Genetic diversity of the annual weed Monochoria vaginalis in southern China detected by random amplified polymorphic DNA and inter-simple sequence repeat analyses

Two molecular genetic screening techniques, RAPD (random amplified polymorphic DNAs) and ISSR (inter-simple sequence repeats), were applied to detect the level and pattern of genetic diversity of Monochoria vaginalis, a common weed of rice fields, in seven populations from southern China. Among these populations, 116 bands were amplified by 18 RAPD primers, of which 34 bands (29.31%) were polymorphic, and 14 ISSR primers produced 111 bands with 87 polymorphic bands (78.38%). Within each population, a relatively low level of genetic diversity was detected by both RAPD and ISSR analyses, with a mean genetic diversity (H) of 0.0348 and 0.0551 respectively. Analysis of molecular variance of the data from the RAPD and ISSR markers detected that the majority of total genetic variation existed among populations (73.50% and 76.70% respectively) and only minor genetic variation within populations (26.50% and 23.30% respectively). Cluster analysis divided the seven populations into two groups, indicating that the genetic relationships among populations have relatively low correlation with their geographical distribution (Mantel test; r = 0.45 and 0.48 respectively). Our results indicated that both RAPD and ISSR markers were effective and reliable for accurately assessing the degree of genetic variation of M. vaginalis. Comparing the two techniques, ISSR markers were more efficient than the RAPD assay. The Mantel test gave r = 0.16, suggesting no correlation between these two molecular markers.     

Genetic diversity of herbicide-resistant and -susceptible Avena fatua populations in North Dakota and Minnesota

Genetic diversity within and among 20 herbicide-resistant (HR) and 16 herbicide-susceptible (HS) Avena fatua multi-field populations was determined using 82 polymorphic loci resulting from two intersimple sequence repeat (ISSR) primers and one long-primer random amplified polymorphic DNA (LP-RAPD) primer. Collections from the Red River Valley of North Dakota and Minnesota, sampled in 1964 and 2000, represented A. fatua populations before and after intensive exposure to herbicides. A 1995 collection from south-west North Dakota represented A. fatua exposed to low herbicide selection. Despite differences in years of herbicide exposure among collections, both HR and HS populations from every collection maintained nearly similar levels of ISSR and RAPD diversity. Genetic differentiation among populations (G_ST) varied from 11% to 13% among HR populations and from 9% to 16% among HS populations, indicating that 84–91% of total variation remained within HS or within HR populations. Minimal difference in gene diversity between HR and HS is consistent with multiple origins of resistance, where HR A. fatua most likely evolved from diverse founding individuals.     

Genetic Structure and Variation in Aggressiveness in European and Australian Populations of the Grapevine Dieback Fungus, Eutypa lata

Eutypa lata is an ascomycete fungus causing a severe dieback in grapevine. The genetic structure of populations of E. lata from seven regions in Australia, France, Italy and Spain was examined using 20 random amplified polymorphic DNA (RAPD) markers. In some regions, populations were subdivided and a total of 14 samples were analysed. A total of 231 RAPD haplotypes were found among the 240 isolates. Vegetative compatibility testing further demonstrated that isolates of the same haplotype were genetically distinct. Gene diversity was the highest in the population from northern Italy and lowest in the Alsace region in France. Linkage disequilibrium between pairs of putative loci was very low and most of the multilocus analyses were consistent with the hypothesis of random association of the loci. This suggests that random mating occurred in every population and that the sexual stage shapes the genetic structure of E. lata populations in the regions sampled. Only 6% of the total variability was attributable to differences between populations. Nevertheless, significant differences in allele frequency appeared with respect to six RAPD markers indicating some genetic differentiation between populations. This differentiation appeared attributable to differences between the Italian and Spanish populations and the other populations. We thus hypothesize that a restriction of gene flow exists within Europe. The population from Australia was genetically closer to the French and Spanish populations than to that from Italy. Genetic diversity is associated with considerable variation in aggressiveness, which was assessed on cuttings in the greenhouse in six populations. All populations included a range of isolates differing in aggressiveness, but the Italian population seemed to have more isolates with low aggressiveness.     

