude, however, did not have any clear effect on genetic differentiation.     

Genetic Diversity Within and Among Lepidium draba Populations from Eastern Anatolia Based on RAPD Analysis

Genetic variation and structure of six natural populations of Lepidium draba L. from Eastern Anatolia were assessed using random amplified polymorphic DNA (RAPD) markers. For RAPD analysis, 12 primers generated 218 reproducible bands across the six populations analyzed, of which 73 bands (33.3%) were polymorphic. The mean Nei’s gene diversity value for all six populations was 0.1771. Shannon’s information index varied with population (0.2278–0.3082), averaging 0.2608. Analysis of molecular variance (AMOVA) showed that genetic diversity was greater within populations (58.66%) than among populations (30.68%). In addition, the variation between groups was 10.33%. The genetic differentiation among populations (G _ST) was 0.3210, indicating that most genetic diversity occurs within populations. Gene flow (Nm) was low, at only 0.5288.     

Genetic variation within the endangered quillwort Isoëtes hypsophila (Isoetaceae) in China as evidenced by ISSR analysis

The genetic diversity of 56 individuals of Isoëtes hypsophila Hand.-Mazz. from China was investigated by ISSR. Twelve primers were screened from 65 primers, and a total of 119 DNA fragments were scored, of these, 82% were polymorphic bands, which indicated that high levels of genetic variation existed in the natural populations. Genetic diversity varied greatly among populations with the percentage of polymorphic band (PPB) values ranging from 8 to 35%. An analysis of molecular variance (AMOVA) was used to apportion the variation between regions, among populations within regions, and within populations. Results indicated that most of the variance (85%) occurred between Yunnan and Sichuan. The variances among populations within regions and within populations, however, were only 5 and 10%, respectively. In the among-population analysis, the larger part of genetic variation (77%) resided among populations, and less (23%) presented differences within populations. UPGMA cluster analysis showed that there was no distinct genetic differentiation between populations from Sichuan province. A number of causes including limited gene flow, genetic drift and inbreeding might have led to these observed genetic profiles of I. hypsophila.     

Genetic diversity within and among populations of Neopicrorhiza scrophulariiflora (Scrophulariaceae) in China,an endangered medicinal plant

Neopicrorhiza scrophulariiflora Pennel (Hong) (Scrophulariaceae) is an endangered medicinal plant, endemic to the Eastern Himalayas and the Hengduan Mountains. Levels of genetic variation and genetic structure of seven populations of N. scrophulariiflora in China were studied using inter-simple sequence repeat (ISSR) markers. Thirteen primers amplified 82 total loci from 7 populations composed of 136 individuals. All 82 loci were polymorphic, showing a percentage of polymorphic bands (PPB) of 100%, indicating considerable genetic variation at the species level. In contrast, a low level of genetic diversity within populations was detected with a mean PPB of 30.56%. In addition, Nei’s genetic diversity analysis (0.4073) and Shannon’s diversity index (0.5917) revealed similar genetic structure. High levels of genetic differentiation (Gst = 0.6955) and restricted gene flow (Nm = 0.2198) among populations were also detected. Anthropologic impacts, together with clonal propagation, genetic drift and geographical isolation might be the reasons which had shaped the genetic structure of this species.     

Genetic diversity within and among populations of the endangered species Taxus fuana (Taxaceae) from Pakistan and implications for its conservation

The West Himalayan yew, Taxus fuana Nan Li & R.R. Mill (Taxaceae), is an endangered species endemic to the Western Himalayas. An investigation of the genetic diversity of wild populations of T. fuana in Pakistan was undertaken. The genetic diversity and genetic structure was quantified using random amplified polymorphic DNA (RAPD) variation in 219 individuals of the 10 populations. Of the 32 universal primers screened 16 produced highly reproducible, clear RAPD bands. Using these primers, 193 discernible DNA fragments were generated, of which 164 (84.97%) were polymorphic. The statistical results indicated that there was a relatively low genetic diversity within populations (with percentages of polymorphic bands, PPB, ranging from 29.53 to 50.26%, with an average of 38.34% and a Nei's genetic diversity index (H_E) of 0.1165), and a high genetic differentiation among populations (G_ST = 0.5842, Φ_ST = 0.5685) within these populations. The gene flow (N_m) was low with only 0.3558.     

