Analysis of diversity in populations of plant pathogens: the barley powdery mildew pathogen across Europe

Understanding population genetics and evolution within species requires recognition of variation within and between populations and the ability to distinguish between the potential causes of an observed distribution of variation. For this aim several established indices of diversity, and a novel one, were applied to population samples of the barley powdery mildew pathogen,Erysiphe graminis f. sp.hordei. Random spore samples were obtained from the air along transects through regions of interest across large parts of Europe in 1990. Significant geographical differences in diversity of virulence genotypes occurred among regional sub-samples. Diversity was highest in the samples from eastern Germany, Denmark and Austria, whereas the lowest values were found in the samples from Italy, southern France and parts of western Germany. Diversity in the pathogen population was generally related to the degree of diversification of host resistance in time and space, although there was considerable variation in ranking among different measures of diversity. Sensitivity to sample size proved to be the major problem with the use of several established indices of diversity. Working with very large sample sizes we used multiple random subsamples of various smaller sizes to determine how the mean index values changed with changing sample size. The Shannon index proved to be considerably affected by sample size, in contrast to the Simpson index that was therefore used as a global measure of diversity. Limits of confidence were estimated for the Simpson index using the bootstrap method of numerical resampling. The two aspects contributing to global diversity, richness and evenness, were considered separately to allow meaningful interpretation of the Simpson index. Random sub-sampling was used to reduce the influence of sample size differences for these measures. Dissimilarity, a novel measure of diversity for use in plant pathology, indicates the average number of major genes for host resistance against which pathotypes in a sample respond differently. It is thus able to account for the genetic relationship among pathotypes, which is not considered by any other index. The approaches developed in this study help to compare major forces driving evolution of large-scale populations of the barley mildew pathogen.     

The Genetic Structure of Australian Populations of Mycosphaerella musicola Suggests Restricted Gene Flow at the Continental Scale

ABSTRACT Mycosphaerella musicola causes Sigatoka disease of banana and is endemic to Australia. The population genetic structure of M. musicola in Australia was examined by applying single-copy restriction fragment length polymorphism probes to hierarchically sampled populations collected along the Australian east coast. The 363 isolates studied were from 16 plantations at 12 sites in four different regions, and comprised 11 populations. These populations displayed moderate levels of gene diversity (H = 0.142 to 0.369) and similar levels of genotypic richness and evenness. Populations were dominated by unique genotypes, but isolates sharing the same genotype (putative clones) were detected. Genotype distribution was highly localized within each population, and the majority of putative clones were detected for isolates sampled from different sporodochia in the same lesion or different lesions on a plant. Multilocus gametic disequilibrium tests provided further evidence of a degree of clonality within the populations at the plant scale. A complex pattern of population differentiation was detected for M. musicola in Australia. Populations sampled from plantations outside the two major production areas were genetically very different to all other populations. Differentiation was much lower between populations of the two major production areas, despite their geographic separation of over 1,000 km. These results suggest low gene flow at the continental scale due to limited spore dispersal and the movement of infected plant material.     

Population structure and reproductive mode of Didymella fabae in Syria

Didymella fabae is a highly destructive fungal pathogen of faba bean (Vicia faba) that represents a significant yield‐limiting biotic constraint in all locations where the crop is grown. However, nothing is known about the population structure of this pathogen anywhere in the world. Population genetic analyses employing 18 sequence‐tagged microsatellite (STMS) markers covering eight genetic linkage groups and a PCR‐based mating type marker were used to elucidate the genetic structure and reproductive mode of the pathogen in three populations in Syria. High gene diversity within populations but low genetic differentiation among populations was observed and the entire collection of isolates was assigned to a single genetic population using a Bayesian clustering algorithm. Independent analyses were performed based on four unlinked sets of STMS markers to infer reproductive mode. A simulation approach was used to estimate which of the repeated multilocus genotypes were probably the result of asexual reproduction and should be clone‐corrected. A 1:1 ratio of mating types could not be rejected in any clone‐corrected population, probably due to small sample sizes. Likewise, frequency of clones and sample size, but not marker linkage, had strong effects on multilocus gametic disequilibrium. The null hypothesis of random mating was rejected in the majority of populations for both non‐clone‐corrected and clone‐corrected samples and with four sets of unlinked markers indicating a predominance of asexual reproduction in these populations. This represents the first detailed screening of clonal and genetic composition of D. fabae populations in Syria.     