Genetic variation within and between southern Ontario populations of Sclerotinia homoeocarpa

Restriction fragment length polymorphisms (RFLP) of the intergenic spacer region (IGS) of rDNA and random amplified polymorphic DNA (RAPD) markers were used to survey genetic variability among 181 isolates of Sclerotinia homoeocarpa from Ontario and 10 isolates from Japan. RAPD and IGS-RFLP analyses revealed polymorphisms within and between populations of S . homoeocarpa , distinguishing 151 genotypes. Both types of markers gave similar results in phenetic analysis of genetic distances between populations. Cluster analysis showed that Japanese isolates of S. homoeocarpa were genetically distinct from Ontario isolates, demonstrating significant intraspecific differentiation. An average genetic similarity of 0.66 was found between Japanese isolates. Among Ontario isolates, average genetic similarity was 0.86, and genotypic diversity analysis showed that 49.3% of the total genetic variation observed within Ontario populations occurred among individuals within populations compared to 50.7% between populations. Gametic linkage disequilibrium analysis within Ontario populations revealed an average 15.6% significant nonrandom associations between putative RAPD loci, and that half of the populations showed signs of significant linkage disequilibrium. These results suggest that both clonal propagation and recombination events occurred in local populations of S. homoeocarpa . The high level of genetic similarity between populations and the low levels of intraspecific genetic variation may reflect a small founding population for southern Ontario isolates of S. homoeocarpa .     

Genetic and morphologic diversity of <Emphasis Type="Italic">Echinochloa crus-galli</Emphasis> populations from different origins

Echinochloa crus-galli (L.) P. Beauv. (barnyardgrass) is an annual weed that is native to Asia and found throughout the world. The broad ecological tolerance and competitive ability of E. crus-galli makes it the most important weed species in rice. Genetic studies of plants are becoming increasingly common because reliable information is necessary to better understand population dynamics, occurrence of herbicide resistance, and demographic data. Echinochloa crus-galli populations from 34 different locations in Turkey were compared with respect to morphological differences and genetic variation. For morphological variation, five seeds of each population were sown in pots and grown in a screenhouse using a randomized block design. Morphological parameters such as germination speed, flowering time, leaf area, plant height, spikelet length, above-ground biomass, root dry weight and number of seeds were measured. Distinct differences among populations with respect to hierarchical cluster analysis were observed. Genetic variations among populations were performed using random amplified polymorphic DNA (RAPD) markers. The seven RAPD primers amplified 55 bands whose molecular weight varied between 200 and 4000 bp. The percentage of polymorphic bands was 74.54%. Results showed high morphological and genetic variability among individual genotypes within geographic locations. Phenotypic and genetic variability among E. crus-galli populations would be influenced by agricultural practices, crop characteristics, geographic location and herbicide pressure. Differences between weed populations may affect response to chemical or biological control.     

Analysis of genetic diversity in <Emphasis Type="Italic">Monilinia fructicola</Emphasis> from the Ebro Valley in Spain using ISSR and RAPD markers

The genetic diversity of Spanish and French field populations of Monilinia fructicola, a quarantine fungal pathogen in Europe, was compared with that of Californian, Uruguayan, and New Zealand M. fructicola populations using inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis and principal component analysis (PCA) of the ISSR data set revealed that the Spanish and French M. fructicola isolates were more closely related between themselves than to the non-European isolates. The levels of genetic diversity in the Spanish and French isolates are lower than those of the non-European isolates, indicating that M. fructicola is a recently introduced pathogen. UPGMA cluster analysis and PCA of the combined ISSR + RAPD data set of the European M. fructicola populations revealed that the Spanish isolates were more closely related among themselves than with the French isolates. Analysis of molecular variance partitioned the genetic variance to among the two regions (Spain and France) (20%), among the regional populations (35%), and within the populations in each region (45%) suggesting restricted gene flow between the three European populations. The observed index of association (I_A) in each European M. fructicola populations indicates that the French and Spanish populations of M. fructicola are mainly asexually reproducing, with the Sudanell population potentially having a teleomorphic stage. The present finding of low genetic diversity in the Spanish and French M. fructicola populations is probably due to founder effects and genetic drift.     