内蒙古地区刺叶柄棘豆(Oxytropis aciphylla Ledeb.)种群遗传多样性分析

用ISSR分子标记对内蒙古地区刺叶柄棘豆(Oxytorpis aciphylla Ledeb.) 5个地理种群进行了种群遗传多样性分析。结果表明：刺叶柄棘豆种群具有较高的遗传多样性,11个ISSR引物扩增出215条带,总的多态位点百分率为98.14%,Shannon多样性指数I=0.2108,Nei基因多样性指数 H=0.341 6,种内总基因多样性(H_t) 为0.2108,种群内基因多样性(H_s)为0.160 4, 大部分遗传变异(76.11%)的遗传变异存在于种群内, 23.89%的遗传变异存在于种群间。遗传分化系数(Gst)为0.238 9,基因流(Nm)为1.592 9。5个居群间已有遗传分化趋势,遗传漂变不会引起遗传分化。UPGMA遗传距离聚类结果表明, 5个地理种群中,植被类型为荒漠草原的4个种群之间遗传距离较近,与1个荒漠种群距离较远。     

白花泡桐种源的遗传多样性和遗传分化研究

利用ISSR技术对白花泡桐38个种源的遗传多样性和遗传分化进行分析。结果显示：（1）从100个ISSR引物中筛选出9个能扩增出清晰带型并具多态性的引物,共扩增出95个条带,其中88条具多态性,多态位点比率为92.63%。（2）在物种水平上,有效等位基因数（N_e）、Nei’s基因多样性指数（H）、Shannon’s信息指数（I）的平均值分别为1.391 0、0.242 4、0.376 5;种源的多态位点比率在32.63%（江西抚州）~56.84%（广西梧州和江西九江）之间,平均为47.16%;基因流（N_m）为0.912 7,种源间遗传分化系数（G_st）为0.353 9,反映出种源间遗传变异占总遗传变异的35.39%,且遗传变异主要来源于种源内的个体间。（3）遗传一致度在0.39~0.82之间,反映出白花泡桐的遗传基础较宽。UPGMA法聚类分析将38个种源分为3组,主坐标分析(PCoA)将其大致分为4组,两种聚类方法的结果有一定的差异,本文做了相关讨论。研究还表明种源间的遗传距离与地理距离相关不显著。     

珍稀濒危植物长叶红砂种群遗传多样性的ISSR分析

采用ISSR分子标记技术,对濒危小灌木长叶红砂(Reaumuria trigyna) 集中分布的5个种群的遗传多样性水平和遗传结构进行了研究。14条引物共检测到114个位点,其中99个为多态位点,多态位点比率为86.84％,长叶红砂种群具有较高的遗传多样性。物种水平上Shannon多样性指数(I)为0.468 8,Nei基因多样性指数(H)为0.308 4;种群水平上,多态位点比率P为77.89%,I为0.410 6,H为0.260 9,基因分化系数Gst为0.106 9,揭示了长叶红砂种群遗传变异多存在于种群内,种群间的遗传分化较小,占10.69%。 基因流(Nm)为4.178 7＞1,说明种群间的基因交流,防止了由于遗传漂变导致的遗传分化。聚类分析表明长叶红砂种群遗传距离与地理距离之间无显著的相关性。研究结果说明遗传多样性水平与物种本身特性和所处不同群落有关,濒危植物并不一定表现为遗传变异水平的降低。     

Population structure and genetic diversity of Stipa grandis P. Smirn,a dominant species in the typical steppe of northern China