Genetic diversity and population structure of Plasmopara viticola in China

Grape downy mildew is a destructive oomycete disease worldwide for viticulture. A total of 440 infected leaf lesions were collected from nineteen vineyards distributing in the major viticulture regions in China. Six specific SSR markers were used to genetically characterize the Plasmopara viticola populations. A total of 60 alleles were generated and 324 distinct genotypes were identified based on these multi-locus markers. Most populations had high levels of genetic and genotypic diversity. AMOVA analysis showed that majority of the total genetic diversity was distributed within the vineyards while moderate to high genetic differentiation was also observed among some P. viticola populations. Three populations (BJ, GX, and GS2) were clearly separated from the rest of the populations by using PCA and Nei’s genetic distance analysis. Mantel test showed no significant correlation between unbiased Nei’s genetic distance and geographical distance.     

Spatial genetic structure and dispersal of the cacao pathogen Moniliophthora perniciosa in the Brazilian Amazon

Moniliophthora perniciosa is the causal agent of witches’ broom in Theobroma cacao (cacao). Three biotypes of M. perniciosa are recognized, differing in host specificity, with two causing symptoms on cacao or Solanaceae species (C‐ and S‐biotypes), and the third found growing endophytically on lianas (L‐biotype). The objectives of this study were to clarify the genetic relationship between the three biotypes, and to identify those regions in the Brazilian Amazon with the greatest genetic diversity for the C‐biotype. Phylogenetic reconstruction based on the rRNA ITS regions showed that the C‐ and S‐biotypes formed a well‐supported clade separated from the L‐biotype. Analysis of 131 isolates genotyped at 11 microsatellite loci found that S‐ and especially L‐biotypes showed a higher genetic diversity. A significant spatial genetic structure was detected for the C‐biotype populations in Amazonia for up to 137 km, suggesting ‘isolation by distance’ mode of dispersal. However, in regions containing extensive cacao plantings, C‐biotype populations were essentially ‘clonal’, as evidenced by high frequency of repeated multilocus genotypes. Among the Amazonian C‐biotype populations, Acre and West Amazon displayed the largest genotypic diversity and might be part of the centre of diversity of the fungus. The pathogen dispersal may have followed the direction of river flow downstream from Acre, Rondônia and West Amazon eastward to the rest of the Amazon valley, where cacao is not endemic. The Bahia population exhibited the lowest genotypic diversity, but high allele richness, suggesting multiple invasions, with origin assigned to Rondônia and West Amazon, possibly through isolates from the Lower Amazon population.     

Genetic structure of populations of Rhizoctonia solani anastomosis group-1 IA from soybean in Brazil

The Basidiomycete fungus Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen of soybean in Brazil, where the average yield losses have reached 30 to 60% in some states in Northern Brazil. No information is currently available concerning levels of genetic diversity and population structure for this pathogen in Brazil. A total of 232 isolates of R. solani AG1 IA were collected from five soybean fields in the most important soybean production areas in central-western, northern, and northeastern Brazil. These isolates were genotyped using 10 microsatellite loci. Most of the multilocus genotypes (MLGTs) were site-specific, with few MLGTs shared among populations. Significant population subdivision was evident. High levels of admixture were observed for populations from Mato Grosso and Tocantins. After removing admixed genotypes, three out of five field populations (Maranhao, Mato Grosso, and Tocantins), were in Hardy-Weinberg (HW) equilibrium, consistent with sexual recombination. HW and gametic disequilibrium were found for the remaining soybean-infecting populations. The findings of low genotypic diversity, departures from HW equilibrium, gametic disequilibrium, and high degree of population subdivision in these R. solani AG-1 IA populations from Brazil are consistent with predominantly asexual reproduction, short-distance dispersal of vegetative propagules (mycelium or sclerotia), and limited long-distance dispersal, possibly via contaminated seed. None of the soybean-infecting populations showed a reduction in population size (bottleneck effect). We detected asymmetric historical migration among the soybean-infecting populations, which could explain the observed levels of subdivision.     

