Molecular diversity and population structure of the forage grass Hemarthria compressa (Poaceae) in south China based on SRAP markers

Hemarthria compressa is one of the most important and widely utilized forage crops in south China, owing to its high forage yield and capability of adaptation to hot and humid conditions. We examined the population structure and genetic variation within and among 12 populations of H. compressa in south China using sequence-related amplified polymorphism (SRAP) markers. High genetic diversity was found in these samples [percentage polymorphic bands (PPB) = 82.21%, Shannon's diversity index (I) = 0.352]. However, there was relatively low level of genetic diversity at the population level (PPB = 29.17%, I = 0.155). A high degree of genetic differentiation among populations was detected based on other measures and molecular markers (Nei's genetic diversity analysis: G(ST) = 54.19%; AMOVA analysis: F(ST) = 53.35%). The SRAP markers were found to be more efficient than ISSR markers for evaluating population diversity. Based on these findings, we propose changes in sampling strategies for appraising and utilizing the genetic resources of this species.     

鸢尾属植物遗传多样性的 RAPD和ISSR分析

应用RAPD和ISSR标记技术,对来自不同产地的鸢尾属(IrisL.)4个野生种的遗传多样性进行了分析。结果表明,12个RAPD和ISSR引物分别扩增出225和196条带,多态性条带分别为215和196条,多态性条带百分率分别为95.56%和100.00%;种间总基因多样度分别为0.368 9和0.357 5、种内基因多样度分别为0.107 7和0.138 0,表明鸢尾属种间遗传多样性较高,且种间变异大于种内变异。4个野生种中,蝴蝶花(I.japonicaThunb.)的遗传组成较为丰富。此外,种内遗传关系与地理分布和环境差异有一定的相关性。     

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.     

广西地不容种质资源的ISSR分析

采用简单序列重复区间扩增(ISSR)分子标记技术对广西地不容3个野生居群和1个引种居群共92个个体进行了遗传多样性研究。10个引物共扩增出61条带,其中60条具多态性,多态性位点百分率为98.36%。4个居群多态性百分率在73.77%～86.89%。Nei’s基因多样性指数(H)为0.3379,Shannon信息多样性指数(Ⅰ)为0.5055。3个野生居群Nei’s遗传分化系数(Gst)表明:83.87%遗传变异分布在居群内,16.13%的遗传变异分布在居群间。引种居群与3个野生居群间的遗传一致度达0.8846。引种居群有效地保护了广西地不容的遗传多样性。     

西双版纳地区流苏石斛遗传多样性的ISSR 分析

采用ISSR 分子标记技术, 对西双版纳分布的兰科濒危植物流苏石斛( Dendrobium fimbriatum) 5 个居群共114 个个体的遗传多样性进行了研究。从100 条引物中筛选出了12 条用于扩增, 共检测到117 个位点, 其中105 个为多态位点。分析结果表明, 流苏石斛居群水平遗传多样性较低。在物种水平上, 流苏石斛多态位点百分率PPB 为89 .74% , Nei′s 基因多样性指数H 为0 . 3227 , Shannon′s 多样性信息指数Hsp 为0 . 4779 ; 在居群水平上, 各个居群的多态位点百分率PPB 差异较大( 6.84% ～ 39.32% ) , 平均值为23.93% , Nei′s 基因多样性指数H 为0 . 0871 , 各个居群的Shannon′s 多样性信息指数Ho 平均为0.1290。AMOVA 分析的结果显示, 流苏石斛的遗传变异大多数存在于居群间, 占总遗传变异的74 . 79%。基于Nei′s遗传多样性分析得出的居群间遗传分化系数Gst = 0 . 7443。各居群间的Nei′s 遗传一致度( I) 范围为0 . 5882～0 . 8331。Mantel 检测发现, 居群间的遗传距离和地理距离之间无显著的正相关关系( r= 0.2419, P=0.2416) 。鉴于流苏石斛的遗传多样性现状和居群遗传结构, 我们建议对流苏石斛居群所有个体实施及时的就地保护, 同时建立迁地保护居群, 促进基因交流。     

