利用SRAP标记分析中国野生石蒜的遗传多样性

采用SRAP（Sequence-related amplified polymorphism,序列相关扩增多态性）标记对中国13个省24份野生石蒜（Lycoris radiata）资源94个样品进行了检测。10个引物组合共扩增出218条带,其中173条为多态性条带,多态性百分比达79.36%。石蒜的观测等位基因数（na）、有效等位基因数（ne）、基因多样性指数（h）、Shannon信息指数（I）分别为1.7936、1.4131、0.2415和0.3664。石蒜不同种源间的遗传分化系数（Gst）达0.9547、基因流（Nm）仅0.0136,表明种源间遗传分化显著,遗传变异主要存在于种源间。根据Nei′s遗传距离对24份种源进行UPGMA聚类,所有石蒜种源聚成两大类,第I大类由7份种源组成,除江苏连云港的石蒜（JS3）外,均来自我国西南或西北地区;其余的17份种源构成第II大类,它们遍及华南、华中和华东地区;各大类中的分支结果与野生石蒜外部形态及生长发育习性有一定联系。将石蒜种源的遗传多样性与其所处的经度、纬度、海拔、年均降雨量、年均温等进行相关性分析,结果显示它们之间的相关性均不显著,即石蒜对环境依赖性小,能分布在各种生境中。根据以上结果,我们认为野生石蒜具有较丰富的遗传多样性,而种源间遗传分化显著的原因主要是基因流的隔离。研究结果对我国的野生石蒜资源的开发利用与保护有重要意义。     

ISSR and SRAP Markers Reveal Genetic Diversity and Population Structure of an Endangered Slipper Orchid,Paphiopedilum micranthum (Orchidaceae)

Paphiopedilum micranthum is an endangered pink slipper orchid mainly distributed in the limestone areas of southwestern China. Wild populations of this species have been seriously threatened by excessive collections, rampant smuggling for export, and habitat destruction. We used 15 ISSR markers and 11 SRAP markers to investigate the genetic diversity and structure of 15 natural populations. A high degree of diversity was observed at the species level (ISSR: PPB=9166%, He=03839; SRAP: PPB=9929%, He=02806). Certain degree of genetic differentiation among populations (ISSR: Gst=02577; SRAP: Gst=02383) was detected maybe caused by low gene flow (ISSR: Nm=07201; SRAP: Nm=07991). Consistent with the results of Principal Coordinate Analysis, the UPGMA dendrogram analysis divided the 15 populations into two main clades. In addition to geographic distance, the difference in elevation was another natural factor contributing to this differentiation. Knowledge about genetic diversity and structure gained from our study will be beneficial for the development of reasonable and efficient strategies to conserve this endangered species.     

Genetic Diversity of Jatropha curcas (Euphorbiaceae) Collected from Southern Yunnan,Detected by Inter-simple Sequence Repeat ( ISSR)

The genetic diversity of 158 individuals from eight semi-wild populations from Yunnan Province was estimated using ISSR method (8 primers). The results revealed an extraordinarily high level of genetic diversity ( at species level,percentage of polymorphic loci PPB = 91.04% , effective number of alleles N_e = 1.5244 , Nei′s (1973 ) gene diversity H_e= 0.3070, and Shannon′s information index H_o = 0 . 4618 ; at population level, PPB = 55. 04% , N_e = 1.3826, Nei′s (1973) gene diversity H_e = 0.2171, and Shannon′s information index H_o = 0.3178). The level of genetic differentiation between populations is lower than that among populations . The low level of genetic differentiation among populations was detected, based on Nei′s genetic diversity analysis (29.44%), and AMOVA (36.50%). There is no associations between geographical distance and genetic identity.We suggest that Jatropha curcas of Yunnan Province might not be introduced from the same place.     