不同生境臭柏种群的遗传多样性分析及其与环境因子的相关性

毛乌素沙地臭柏群体是一个生态过渡带。为了进一步阐明分子变异和基因流与生境或生态过渡带的联系,应用RAPD标记开展了臭柏群体的分子生态学研究。采用随机扩增多态性DNA(RAPD)方法对臭柏(Sabina vulgaris.)的3个种群进行了研究.用11个随机引物扩增出129条清晰谱带,其中117条为多态性谱带。利用POPGENE3.2软件对数据进行处理,结果如下:(1)臭柏有着较丰富的遗传多态性,多态位点百分率达90.70%,各种群多态位点百分比在69.77%~72.87%之间.(2)臭柏的种群间分化较小Gst=0.1872,81.38%的遗传变异存在于种群内,各种群的遗传一致度都在86.22%.(3)聚类分析显示,生境相近的种群被聚到了一起,反映了臭柏种群的遗传分化和生境有着一定的相关性.又利用Nei,s指数统计了RAPD数据,也证实了大部分的遗传变异存在于群体之内。臭柏群体内的遗传多样性与土壤总钾呈显著的负相关。     

Genetic Variability and Population Structure of the Wheat Foot Rot Fungus, Fusarium culmorum, in Tunisia

The random amplified polymorphic DNA (RAPD) method was used to investigate the genetic variability and population structure of Fusarium culmorum isolated from wheat stem bases. A total of 108 isolates, representing seven geographically distinct populations, was collected from five climatic regions in Tunisia. Pseudo-allelic frequencies were estimated at each of the 25 putative RAPD loci analyzed by scoring for the presence or absence of amplified fragments; 92 haplotypes were found among the 108 strains. The analysis of the population structure did not reveal any trend with regard to geographic origin. Total gene diversity (H_T ^* = 0.318) was mostly attributable to diversity within populations (H_S ^* = 0.308). Analysis of molecular variance confirmed that most of the genetic variability was within populations. Genetic differentiation among populations was low to moderate (G_ST ^* ranged from 0 to 0.190 and averaged 0.041 over all loci). Cluster analysis with UPGMA using genetic distances did not reveal any spatial clustering of the isolates collected from the different geographic regions. Based on these results, we conclude that the F. culmorum isolates recovered from different regions in Tunisia might be part of a single population pool.     

不同干扰生境中荒漠小灌木红砂种群遗传多样性研究

应用RAPD标记技术对荒漠小灌木红砂(Reaumuria soongorica)种群在不同扰动下的遗传多样性进行了分析。18条随机引物对红砂6个种群的120个个体进行扩增,共检测102个位点,其中多态位点99个。研究结果表明:红砂种群的多态位点比率(P)为96.86%,显示了不同生境中红砂种群内存在较高的遗传多样性。Shannon多样性指数(0.5007)、Nei基因多样性指数(0.3307)和基因分化系数(Gst=0.1952)揭示了红砂种群遗传变异多存在于种群内,种群间的遗传分化则较小。聚类分析表明:红砂种群遗传距离与地理距离之间存在一定相关性;遗传多样性水平与物种特性和不同干扰生境有关,与生态因子无相关性。     

内蒙古亚洲小车蝗种群遗传多样性和遗传分化的ISSR分析

亚洲小车蝗Oedaleus asiaticus Bei-Bienko是我国北方草原和农牧交错区的主要害虫。为评价内蒙古地区亚洲小车蝗种群的遗传多样性和遗传分化,应用ISSR标记方法对内蒙古15个亚洲小车蝗种群遗传多样性及遗传分化进行了分析。结果表明,7条引物扩增出85条ISSR条带,均为多态性条带。多态性比例（P）、Nei''s遗传多样性指数（H）和香农多样性指数（I）分别为82.59%、0.2319和0.3421,表明亚洲小车蝗种群具有较高的遗传多样性。基因流（Nm）和基因分化系数（Gst）分别为1.2298和0.3352,表明亚洲小车蝗不同地理种群具有明显的遗传分化。遗传距离与地理距离呈极显著正相关关系。表明地理距离和地形差异可能是形成亚洲小车蝗种群遗传分化的主要原因。     