Inter and intraspecific genetic diversity (RAPD) among three most frequent species of macrofungi (Ganoderma lucidum,Leucoagricus sp. and Lentinus sp.) of Tropical forest of Central India

In present study seven RAPD primers were used to access the diversity within and among twelve populations of three mushroom species Ganoderma lucidum, leucoagaricus sp. and Lentinus sp. Total of 111 bands were scored by 7 RAPD primers in 30 accessions of three mushroom species collected from different sampling sites of central India. Total 111 bands were generated using seven primers which were F-1, OPG-06, OPC-07, OPD-08, OPA-02, OPD-02, OPB-10. All 111 bands were polymorphic in nature (100%). Therefore, it revealed that the used primers had sufficient potency for population studies and 30 accessions had higher genetic differences among each other. In best of the knowledge, this is the first report, which accesses the genetic diversity between three mushroom species (Gd Ganoderma lucidum, Lg Leucoagaricus sp., Ls Lentinus). The polymorphic percentage ranged from 3.60 to 23% within twelve populations, while polymorphic percentage among group was 40.56, among population within groups was 41.12 and within population was 18.32. This indicated that the genetic diversity within the population was very low, but slightly higher in the populations of three species. Among three groups representing Gd., Lg and Ls, Among populations within groups shown highest percentage of variation (Pv?=?41.12) while within populations, the lowest percentage of variation (18.32) was observed. This result also support that the highest genetic variation was present among groups in comparison to among the population within a species and lowest genetic variation was observed within the population.     

利用ISSR标记对新疆白梭梭居群的遗传多样性分析

利用ISSR分子标记对新疆白梭梭4个居群,105个个体进行了遗传多样性的比较分析。在供试材料中,11个引物共扩增出171个多态位点,多态位点百分率为84．85％,4个居群的多态位点百分率差异在33．92％．40．35％之间。Shannon多样性指数（I）为0．3518,物种水平的Nei基因多样度（h）为0．3482。遗传变异分析表明,物种水平的居群间遗传分化系数Gst为0．6238,居群间的基因流Nm为0．3016。遗传分析表明吐鲁番居群和甘家湖居群的遗传距离最近。     

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。     

Genetic Variation and Clonal Diversity of Psammochloa villosa(Poaceae) Detected by ISSR Markers

Genetic variation and clonal diversity of seven Psammochloavillosa(Poaceae) populations from northwest China were investigatedusing inter simple sequence repeat (ISSR) markers. Of the 84primers screened, 12 produced highly reproducible ISSR bands.Using these primers, 173 discernible DNA fragments were generatedwith 122 (70.5%) being polymorphic, indicating considerablegenetic variation at the species level. In contrast, there wererelatively low levels of polymorphism at the population levelwith the percentage of polymorphic bands (PPB) ranging from6.1 to 26.8. Analysis of molecular variance (AMOVA) showed thata large proportion of genetic variation (87.46%) resided amongpopulations, while only 12.54% resided among individuals withinpopulations. Clonal diversity was also high with 98 genets beingdetected from among 157 individuals using 12 ISSR primers. Theevenness of distribution of genotypes in P. villosa populationsvaried greatly, with all of the genotypes being local ones.No significant differences in genetic or clonal diversity werefound between populations in mobile or fixed dunes. The mainfactor responsible for the high level of differentiation amongpopulations and the low level of diversity within populationsis probably the clonal nature of this species, although selfingmay also affect the population genetic structure to some extent.The efficiency of ISSRs in identifying genetic individuals wasmuch higher than that of allozymes. An approximately asymptoticcorrelation was found between the number of genets detectedand the number of polymorphic loci used, suggesting that useof a high number of polymorphic bands is critical in genet identification.Copyright 2001 Annals of Botany Company Psammochloa villosa, ISSRs, genetic variation, clonal diversity     