野生地椒的斑块多样性及空间结构

将ISSR、SRAP分子标记与空间自相关分析技术相结合,对我国野生百里香属植物分布最南端 的怀远3个地椒居群进行了以斑块为单位的遗传多样性、克隆多样性和克隆结构、空间结构的研究.结果表明：地椒野生居群内不同斑块间存在较高的遗传多样性和克隆多样性,多样性条带百分率为75.75％,Nei基因多样性指数为0.2537, Shannon信息多样性指数为0.3811,基因型比率平均为0.61,Simpson指数平均为0.96,Fager均匀性指数平均为0.91.居群间的遗传分化较低,在总的遗传多样性中,90.35%来自居群内斑块间的变异,居群间占9.65％.野生地椒居群间无共有基因型斑块,居群内不同斑块间在一定范围内具有镶嵌性,克隆斑块间的分布范围主要集中在0～25 m.该地区地椒居群除了在部分位点呈现一定相关性外,总体缺乏空间结构.该地区野生地椒种群斑块的建立应为种子入侵所致,其后克隆繁殖对斑块的发展及种群的扩张起到了主要作用.     

云南南部不同种源地小桐子遗传多样性的ISSR 分析

应用ISSR 分子标记方法对采自云南的8 个居群的小桐子( Jatropha curcas) 共158 个个体进行遗传多样性分析。8 个ISSR 引物共扩增到了67 个位点, 其中61 个是多态性位点。分析结果表明: (1) 云南小桐子的遗传多样性水平很高。在物种水平上, 平均每个位点的多态位点百分率PPB = 91.04% , 有效等位基因数N_e = 1.5244, Nei′s 基因多样性指数H_e= 0.3070, Shannon 多样性信息指数H_o = 0.4618; 在居群水平上, PPB = 55.04%, N_e = 1.3826, H_e = 0.2171, Shannon 多样性信息指数H_o = 0.3178。(2) 居群间的遗传分化低于居群内的遗传分化。基于Nei''s 遗传多样性分析得出的居群间遗传多样性分化系数G_st = 0.2944。AMOVA分析显示: 云南小桐子的遗传变异主要存在于居群内, 占总变异的63.50%, 居群间的遗传变异占36.50%。(3) 居群间的地理距离及遗传一致度并不存在相关性。鉴于以上指标, 我们推测云南小桐子可能来自不同的地区。     

基于SSR分子标记的73份山葡萄及杂交后代的遗传多样性分析

采用SSR分子标记技术,分析俄罗斯葡萄资源及东北山葡萄资源的遗传多样性及亲缘关系,旨在为葡萄种质资源利用与创新及分子标记辅助育种提供依据。筛选11对多态性好的SSR引物分析了10份东北山葡萄品种和63份俄罗斯引种葡萄的遗传多样性及亲缘关系。11对引物在73份葡萄资源中共检测到75个等位基因,每个位点扩增3(VVIN31)-10(VVS2)个等位基因,平均等位基因6.8182个,有效等位基因(Ne)在5.280(VVS2)-1.3050(VVIN31)之间,平均值为3.5196;Shannon多态性信息指数(I)范围1.8830(VVS2)-0.4678(VVIN31),平均值1.3736;各位点多态性信息含量(PIC)变化范围为0.2337(VVIN31)-0.8098(VVS2)平均值0.6440,其中VVIN31、VMCA12位点只具有低中度多态性;Nei’s遗传多样指数在0.8098(VVS2)-0.2337(VVIN31)之间,平均值0.6444,表明各位点遗传多样性存在较大差异,等位基因在群体内的分布不均匀;观测杂合度变化范围为0.1667-0.9315,平均值0.4642,期望杂合度变化范围0.8154-0.2353,平均值为0.6489,不同位点杂合度差异较大,平均观测杂合度低于期望杂合度,表示种群内存在一定的近交率,杂合体缺失,纯合体较多;遗传分化系数Fst平均值为0.1183。基因流Nm平均值为1.8641,种质中度遗传分化,基因流较大。聚类分析结果表明东北山葡萄资源与俄罗斯野生葡萄资源亲缘关系较近,与俄罗斯选育葡萄资源亲缘关系较远;俄罗斯选育品种的遗传多样性高于山葡萄品种与俄罗斯野生葡萄资源。11对SSR引物含有丰富的多态性信息,73份葡萄资源产生了中度的遗传分化,基因流较丰富,俄罗斯葡萄资源的遗传多样性较丰富,可用于山葡萄新品种选育。     