Random amplified polymorphic DNA (RAPD) analysis of Phytophthora infestans isolates collected in Canada during 1994 to 1996

Mating type, glucose-6-phosphate isomerase ( Gpi ) allozyme banding patterns, response to the fungicide metalaxyl and random amplified polymorphic DNA (RAPD) markers were used to characterize genetic variability among 141 Canadian isolates of Phytophthora infestans collected between 1994 and 1996. Multiple correspondence analysis of RAPD profiles separated isolates into 21 groups that were not correlated to groups defined by mating type, Gpi allozyme banding patterns or response to metalaxyl. Population subdivision analysis showed that 97% of the total genetic variation was found among individuals within populations, compared with 3% among populations. The average similarity coefficient among isolates was 80%. No significant differences in haplotypic diversity were observed among the years under study, but levels of genetic diversity among local populations of P. infestans were high (0.76). All classes of response to the fungicide metalaxyl were observed, with 55% of isolates displaying moderate levels of insensitivity. The high level of genetic diversity detected within populations indicates that migration and sexual recombination probably play important roles in the population biology of P. infestans in Canada.     

Molecular evidence supports hypervariability in Phytophthora colocasiae associated with leaf blight of taro

The oomycete Phytophthora colocasiae that causes taro leaf blight is the most devastating disease of taro and is widely distributed worldwide. Molecular and phenotypic techniques were employed for assessing and exploiting the genetic variability among four populations of P. colocasiae obtained from a fine spatial scale (multiple leaf blight lesions on single taro leaf). Phenotypic characters such as virulence, morphology and mating type showed no variation. ITS characterization revealed detectable polymorphism among isolates of P. colocasiae. The mean number of haplotypes (H), haplotype diversity (HD), nucleotide diversity (π), and nucleotide substitution rate (θ) among analyzed sequences were 6.75, 1.00, 0.069, and 0.088 respectively. High levels of inter and intra specific variation were detected by random amplified polymorphic DNA (RAPD) assays. Moderate genetic diversity (H?=?0.2651) was observed among populations of P. colocasiae. Analysis of molecular variance (AMOVA) confirmed that most of the genetic variability was confined to within a population (63.54 %). The coefficient of genetic differentiation among populations (G _ST ) was 0.2007 and estimates of gene flow (Nm) among populations was 1.991 migrants per generation. Cluster analysis using UPGMA revealed that individuals from the same population failed to cluster in one distinct group. The results of the study reveal considerable genetic diversity among and within populations of P. colocasiae obtained from fine spatial scale. The possible mechanisms and implications of this genetic variation are discussed.     

Genetic Structure of Mycosphaerella populorum (Anamorph Septoria musiva) Populations in North-Central and Northeastern North America

ABSTRACT In order to characterize the genetic variation of the poplar pathogen Mycosphaerella populorum (anamorph Septoria musiva), we have studied seven North American populations using the polymerase chain reaction random amplified polymorphic DNA (RAPD) technique. The fungal populations were sampled in 2001 and 2002 by obtaining 352 isolates from cankers and leaf spots in hybrid poplar plantations and adjacent eastern cottonwood (Populus deltoides). A total of 21 polymorphic RAPD markers were obtained with the six RAPD primers used. A fine-level scale analysis of the genetic structure within the populations revealed that subpopulations sampled on P. deltoides and on hybrid trees were not significantly differentiated. In contrast, analyses performed on the entire data set showed high levels of haplotypic diversity and moderate to high genetic differentiation, with 20% of the expected genetic diversity found at the interpopulation level. Moreover, a high and significant correlation between genetic and geographic distances among populations was found, suggesting isolation by distance of the sampled populations. Although the occurrence of the sexual stage of this fungus remained unclear in field populations, five of the six populations were at gametic equilibrium for RAPD loci, suggesting the occurrence of recombination episodes in Septoria musiva populations. Overall, S. musiva appears to consist of differentiated subpopulations, with both asexual and sexual recombination contributing to the local level of genetic structure.     