采用RAPD和ISSR标记研究古尔班通古特沙漠东南缘梭梭种群的遗传结构

梭梭(Haloxylon ammodendron(CA Mey.)Bunge)是一种沙漠旱生优势树种,具有重要的生态和经济价值,然而,我们对梭梭种群的遗传多样性和遗传结构所知甚少.本文采用RAPD和ISSR标记对来自古尔班通古特沙漠东南缘的4个天然梭梭种群的遗传多样性和遗传结构进行了检测.5个RAPD引物和8个ISSR引物分别扩增出61和195条带,多态性位点比率分别为83.6%和89.7%,Shannon信息指数分别为0.333和0.367,RAPD和ISSR分析均表明梭梭种群的遗传多样性水平较高.利用分子方差分析(AMOVA)研究梭梭种群的遗传结构,结果表明,大部分遗传变异存在于种群内,通过RAPD分析发现138.2%的遗传变异发生在种群内;通过ISSR分析发现89.4%的遗传变异发生在种群内;而种群间的遗传分化很小.通过RAPD标记没有检测到种群间的遗传分化,ISSR分析表明10.6%的遗传变异发生在种群内.我们推测梭梭种群较高的遗传多样性水平可能源于对异质、高胁迫环境的长期适应,但还需要进一步的研究加以证实.种群间遗传分异低的主要原因是种群间存在强大的基因流.     

滇牡丹遗传多样性的ISSR分析

应用ISSR标记对中国西南地区特有植物滇牡丹(Paeonia delavayi)的遗传多样性进行了研究。从100个引物中筛选出10个用于正式扩增,在取自16个自然居群和1个迁地保护居群的511个个体中,检测到92个多态位点。在居群水平上,多态位点百分率（PPB）为44.61%,Nei′s基因多样性指数（H）和Shannon信息指数（I）分别为0.1657和0.2448。在物种水平上,多态位点百分率（PPB）为79.31%,Nei′s基因多样性指数（H）和Shannon信息指数（I）分别为0.2947和0.4355。居群间的遗传分化系数(G_ST)达0.4349。结果表明：滇牡丹遗传多样性水平较高,居群间遗传分化较大。结合以前的研究结果,对滇牡丹的现状进行评估的结果显示,滇牡丹并不濒危。     

用扩增片段的长度多态性分子标记探讨盾叶薯蓣的遗传多样性

用扩增片段的长度多态性(amplified fragment length polymorphism,AFLP)标记分析研究了中国5个盾叶薯蓣居群30个个体的遗传多样性。筛选出9对AFLP引物,从中检测到14698条清晰可见的条带,其中多态性带12628条,多态性比率85.92%。Shannon信息指数(I)为0.3656±0.1721,物种水平的Nei基因多样性(H)为0.2322±0.2200。遗传变异分析表明,物种水平的遗传分化系数Gst为0.4827,说明其群体间存在一定的遗传分化,居群间的基因流Nm为0.5358,居群间遗传交换较小。聚类分析结果显示5个居群盾叶薯蓣有较为丰富的遗传变异,且与地理分布有相关性。     

Genetic diversity and geographic differentiation in Tacca chantrieri (Taccaceae): an autonomous selfing plant with showy floral display

BACKGROUND AND AIMS: Despite considerable investment in elaborate floral displays, Tacca chantrieri populations are predominantly selfing. It is hypothesized that this species might possess considerable spatial or temporal variation in outcrossing rates among populations. To test this hypothesis, genetic variability and genetic differentiation within and among T. chantrieri populations were investigated to find out if they are in agreement with expectations based on a predominantly inbred mating system. METHODS: Genetic diversity was quantified using inter-simple sequence repeats (ISSR) in 303 individuals from 13 populations taken from known locations of T. chantrieri in China, and from one population in Thailand. KEY RESULTS: Of the 113 primers screened, 24 produced highly reproducible ISSR bands. Using these primers, 160 discernible DNA fragments were generated, of which 145 (90.62 %) were polymorphic. This indicated considerable genetic variation at the species level. However, there were relatively low levels of polymorphism at population levels, with percentages of polymorphic bands (PPB) ranging from 8.75 % to 55 %. A high level of genetic differentiation among populations was detected based on different measures (Nei's genetic diversity analysis: G(ST) = 0.5835; AMOVA analysis: F(ST) = 0.6989). Furthermore, based on levels of genetic differentiation, the 14 populations clustered into two distinct groups separated by the Tanaka Line. CONCLUSIONS: High levels of differentiation among populations and low levels of diversity within populations at large spatial scales are consistent with earlier small-scale studies of mating patterns detected by allozymes which showed that T. chantrieri populations are predominantly selfing. However, it appears that T. chantrieri has a mixed-mating system in which self-fertilization predominates, but there is occasional outcrossing. Significant genetic differences between the two distinct regions might be attributed to vicariance along the Tanaka Line. Finally, possible mechanisms of geographic patterns based on genetic differentiation of T. chantrieri are discussed.     