Use of SRAP markers to assess genetic diversity and population structure of wild, cultivated, and ornamental pomegranates (Punica granatum L.) in different regions of Iran

Sequence-related amplified polymorphism (SRAP) was used to assess the genetic diversity of 63 cultivated, wild, and ornamental pomegranate genotypes from five different geographical regions of Iran. A total of 250 fragments were amplified using 13 primer combinations; among these, 133 bands (53?%) were polymorphic. The average PIC value was 0.28 over all PCs. The genetic distance among genotypes ranged from 0.10 to 0.37 with an average of 0.24. Cluster analysis using the neighbor-joining (NJ) method suggested there are close relationships between ornamental and some wild genotypes. Although AMOVA results revealed significant differences in the genetic diversity among the regions (P?=?0.0048), the genetic variation was mainly caused by variation of intra regions. The results indicated low genetic differentiation (Fst?=?0.025) and high gene flow (Nm?=?2.28) among regions. These results confirmed that SRAP markers could be powerful tools and an effective marker system for determining the genetic diversity and population genetic structure of the pomegranate.     

野生狗牙根种质遗传多样性的SRAP研究

采用SRAP分子标记技术, 对采自中国四川、重庆、贵州、西藏四省区的32份野生狗牙根(Cynodon dactylon)材料进行遗传多样性分析, 获得下述结果：(1)用14对引物组合共得到132条多态性条带, 平均每对引物扩增出9.4条多态带, 多态性位点百分率为79.8%, 材料间的遗传相似系数范围在0.591到0.957之间, 平均GS值为0.759, 这些结果说明, 供试野生狗牙根具有较为丰富的遗传多样性; (2)对所有材料进行聚类分析, 可聚为4类, 大部分来自相同或相似生态地理环境的材料聚为一类, 表明供试材料的聚类和其生态地理环境间有一定的相关性; (3)基于Shannon多样性指数估算了6个狗牙根生态地理类群内和类群间的遗传分化, 发现类群内遗传变异占总变异的65.56%, 而类群间遗传变异占总变异的34.44%; (4)对各生态地理类群基于Nei氏无偏估计的遗传一致度的聚类分析表明, 各生态地理类群间的遗传分化与其所处的生态地理环境具有一定的相关性。     

Genetic diversity and peculiarity of annual wild soybean (<Emphasis Type="Italic">G. soja</Emphasis> Sieb. et Zucc.) from various eco-regions in China

Annual wild soybean (Glycine soja Sieb. et Zucc.) is believed to be a potential gene source for future soybean improvement in coping with the world climate change for food security. To evaluate the wild soybean genetic diversity and differentiation, we analyzed allelic profiles at 60 simple-sequence repeat (SSR) loci and variation of eight morph-biological traits of a representative sample with 196 accessions from the natural growing area in China. For comparison, a representative sample with 200 landraces of Chinese cultivated soybean was included in this study. The SSR loci produced 1,067 alleles (17.8 per locus) with a mean gene diversity of 0.857 in the wild sample, which indicated the genetic diversity of G. soja was much higher than that of its cultivated counterpart (total 826 alleles, 13.7 per locus, mean gene diversity 0.727). After domestication, the genetic diversity of the cultigens decreased, with its 65.5% alleles inherited from the wild soybean, while 34.5% alleles newly emerged. AMOVA analysis showed that significant variance did exist among Northeast China, Huang-Huai-Hai Valleys and Southern China subpopulations. UPGMA cluster analysis indicated very significant association between the geographic grouping and genetic clustering, which demonstrated the geographic differentiation of the wild population had its relevant genetic bases. In comparison with the other two subpopulations, the Southern China subpopulation showed the highest allelic richness, diversity index and largest number of specific-present alleles, which suggests Southern China should be the major center of diversity for annual wild soybean. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