Genetic structure and diversity of Phakopsora pachyrhizi isolates from soyabean

Simple sequence repeat (SSR) markers were used to classify 116 isolates of Phakopsora pachyrhizi, the cause of soyabean rust, collected from infected soyabean leaves in four agroecological zones in Nigeria. A high degree of genetic variation was observed within the sampled populations of P. pachyrhizi. Eighty‐four distinct genotypes were identified among three of the four agroecological zones. Nei’s average genetic diversity across geographical regions was 0·22. Hierarchical analysis of molecular variance showed low genetic differentiation among all populations of P. pachyrhizi. The majority (> 90%) of the genetic diversity was distributed within each soyabean field, while approximately 6% of the genetic diversity was distributed among fields within geographic regions. Low population differentiation was indicated by the low F_ST values among populations, suggesting a wide dispersal of identical genotypes on a regional scale. Phylogenetic analysis indicated a strictly clonal structure of the populations and five main groups were observed, with group II accounting for 30% of the entire population. Because of the asexual reproduction of P. pachyrhizi, single‐step mutations in SSR genotypes are likely to account for the genetic differences within each group.     

Diversity of Phytophthora Clandestina Isolated From Subterranean Clover in Southern Australia: Analysis of Virulence and RAPD Profiles

The virulence spectrum of 112 isolates of Phytophthora clandestina collected from 56 sites in four subterranean clover-growing states in southern Australia was determined using differential cultivars of subterranean clover. Five races were detected, with race 0 in all states except New South Wales, race 1 in all states, race 2 only in Victoria, race 3 only in New South Wales, and race 4 in Victoria and Western Australia. The level of genotypic diversity among the different P. clandestina populations was investigated using five RAPD primers. Among 30 bands amplified, only two were polymorphic. This enabled identification of four multilocus RAPD genotypes. Three of the four genotypes occurred in all four states. Races 2 and 3 occurred with RAPD genotypes 1 and 2 only whereas races 0 and 1 occurred in all four multilocus RAPD genotypes. These results indicate that the pathogenicity spectrum of P. clandestina can change rapidly.     

Genetic diversity of Solanum elaeagnifolium,an invasive problematic weed in Jordan

Solanum elaeagnifolium (silverleaf nightshade) is a problematic weed that is common in Jordan and difficult to control. The weed exhibits distinct morphological variations in growth habit, leaf shape, leaf margins, flower colour and presence or absence of spines between individuals among and within populations suggesting genetic differences. Genetic variations among 61 samples of S. elaeagnifolium collected from heavily infested sites in the central Jordan Valley were investigated using six simple sequence repeat (SSR) markers and eight amplified fragment length polymorphism (AFLP) primer combinations. Results showed that 111 out of 675 AFLP bands were polymorphic generating polymorphism information content (PIC) of 38.0%, while 23 SSR polymorphic alleles were detected generating a PIC of 30.8%. Phylogenetic analysis using RaxML software identified four major clades with a clear clustering of the samples with their collection sites. Genetic analysis using both techniques revealed high level of genetic diversity among S. elaeagnifolium samples collected from a small geographical area indicating that a range of genetic diversity may be detected in weed populations across the country that may complicate its management.     