Genotypic variation and population structure of Sclerotinia trifoliorum infecting chickpea in California

Sclerotinia trifoliorum, an important pathogen of cool season legumes, displays both homothallism and heterothallism in its life cycle, unique among members of the genus Sclerotinia. Very little is known about its genetic diversity and population structure. A sample of 129 isolates of S. trifoliorum from diseased chickpea in California was investigated for genetic diversity, population differentiation and reproductive mode. Genetic diversity was estimated using mycelial compatibility (MCG) phenotypes, rDNA intron variation, and allelic diversity at seven microsatellite loci. Genetic analysis revealed high levels of genotypic diversity demonstrated by high genotypic richness (0·88). Similarly, high levels of gene diversity (mean expected heterozygosity H_E = 0·68) were observed at the microsatellite loci. Geographic populations of S. trifoliorum were highly admixed as evident from low F_ST values (0–0·11), suggesting high contemporary or historical gene flow. Hierarchical analysis of molecular variance showed that more than 92% of the genetic variation occurred among isolates within populations. Bayesian clustering analysis identified four cryptic genetic populations that were not correlated to geographic location, and index of multilocus association was non‐significant in each of the four genetic populations. However, the presence of identical haplotypes within and among populations indicates clonal reproduction. The high levels of haplotype diversity and population heterogeneity, a lack of correspondence between MCG and microsatellite haplotype, and low levels of population differentiation suggest that populations of S. trifoliorum in chickpea have been undergoing extensive outcrossing and migration events probably shaped by human‐mediated dissemination, the underlying diverse cropping systems, and chickpea disease management practices.     

克拉玛依植物群落结构和物种多样性研究

采用多样性指数,丰富度指数和均匀度指数对克拉玛依植物群落物种多样性进行了研究。结果表明:各群落类型的物种多样性指数的顺序为:梭梭+碱蓬>花花柴、胡杨>碱蓬+麻黄>柽柳>琵琶柴>猪毛菜>梭梭>芦苇>盐节木>白刺+柽柳;灌木和乔木群落多样性指数和丰富度指数大于草本群落,而均匀度指数在乔木,灌木和草本群落中则表现出多样化的趋势。     

Epidemiology in mixed host populations

ABSTRACT Although plant disease epidemiology has focused on populations in which all host plants have the same genotype, mixtures of host genotypes are more typical of natural populations and offer promising options for deployment of resistance genes in agriculture. In this review, we discuss Leonard's classic model of the effects of host genotype diversity on disease and its predictions of disease level based on the proportion of susceptible host tissue. As a refinement to Leonard's model, the spatial structure of host and pathogen population can be taken into account by considering factors such as autoinfection, interaction between host size and pathogen dispersal gradients, lesion expansion, and host carrying capacity for disease. The genetic composition of the host population also can be taken into account by considering differences in race-specific resistance among host genotypes, compensation, plant competition, and competitive interactions among pathogen genotypes. The magnitude of host-diversity effects for particular host-pathogen systems can be predicted by considering how the inherent characteristics of a system causes it to differ from the assumptions of the classic model. Because of the limited number of studies comparing host-diversity effects in different systems, it is difficult at this point to make more than qualitative predictions. Environmental conditions and management decisions also influence host-diversity effects on disease through their effect on factors such as host density and epidemic length and intensity.     

人工绿洲防护林林下植物多样性研究

采用"标准地+样方"法,对克拉玛依农业综合开发区防护林林下植物群落进行调查,统计并计算林下植物的丰富度、物种多样性及均匀度。结果表明:(1)研究区防护林林下植物共有33种,主要以农田杂草为主;(2)研究区防护林林下植物物种多样性以紫穗槐林为最高,沙棘、沙枣林和柽柳林次之,杨树林和榆树林最小;(3)高郁闭度的乔木防护林对林下植物的生长有较强的抑制作用,林下植物多样性低,中等郁闭度的乔木防护林林下植物多样性最高,而灌木防护林林下植物多样性和均匀性都比较高,多样性在不同郁闭度下差异不大。文中旨在了解干旱区不同防护林林下植物群落的现状,为该地区防护林建设和经营提供科学依据。     

Population Genetic Structure of Septoria passerinii in Northern Great Plains Barley