山西霍山五角枫不同海拔种群遗传多样性研究

利用SRAP分子标记分析山西霍山不同海拔五角枫种群的遗传多样性和遗传结构。11对引物组合共得到88个重复性好的位点;Nei基因多样性指数（ h）在0.1996～0.3163之间,平均为0.2373;Shannon多样性指数（ I）范围为0.2995～0.4936,平均为0.3535;在物种水平上,多态位点百分率（ PPB）为98.86％,表现出较高地遗传多样性。 ANOVA分析表明,遗传变异主要存在于五角枫种群内（79％）,21％的分子变异分布在种群间。基于遗传距离进行UPGMA聚类分析,5个五角枫种群聚为明显的2支。相关分析显示：五角枫的多样性指数与地理梯度均无显著或极显著相关。     

基于SRAP标记的山药种质资源遗传多样性分析

目的:研究我国山药种质资源遗传多样性,为合理利用资源和开展选育种工作提供理论依据。方法:以国内94份山药种质资源为材料,采用SRAP标记并通过NTSYS2.10软件进行SHAN聚类分析、PROJECTION主成分分析;利用POPGENE软件估算遗传多样性参数。结果:从49对SRAP引物中筛选出30对能产生稳定清晰可辨的扩增产物的引物,共扩增出754条DNA带,其中多态性条带616条,占总条带的81.7%。聚类结果表明:当遗传相似系数(GS)为0.822时,可将94份资源分为5类:第Ⅰ类20份、第Ⅱ类43份、第Ⅲ类7份、第Ⅳ类3份、第Ⅴ类21份。第Ⅰ、Ⅱ、Ⅲ、Ⅴ类分别为薯蓣、褐苞薯蓣、山薯和参薯。主成分分析结果显示:第一与第二主成分可解释88.34%(82.10%和6.24%)的遗传总变异。遗传多样性参数分析表明:比较5个遗传多样性参数值,5个群体的遗传多样性水平表现为Ⅰ>Ⅴ>Ⅲ>Ⅱ>Ⅳ,第Ⅰ类(薯蓣)遗传多样性水平高;山药遗传群体间遗传分化系数为51.88%,大部分差异存在于群体之间,群体间遗传分化高。结论:山药种质资源丰富且群体遗传分化高,有利于山药新品种的选育。SRAP标记可有效应用于山药种质资源的鉴别和遗传多样性分析。通过DNA指纹鉴定技术鉴别山药品种具有重要性与紧迫性。     

蕙兰SSR引物开发及渝贵川地区兰属遗传多样性研究

采用磁珠富集法对野生蕙兰DNA进行SSR引物开发,并以开发出的多态性引物为研究工具,选取来自渝、责、川3省(市)的9个野生兰属居群为研究对象,探讨遗传多样性与其地理位置分布的关系,从而在分子水平上为如何保护兰属植物提供有利参考.结果 显示:8对SSR引物共扩增出53个等位基因,平均每个位点的等位基因为6.6250个,平...     