Random amplified polymorphic DNA (RAPD) markers were used to characterize genetic heterogeneity within and among five populations of Stipa grandis in the Xilingol Plateau. Estimates of the percentage of polymorphic bands, Shannon's diversity information index and Nei's gene diversity index were comparatively high in the five populations, and the Population GSM was found to have the highest genetic diversity among all populations. An analysis of molecular variance indicated that the majority of variation existed within populations (74.12%), and that there was significant differentiation among populations (Φ_ST = 25.88%, P < 0.001). Genetic distance (Φ_ST) ranged from 0.198 to 0.310 and the differentiation between pair-wise populations was significant when individual pairs of populations were compared. Based on the Φ_ST values, gene flow (Nm) was estimated and was found to vary from 0.556 to 1.013 between pair-wise populations and 0.7412 among populations. The results of UPGMA cluster analysis and nonmetric multi-dimensional scaling analysis indicated that most variation occurred within populations and that genetic differentiation had happened between populations. These findings are important for a better understanding of the adaptive strategy of S. grandis in northern China and will be useful for conservation managers to work out an effective strategy to protect this important species.     

珍稀濒危植物金毛狗的SRAP分析

利用SRAP分子标记技术,对7个居群79株金毛狗进行遗传多样性分析。结果表明:10对SRAP引物组合共得到107条扩增条带,多态性条带比率为85.98%,Nei’s基因多样性指数为0.229 6,Shannon’s多样性指数为0.358 6,表明金毛狗居群水平具有较高的遗传多样性;金毛狗7个居群的总基因多样度为0.229 6,居群内遗传多样度为0.135 4,居群间的遗传分化指数为0.410 6,表明有41.06%的变异存在于居群间,有58.94%的变异存在于居群内;居群间基因流为0.717 8,表明居群间基因交流频率较低;遗传一致度和UPGMA聚类分析结果显示,生境条件相似的居群优先聚集,说明金毛狗种质亲缘关系与地理分布相关性不显著。     

中华水韭遗传多样性的RAPD分析

采用RAPD方法对珍稀濒危植物中华水韭(Isoetes sinensis)4个自然居群的48个样品进行了DNA多态性分析。从60个随机引物中筛选出14个有效引物,共产生124条DNA片段,其中72条为多态性条带,总的多态位点百分率(PPB)为58．06％。各居群间多态位点百分率差异显著(0．81％-12．90％)。AMOVA分析结果表明,4个居群间基因分化系数Фst=0．5894,即遗传变异中有相当一部分来源于群体间(58．94％)。日益缩小的种群规模而导致的居群内近交和遗传漂变的发生以及居群间有限的基因交流可能是中华水韭目前遗传结构的主要成因。鉴于目前中华水韭居群内个体数偏少、遗传多样性较低的现状,建议对其进行就地保护并保护尽可能多的生境,对不同自然居群内的个体进行植株相互移栽和育苗移栽,以提高不同居群间的基因交流,尽可能地保护中华水韭的遗传多样性。     

广东省五节芒遗传多样性的ISSR分析

采用ISSR分子标记技术,对广东省内分布的能源植物五节芒(Miscanthus floridulus)13个野生居群共215个个体的遗传多样性进行了研究.9个ISSR引物共扩增到了81个位点,其中76个是多态性位点.结果表明,广东五节芒的遗传多样性水平很高,物种水平上,多态位点百分率(PPB)为93.83％,Nei's...     