西南地区稻瘟病菌群体遗传多样性分析

为明确西南地区稻瘟病菌Magnaporthe grisea(Hebert)Barr群体遗传结构及其多样性水平,选用13对SSR引物对来自18个县(市)的221个稻瘟病菌单孢菌株进行PCR扩增,利用最长距离法和生物学软件进行聚类分析和群体遗传多样性分析。结果显示,13对SSR引物均能扩增出一条大小相同且清晰的条带,多态位点百分率高达100%。221个菌株在0.16相异水平上可划分为13个遗传宗谱,宗谱SCL01含205个菌株,占总菌株数的92.76%,为优势宗谱;宗谱SCL02~SCL013为劣势宗谱,差异极大。在群体水平上,菌源丰富的8个区域稻瘟病菌群体的Nei’s基因多样性指数为0.2133,Shannon信息指数为0.3588,具有丰富的遗传多样性,且群体间差异较大;这8个种群基于UPGMA法大都聚为一类,种群遗传谱系与地理区域分布呈一定相关性,群体遗传多样性均值为0.2518,存在一定的遗传分化,且群体内多样性大于群体间,总遗传变异的59.37%存在于群体内。总体上,西南地区稻瘟病菌群体结构既有明显的优势宗谱,又存在许多复杂多变的特异性小宗谱,具有丰富的遗传多样性,与地理分布关系较为密切。     

Genotypic Diversity of the Wheat Leaf Blotch Pathogen Mycosphaerella Graminicola (anamorph) Septoria Tritici in Germany

The population structure and genotypic diversity of Mycosphaerella graminicola from six natural field populations in Germany were studied with molecular markers. To reveal the potential effects of plant host resistance on the pathogen population, hierarchical samples were taken from susceptible and resistant cultivars. A total of 203 single spore isolates was subjected to molecular marker analysis using the amplified fragment length polymorphism technique (AFLP). Among the 203 isolates analyzed, 142 different multilocus haplotypes (MLH) were identified revealing a high degree of genotypic diversity of the M. graminicola population. On average, a F _ST value of 0.04 was found, indicating a low genetic differentiation with only 4% of the genetic variation between the local populations but leaving 96% of the genetic variation within the populations. According to the low F _ST value, a high migration rate of Nm 12 was found. The observed high within-population diversity, and the significant migration between populations, prevented genetic isolation and differentiation of putative geographically separated populations. Furthermore, plant host resistance had no obvious effect on the population structure and diversity of M. graminicola. Genotypic variability can be attributed to sexual recombination which appears to have a considerably larger influence on the population structure. Gene flow on this scale could have significant implications for plant breeding and fungicide spraying programmes.     

Comparison of Genetic and Virulence Diversity of Melampsora larici-populina Populations on Wild and Cultivated Poplar and Influence of the Alternate Host

ABSTRACT The aims of this study were, first, to compare the genetic and virulence diversity between populations of the rust fungus Melampsora larici-populina on wild and cultivated poplar stands and, second, to investigate the influence of the presence of the alternate host of the pathogen, larch, on which its sexual reproduction occurs, on these diversities. Nine French M. larici-populina populations collected from poplar trees in autumn and four populations collected from larch trees during the following spring were analyzed using both virulence factors and neutral markers. In all, 30 pathotypes were identified within the 13 populations studied. The pathotypic structure clearly distinguished the cultivated stands with high richness and complexity from the wild stands with low richness and complexity. High linkage disequilibria between virulences indicated preferential virulence associations, probably due to selection by the host. In all, 19 random amplified polymorphic DNA (RAPD) markers were used, which revealed a very high genetic diversity in the 743 isolates analyzed. The nine populations from poplar appeared moderately differentiated, indicating long-distance gene flow, and no isolation by distance was found. Linkage disequilibria between RAPD markers generally were low, indicating frequent recombination, but they were not lower in populations located near larch, probably due to long-distance dispersal.     

玉米新月弯孢菌(Curvularia lunata)的RAPD分析

 对分离自玉米弯孢菌叶斑病标样中的77株新月弯孢菌和1株来自水稻的新月弯孢菌进行RAPD分析表明,菌株间具有丰富的遗传多样性,在相似系数约0.60处,所有菌株被聚为3个组,但88.0%的菌株聚入第Ⅰ组内,其余菌株被聚入另外2个组内。第Ⅰ组内共有69个菌株,包含来自不同区域的致病性较强的菌株,是玉米弯孢菌叶斑病的优势类群,其余2个类群主要是一些致病能力较弱或不致病的菌株。结果表明,新月弯孢菌种内菌株的遗传多样性与致病性相关,但与菌株地理来源无明显的直接关系。