Population genetics of wild Hizikia fusiformis (Sargassaceae, Phaeophyta) along China’s coast

Hizikia fusiformis is one of the important commercially cultivated seaweeds in China. Inter-simple sequence repeats (ISSR) and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic structure of nine wild H. fusiformis populations collected along the coast of China. Of the 255 bands generated by 21 ISSR primers, 99.61% were polymorphic and 99.71% of 344 bands amplified by 30 SRAP primers were polymorphic. The tested high genetic diversities show that the average Nei’s genetic diversity (H) were 0.1519 and 0.1624, and average Shannon’s information index (I) were 0.2248 and 0.2400 in ISSR and SRAP analyses, respectively. Unweighted pair group method with arithmetic mean (UPGMA) dendrograms of the nine populations were divided into two main groups. The ISSR and SRAP analyses values of gene differentiation (G _ST, 0.5955, 0.5486, respectively) indicate that high variation exists among the nine populations, likely due to external interferences and limitation of gene flow (N _m?=?0.3397, 0.4114). Our study indicated that human activities and herbivore overgrazing had influenced the natural Hizikia populations and that the understanding of population genetics would be helpful in sustainable utilization and biomass conservation of Sargassaceae resources.     

香稻资源遗传多样性的比较

利用60个水稻SSR标记, 对来自国内外的370份香稻材料的遗传多样性进行了比较分析。结果共检测到361个等位基因, 每个位点的等位基因变幅为2~10个, 平均Nei基因多样性指数(He)为0.663, 变幅为0.104(RM308)~0.885(RM2634)。籼粳亚种间的遗传多样性具有明显差异, 籼稻的等位基因数和Nei基因多样性指数均高于粳稻。地方品种的遗传多样性高于选育品种, 选育品种等位基因数仅为地方品种的86.5%。分子方差分析表明, 香稻材料中总变异的43.08%是由于亚种间的遗传差异引起的。不同稻区的遗传分化程度总体介于1.69%~14.40%之间。其中, 华南与西南、华中与西南地方品种间遗传差异的分化程度达显著水平。聚类分析将参试材料明显分为籼粳两大类, 同时地域相同(稻区)、相邻省份的香稻材料基本归为同一类群。     

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。     

Evaluation of genetic diversity in Piper spp using RAPD and SRAP markers

Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) analysis were applied to 74 individual plants of Piper spp in Hainan Island. The results showed that the SRAP technique may be more informative and more efficient and effective for studying genetic diversity of Piper spp than the RAPD technique. The overall level of genetic diversity among Piper spp in Hainan was relatively high, with the mean Shannon diversity index being 0.2822 and 0.2909, and the mean Nei's genetic diversity being 0.1880 and 0.1947, calculated with RAPD and SRAP data, respectively. The ranges of the genetic similarity coefficient were 0.486-0.991 and 0.520-1.000 for 74 individual plants of Piper spp (the mean genetic distance was 0.505 and 0.480) and the within-species genetic distance ranged from 0.063 to 0.291 and from 0.096 to 0.234, estimated with RAPD and SRAP data, respectively. These genetic indices indicated that these species are closely related genetically. The dendrogram generated with the RAPD markers was topologically different from the dendrogram based on SRAP markers, but the SRAP technique clearly distinguished all Piper spp from each other. Evaluation of genetic variation levels of six populations showed that the effective number of alleles, Nei's gene diversity and the Shannon information index within Jianfengling and Diaoluoshan populations are higher than those elsewhere; consequently conservation of wild resources of Piper in these two regions should have priority.     

Genetic diversity and population structure of Butea monosperma (Lam.) Taub.- a potential medicinal legume tree

Three molecular marker systems, Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeats (ISSR) and Sequence-Related Amplified Polymorphism (SRAP) were employed to investigate the genetic structure and diversity among the 14 natural populations of Butea monosperma collected from different geographical regions of India. Detected by 17 RAPD, 15 ISSR and 11 SRAP primer combinations, the proportions of polymorphic bands were 84.2 %, 77.2 % and 91.9 %, respectively, and the mean Nei’s genetic distances among the populations were 0.13, 0.10 and 0.13, respectively. Partitioning of genetic variability by Analysis of molecular variance (AMOVA) revealed that the high genetic diversity was distributed within the populations. AMOVA also revealed that the coefficient of gene differentiation among populations based on F_ST was very high irrespective of markers used. The overall gene flow among populations (Nm) was very low. Cophenetic correlation coefficients of Nei’s distance values and clustering pattern by Mental test were statistically significant for all three marker systems used but poor fit for ISSR data than for RAPD, SRAP and combined data set of all three markers. For all markers, a high similarity in dendrogram topologies was obtained, although some differences were observed with ISSR. The dendrogram obtained by RAPD, SRAP and combined data set of all three markers reflect relationship of most of the populations according to their geographic distribution.     