中国特有植物卧龙沙棘自然群体的RAPD分析

应用12个随机引物对卧龙沙棘全部2居群共28个个体进行了RAPD分析。结果表明,卧龙沙棘具有较丰富的遗传多样性,多态位点百分率为78.05%,Nei’s基因多样性h=0.2553,Shannon’s多态性信息指数Ι=0.3841。分布范围狭窄的卧龙沙棘在亚种水平的遗传多样性明显高于分布较广的中国沙棘。在居群水平上,卧龙沙棘同样具有很高的遗传多样性,平均多态位点百分率为63.42%,Nei’s基因多样性h=0.2193,Shannon’s多态性信息指数I=0.3287。卧龙沙棘的基因分化系数Gst=0.1425,表明遗传变异主要存在于居群内。AMOVA的结果也表明,在全部的遗传变异中,19.18%的遗传变异存在于居群之间,与Gst值基本一致。这一结果符合卧龙沙棘风媒、异交的繁育系统特点。     

Genetic diversity analysis of Pinellia ternata based on SRAP and TRAP markers

An assessment of the genetic diversity and variation of Pinellia ternata collected from 43 populations in China was undertaken using SRAP + TRAP markers. A total of 13 SRAP primers in addition to 3 TRAP primer combinations yielded 292 bands in total of which 286 were polymorphic (98.0%), with an average of 16 for each. The PIC value ranged from 0.88 to 0.95, with a mean polymorphic information content (PIC) of 0.92 over all the primers. A cluster analysis was conducted based on the unweighted pair group method with arithmetic average (UPGMA), and a principle coordinate analysis (PCA) was performed relying on Nei's genetic distance, both of which showed similar outcomes in that the results of clustering did not correlate to the geography locations but showed an association with morphology. An analysis of molecular variance (AMOVA) was performed to detect the source of variation; the results indicated that the main variation existed within populations (67.2%), whereas there was still 32.8% differentiation existing among the populations.     

Genetic diversity of Astragalus nitidiflorus, a critically endangered endemic of SE Spain,and implications for its conservation

Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population structure in five populations of Astragalus nitidiflorus, a critically endangered species endemic to southeast Spain. Eight primers amplified 78 bands with 40 (51.3%) being polymorphic. Statistical results indicated a low genetic diversity at the population and species level, with percentages of polymorphic bands (PPB) ranging from 28.2 to 37.2% (an average of 31.8%), and means of gene diversity (H_E) of 0.129 and 0.171 respectively. The Shannon’s index (SI) ranged from 0.160 to 0.214 at the population level and was 0.260 at the species level. A low level of genetic differentiation among populations was detected, based on the Shannon’s information index (0.297), the coefficient of genetic differentiation between populations (G_ST = 0.2418) and AMOVA analysis (Φ_ST = 0.255). The estimated gene flow (Nm) was 0.789. The high genetic connectivity found among populations of A. nitidiflorus is an evidence of a recent habitat fragmentation. In addition, a bottleneck event in the past has been revealed, with a subsequent reduction of population size and a loss of genetic variation. Based on these results, the conservation strategy of A. nitidiflorus was proposed.     

ISSR analysis of genetic diversity of the Qinghai-Tibet Plateau endemic Rhodiola chrysanthemifolia (Crassulaceae)

Inter-simple sequence repeat markers (ISSR) were used to estimate genetic diversity within and among 10 populations of Rhodiola chrysanthemifolia along Nianqingtangula Mountains and Brahmaputra, a species endemic to the Qinghai-Tibet Plateau and an endangered medicinal plant. Of the 100 primers screened, 13 produced highly polymorphic DNA fragments. Using these primers, 116 discernible DNA fragments were generated of which 104 (89.7%) were polymorphic, indicating substantial genetic diversity at the species level. Genetic diversity measured by the percentage of polymorphic bands (PPB) at the population level ranged from 21.97% to 48.8%. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly among populations (77.3%), but no regional differentiation was discernible. Variance within populations was only 22.7%. The main factor responsible for this high level of differentiation among populations is probably the historical geographical and genetic isolation of populations in a harsh mountainous environment. Concerning the management of R. chrysanthemifolia, the high genetic differentiation of populations indicates the necessity of conserving the maximum possible number of populations.     