采用RAPD标记探讨瓣蕊唐松草(毛茛科唐松草属)的遗传多样性及其地理分布格局(英文)

Random amplified polymerphic DNA(RAPD)method was applied to assessg enetic variation and population structure of Thahctrum petalotdeum L(Ranunoulaceae),Two hundred and forty-six individuals from 11 populations of the species were investigated by RAPD profiles Twenty selected RAPD primers generated 125 bands．in which 120 were polymorphic Ther esults revealed a high level of genetic variation(ercentage of polymorphIc bands(PPB was 96％．Nei’s gene diversity(りwas 03502 and shannon’s information index(I) was 0．5199 at the species level) The differentiation among the populations was high(Gst=0．3511)in this species．Result of analyzing of molecularvariance(AMOVA)showedthat38．88％of genetic variance was found among the populations Positive correlation withr r=01945(P=00002)was found between genetic distance and geographic distance amongpo pulations Two populations distributed in the drainage basin of YanELz River affined genedcally and formed one clada and the rest nine populations formed the other clade in both unweighted pair-group method using arithmetic average(UPGMA)trees made by two different method different methods. It was yen/clear that these two populations were very special, andmust be closely related in history, despite the fact that they now share quite weak link to the restpopulations through gene communication.     

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.     

濒危植物长叶榧群体遗传多样性的RAPD分析

借助随机扩增多态DNA方法,分析了中国特有的濒危植物长叶榧的遗传多样性和遗传分化．结果表明：12个随机引物在9个长叶榧自然群体180个样品中可检测到180个可重复位点,其中多态位点119个．长叶榧物种水平的遗传多样性较高,多态位点百分率（P）为66．11％,Shannon信息指数（,）为0．3087,Nei指数（h）为0．2015;而群体水平的遗传多样性较低,P、I和h分别平均为23．76％、0．1221和0．0813．AMOVA分子变异显示,42．57％变异来源于群体内,57．43％变异来源于群体间,群体间的遗传分化系数（Gst）为0．5965,群体间的遗传分化程度高．长叶榧群体间的基因流很低,为0．3382．瓶颈效应、群体隔离和群体间基因流低等因素都加剧了长叶榧群体间的遗传分化．9个长叶榧群体间的平均遗传距离为0．1630．通过UPGMA进行聚类,可将9个长叶榧群体分为浙江和福建两大类群．建议在迁地保护时应尽量避免在群体之间实施种质迁移．     

Assessing genetic diversity of Elymus sibiricus (Poaceae: Triticeae) populations from Qinghai-Tibet Plateau by ISSR markers

Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population structure in eight populations of Elymus sibiricus L. from the southeast of Qinghai-Tibet Plateau of China. Of the 100 primers screened, 13 produced highly reproducible ISSR bands. Using these primers, 193 discernible DNA fragments were generated with 149 (77.2%) being 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 44.04 to 54.92%. The mean gene diversity (H_E) was estimated to be 0.181 within populations (range 0.164–0.200), and 0.274 at the species level. A high level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (33.1%), Shannon's index analysis (34.5%), Bayesian method (33.2%) and AMOVA analysis (42.5%). No significant statistical differences (analysis of molecular variance [AMOVA], P = 0.08) in ISSR variation were found between the sample collection regions. However, among populations (42.5% of the variance) and within populations (57.5% of the variance), there were significant differences (P < 0.001). Populations shared high levels of genetic identity. This pattern of genetic variation was different from that for most of inbreeding Triticeae species reported. In addition, a geographical pattern of population differentiation, where the populations from south and north of sampling sites were clearly separated from each other, was revealed by both the cluster and principal coordinates analyses. Generally, the result of this study indicates that E. sibiricus contains high molecular variation in its populations. The implications of these results for the conservation of the species are discussed.     