Genetic diversity in Vicia amoena (Fabaceae) germplasm resource in China using SRAP and ISSR markers

The genetic diversity in 17 germplasms of Vicia amoena L. from north China was analyzed using SRAP and ISSR markers. Three hundred and sixty-eight (94.11%) polymorphic bands (211 and 157 obtained from 20 pairs of SRAP and ISSR primers, respectively) were scored. Although SRAP was more effective than ISSR markers with higher PIC, RP and larger variation range of genetic distance, both the markers were useful for assessing V. amoena genetic diversity. Cluster analysis showed that the 17 germplasms were clustered into 5 groups. The results of principal coordinate analysis supported UPGMA clustering. The germplasms from source areas where the annual average temperature ranged from −1.0 to 5 °C exhibited the highest level of genetic diversity with the highest PPI, I and H. These results have important implications in genome mapping, breeding purposes, and germplasm conservation.     

濒危植物翅果油树种群的遗传多样性和遗传分化研究

利用微卫星（SSR）标记对来自山西和陕西两省的7个翅果油树（Elaeagnus mollisDiels）种群进行遗传多样性和遗传结构研究。10对SSR标记共检测到126个位点,其中多态位点114个。在物种水平上,平均多态位点百分率为90.79%,有效等位基因数（Ne）、Nei基因多样性指数（H）和Shannon多样性指数（I）分别为1.6072、0.3166、0.4603;在种群水平上,多态位点百分率为61.99%,有效等位基因数（Ne）、Nei’s基因多样性指数（H）、Shannon多样性指数（I）分别为1.5445、0.2683、0.3815。遗传分化系数GST为0.2074,表明了翅果油树种群的遗传变异主要存在于种群内。基因流Nm为1.9111〉1,说明种群间基因交流可以阻止由于遗传漂变导致的遗传分化。聚类结果表明,翅果油树种群间的遗传距离与地理距离有一定的相关性,经Mantel检验,种群的地理距离与遗传距离之间呈正相关,但未达到显著水平（p〉0.05）。结果表明,遗传多样性水平与物种本身特性和不同干扰生境有关,濒危植物并不一定表现为遗传变异水平的降低。     

Genetic Diversity of Global Aromatic Rice Varieties

Genetic diversity of 434 rice accessions collected from 16 countries, including 345 fragrance rice varieties and 89 non fragrance rice varieties, have been analyzed. A total of 573 alleles were detected by using 77 simple sequence repeats (SSR) primer pairs covering all rice 12 chromosomes. The value of allelic polymorphism information content (PIC) ranged from 0090 to 0845, with an average of 0516 per locus; Gene diversity (GD) varied from 0091 to 0859, with an average of 0573; The mean value of major allele frequencies (MAF) was 0540, covering from 0251 to 0953. In addition, 434 rice accessions are divided into three sub populations by cluster and population structure analysis, and FST between sub populations showed a mean of -0116, ranging from -0623 to 0494; The score of genetic distance calculated by Nei′s method appeared from 0207 to 0355. Major allele frequencies within each sub population distributed from 0408 to 0746, and gene diversity level from 0354 to 0699, while PIC from 0320 to 0658. Sequencing 6 mitochondrion genes in 18 rice varieties exhibited no different in 5 genes, whereas Mit4 contains a 3 SNPs in the gene body, which acts as an important marker to understanding the relationship between Indica/Japonica differentiation and the evolution of fragrant gene. Finally, genetic diversity and mitochondrion gene sequencing would help to know about the origin of fragrant resource and benefit rice breeding.