ABSTRACT The genetic structure of Septoria passerinii from nine field populations was examined at several scales (within lesions, among lesions in a leaf, among leaves in a field, and among fields in North Dakota and western Minnesota) by using amplified fragment length polymorphism (AFLP) markers. A total of 390 isolates were sampled from seven barley fields located in North Dakota and two barley fields located nearby in western Minnesota in 2003 and 2004. Based on 57 polymorphic AFLP markers, AFLP DNA fingerprints identified 176 different genotypes among 390 (non-clone-corrected) isolates in nine different fields. In two intensively sampled sites, ND16 (Williston, ND) and ND17 (Langdon, ND), only one to four different genotypes were found within a lesion. A higher level of genetic and genotypic diversity was found within a leaf in which six to nine different genotypes were found from lesions on a leaf. The genetic diversity within a leaf was similar to the genetic diversity within a field. The average genetic diversity (H) within a field across all AFLP loci was approximately 0.3, except at site ND12 (Carrington, ND) where it was 0.16. Genotypic diversity was high in all populations, and with the exception of ND15 (Rothsay, MN), very low multilocus linkage disequilibrium values ( r(d)) were found in all populations. The population differentiation, G(ST), was relatively high (G(ST) = 0.238) among the nine populations due to the high G(ST) in ND12, ND14 (Twin Valley, MN), and ND15. Population differentiation without those three populations was 0.09. A lack of correlation between geographical distance and genetic distance was found, suggesting the potential for a high level of gene flow between different geographical regions. The population genetic structure described in this study for S. passerinii in North Dakota and western Minnesota is consistent with that of a sexually reproducing fungus.     

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.     

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 .     

河北省坝上红松洼草原蝗虫群落结构与多样性调查

为明确不同分区治理下河北省坝上红松洼草原生态环境对蝗虫群落多样性的影响,采用样方法于2019-2020年在不同草原类型和不同功能分区对蝗虫群落进行调查,通过丰富度、个体数、多样性指数以及均匀度指数分析蝗虫的多样性,并对不同生态因子和蝗虫多样性指标进行相关性分析.结果 表明:该地区蝗虫发生种类共有5科8亚科14属25种,...     

新疆北部地区农林复合生境瓢虫群落多样性及其季节动态分析

新疆特有天敌资源丰富,具有重要的开发潜力和利用前景。本文于2019年5—9月采用扫网法,对北疆地区麦田、玉米田、苜蓿田、棉花田、农田防护林以及果园等6种典型生境的瓢虫群落多样性及其季节动态变化特征进行分析。结果表明,共获瓢虫标本5501号,隶属3个亚科6族13属23种,其中多异瓢虫Adonia variegata（28.52%）、方斑瓢虫Propylea quaturodecimpunctata（20.21%）以及深点食螨瓢虫Stethorus（Stethorus）punctillum（16.51%）三种为优势种群;不同生境瓢虫群落的个体数和类群数在季节动态分布上存在明显差异,其中苜蓿田个体数量分布最多（262号/样地/次）、种类也最为丰富（20种）,棉花田个体数量（48号/样地/次）及物种数（4种）最为稀少;群落多样性分析表明,Shannon-Wiener多样性指数、Margalef丰富度指数和Pielou均匀度指数依次为8月上半月>7月下半月>5月下半月>8月下半月>7月上半月>6月下半月>9月上半月>6月上半月。各生境中,防护林多样性指数（0.62）、丰富度指数（2.06）、均匀度指数（0.72）在整个生长期中维持着最高的水平,其次是苜蓿田生境的多样性水平较高（0.55、2.35、0.49）,而棉花田生境多样性指数（0.21）、丰富度指数（0.46）和均匀度指数（0.57）平均水平最低,但优势度指数（0.70）最高;相似性分析表明,群落相似性系数在不同生境之间属于中等相似（0.5≤q≤0.75）。不同月份间相似性程度较高,28个不同月份组中,8月下半月与9月上半月间的瓢虫相似性系数最高（0.94）,共同种有深点食螨瓢虫、多异瓢虫等15种,其他月份间属于中等相似或极相似。新疆北部地区瓢虫群落个体数和类群数较为丰富,不同月份间分布相对均匀,自然控制能力较强,尤其是防护林和苜蓿田生境,应加强保护与利用当地天敌资源,为促进绿色农业的可持续发展提供科学依据。     

An investigation of genetic variation in Cirsium arvense field patches

The genetic structure of typical Cirsium arvense patch populations in two arable fields was examined. Patches were mapped and plant samples were taken in these patches. Plants of a central patch and four surrounding patches were sampled in 1 year to investigate the influence of root fragment dispersal. Plants of another patch were sampled in three subsequent years to investigate the patch development. The genotypes of the plants were examined using repetitive enterogenic primer (REP) and inter simple sequence repeat (ISSR) analysis. The mean proportion of distinguishable genotypes ranged from 0.13 to 0.67 and the evenness index ranged from 0.58 to 1.00. Differences in genotypes between neighbouring patches indicated that root fragment dispersal via soil cultivation was of minor importance. Three years sampling within a patch showed that the patch mainly ‘grew’ via the establishment of new clones rather than by clonal growth of one genotype. The influence of various factors caused by population demography or arable practice on patch development in an arable field is discussed. Although various factors can help to maintain genetic diversity, there is strong evidence for regular seedling establishment in arable fields.     