Population Genetic Study of Fagopyrum tataricum from Western Himalaya Using ISSR Markers

Inter-simple sequence repeat (ISSR) markers were used to analyze genetic diversity and relatedness of 15 germplasms of Fagopyrum tataricum. Samples representing 75 individuals were collected from a range of altitudes in the Western Himalaya. The 13 ISSR primers revealed 98.1% polymorphism among populations, whereas average polymorphism was extremely low (2.18%) within populations. The coefficient of population differentiation was 0.9750, with limited gene flow (N _m) of 0.0128. The average PIC value of the ISSR markers was high (0.812), with a marker ratio of 0.65 and marker index of 6.66. The genetic diversity of F. tataricum significantly correlated with altitude and gene diversity, Shannon’s index, and the percentage of polymorphic bands. The genetic diversity among populations showed broad genetic base and provided a developmental strategy for crop improvement.     

短柄枹种群遗传多样性的ISSR分析

利用ISSR分子标记方法对分布在浙江省境内的7个短柄枹种群的遗传多样性和遗传分化进行了分析。从100个引物中筛选出12个用于正式扩增的ISSR引物,在7个种群140个个体中共检测到132个位点,其中多态位点118个,多态位点百分率(P)为89.39%,各种群P平均为58.87%。短柄枹总的Shannon信息指数(I)为0.493 3、Nei指数(h)为0.334 7,各种群I平均为0.336 2、h平均为0.229 1。P、I、h均显示云峰种群最高,天台山种群最低。AMOVA分子差异分析表明,67.97%的变异存在于种群内,32.03%的变异存在于种群间,种群间的基因分化系数(G_ST)为0.315 4。短柄枹种群间的基因流为(N_m)为1.085 3。7个种群的平均遗传距离为0.173 9。利用UPGMA法对7个种群进行聚类,结果显示天台山和雪窦山种群聚成一类,其它5个种群聚成另一类。     

Analysis of genetic variability and population structure of the endemic medicinal Limonium sinense using molecular markers

Limonium sinense is an endemic medicinal herb used to treat fever, hemorrhage and other disorders. In the present study, population genetic diversity was elucidated using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) primers. Percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at species level. The analysis of molecular variance revealed that 69.88% (RAPD), 71.19% (ISSR) and 70.97% (AFLP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Gst (0.3849/0.3577/0.3670). Gene flow number (Nm) was 0.581/0.618/0.612, which indicated that there was a limited gene exchange between populations. The UPGMA clustering results showed that the genetic distance had no significant correlation with geographic distance. These results indicate that these markers were reliable tools for the differentiation and determination of the genetic diversity among the populations of L. sinense and the conservation of existing natural population is necessary.     

Genetic diversity and biogeography of the traditional Chinese medicine, Gardenia jasminoides, based on AFLP markers

Gardenia jasminoides Ellis is used in traditional Chinese medicine (TCM) in China. Levels of genetic variation and patterns of population structure within and among eight wild or cultivated populations of G. jasminoides Ellis in China were investigated using amplified fragment length polymorphism (AFLP) markers. Of the 11 primers screened, four produced highly reproducible AFLP bands. Using these primers, 244 discernible DNA fragments were generated with 165 bands (67.6%), were polymorphic, indicating considerable genetic variation at the species level. In contrast, there were relatively low levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 36.89% to 59.43%. Genetic diversity within populations ranged from 0.2086 to 0.3108, averaging 0.2392 at the species level. A high level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (76.59%), Shannon's index analysis (64.8%) and AMOVA analysis (72.75%). No significant statistical differences (analysis of molecular variance [AMOVA], p = 0.0639) in AFLP variation were found between regions. However, the variance among populations and within populations differed significantly (p < 0.001). An indirect estimate of historical levels of gene flow (N_m = 1.7448) was consistent with the high mean genetic identity (mean I = 0.9263) found among populations. There is an association between geographic and genetic distances between populations. Presently gene change exists between populations.