西双版纳地区流苏石斛遗传多样性的ISSR分析

采用ISSR分子标记技术,对西双版纳分布的兰科濒危植物流苏石斛（Dendrobium fimbriatum）5个居群共114个个体的遗传多样性进行了研究。从100条引物中筛选出了12条用于扩增,共检测到117个位点,其中105个为多态位点。分析结果表明,流苏石斛居群水平遗传多样性较低。在物种水平上,流苏石斛多态位点百分率PPB为89．74％,Nei’s基因多样性指数日为0．3227,Shannon’s多样性信息指数见。为0．4779;在居群水平上,各个居群的多态位点百分率PPB差异较大（6．84％～39．32％）,平均值为23．93％,Nei’s基因多样性指数H为0．0871,各个居群的Shannon’s多样性信息指数见平均为0．1290。AMOVA分析的结果显示,流苏石斛的遗传变异大多数存在于居群间,占总遗传变异的74．79％。基于Nei’s遗传多样性分析得出的居群间遗传分化系数Gst=0．7443。各居群间的Nei’s遗传一致度（I）范围为0．5882～0．8331。Mantel检测发现,居群间的遗传距离和地理距离之间无显著的正相关关系（r=0．2419,P=0．2416）。鉴于流苏石斛的遗传多样性现状和居群遗传结构,我们建议对流苏石斛居群所有个体实施及时的就地保护,同时建立迁地保护居群,促进基因交流。     

我国盾叶薯蓣居群遗传结构分析

利用随机扩增多态DNA(RAPD)标记,分析研究了中国11个盾叶薯蓣居群82个个体的遗传多样性与遗传结构,15个寡聚核苷酸引物扩增共得到108条带,其中96条为多态带,占88．89％。Shannon多样性指数(I)为0．3093,居群水平的变异从0．1564到0．3098,物种水平的Nei基因多样度(h)为0．2499,居群水平的变化范围为0．1607到0．2137。遗传变异分析表明,物种水平的基因分化系数Gst为0．3415,居群间的基因流Nm为0．9641,居群间遗传交换小。分子方差分析(AMOVA)表明,居群内变异为68．96％,地区间变异为19．45％,居群问变异为11．58％。聚类结果以长江为界,将盾叶薯蓣分为南北两个大类群。研究结果对盾叶薯蓣种质的迁地保护有重要意义。     

Genetic diversity of forest arabica coffee (Coffea arabica L.) in Ethiopia as revealed by random amplified polymorphic DNA (RAPD) analysis

Genetic diversity within the forest Coffea arabica L. gene pool in Ethiopia has not been extensively examined with molecular markers. In the present study, a total of 75 polymorphic RAPD bands generated by twelve random primers were used to assess genetic diversity among 144 genotypes representing 16 C. arabica populations. The number of polymorphic bands detected with each primer ranged from 2 to 9 with a mean of 6.25 bands per primer. Banding patterns ranged in percentage polymorphism from 37% to 73% with an overall mean of 56% for the populations analyzed. The amount of genetic variation among populations estimated by Shannon-Weaver diversity index was (H = 0.30). The within population and between populations differentiation values were 0.65 and 0.35, respectively. Genetic differentiations within and between zones of sample collection sites were 0.80 and 0.20, respectively. Within population average similarities estimated by simple matching coefficients ranged from 0.72 to 0.85, with an overall average of 0.78. In the cluster analysis that used individual samples as operational taxonomic units, most of the representatives of the same population failed to cluster before they joined members of other populations. Nevertheless, most of the populations were clustered on the basis of their geographic closeness and an east west differentiation was observed at approximately 75% similarity. The results obtained provide information on how to select sites for in situ conservation of C. arabica germplasm.