Genetic structure of Mycosphaerella fijiensis populations from Australia, Papua New Guinea and the Pacific Islands

Single-copy restriction fragment length polymorphism (RFLP) markers were used to determine the genetic structure of Mycosphaerella fijiensis , the cause of black leaf streak (black Sigatoka) disease of banana and plantain, in the Torres Strait, Papua New Guinea (PNG), and the Pacific Islands. A moderate level of genetic variation was observed in all populations with genotypic diversity values of 60–78% of the theoretical maximum, and gene diversity ( H ) values between 0·269 and 0·336. All populations were at gametic equilibrium, and with the high level of genotypic diversity observed this indicated that sexual reproduction has a major role in the genetic structure of the M. fijiensis populations examined. Population differentiation was tested on several hierarchical scales. No evidence of population differentiation was observed between sites on Mer Island. A moderate level of population differentiation was observed within the Torres Strait, between Badu and Mer Islands ( F _ST = 0·097). On a regional scale, the greatest differentiation was found between the populations of the Torres Strait and the Pacific. Populations from these regions were more closely related to the PNG population than to each other, suggesting they were founded in separate events from the same population.     

Hierarchical Analysis of Diversity, Selfing, and Genetic Differentiation in Populations of the Oomycete Aphanomyces euteiches

ABSTRACT Relatively little is known about the population biology of the legume pathogen Aphanomyces euteiches. A. euteiches is a soilborne pathogen causing Aphanomyces root rot of several legumes, including alfalfa, bean, lentil, and pea. Our objectives were to assess the degree of diversity, selfing, and population differentiation in A. euteiches. We contrasted populations within and among two geographically separated fields with a history of pea production. Molecular genotyping relied on amplified fragment length polymorphism analysis. Samples of A. euteiches recovered from two fields in northeast Oregon and western Washington confirmed previous reports of moderately high genetic diversity in populations of A. euteiches at the regional scale, but revealed higher-than-expected genotypic diversity within individual soil samples. Populations of A. euteiches were significantly differentiated at the soil sample, field, and regional level. The population structure appears to be patterned by regular selfing via oospores, a mixed reproductive system including both asexual and sexual reproduction, with occasional migration of novel genotypes or outcrossing.     

荒漠草原不同放牧制度群落多样性研究

在内蒙古苏尼特右旗荒漠草原,通过划区轮牧与自由放牧的比较试验,研究不同放牧制度下群落α多样性和β多样性。结果表明:①对照区、轮牧区和自由放牧区的植物种类丰富度和多样性均较前一年均有所增加,优势度指数除对照区有所增加,轮牧区和自由放牧区基本不变化;均匀度指数轮牧区和自由放牧区均略有下降。②物种丰富度指数与均匀度指数呈负相关,荒漠草原植物群落多样性更多地受丰富度的影响。③对照区、轮牧区和自由放牧区群落β多样性指数随取样面积增加而降低;荒漠草原在不放牧、自由放牧和划区轮牧下,轮牧区β多样性指数最高,其次为对照区和自由放牧区;④2004年轮牧区与自由放牧区的相似性系数为最高,其次为轮牧区与对照区;自由放牧区与对照区差异最大。到了2005年,除轮牧区与自由区的相似性系数降低外,轮牧区与对照区、自由区与对照区的相似性系数均有所增加。     

银川平原不同种植模式下苜蓿田地表蜘蛛群落多样性及时间动态模拟

为探究不同种植模式对苜蓿田地表蜘蛛群落多样性及个体数量的影响,采用陷阱法对银川平原苜蓿-小麦邻作、苜蓿-玉米邻作和苜蓿-果园间作3种不同种植模式下的人工苜蓿田地表蜘蛛群落进行了调查,研究其多样性、丰富度、均匀度及优势度指数的差异和变化,并利用Gaussian函数对各指数进行时间序列动态拟合,分析了3种种植模式下人工苜蓿田地表蜘蛛群落总个体数量的时间动态变化。结果显示,该地区共收集到蜘蛛标本2 761头,隶属12科19属28种,其中优势种为星豹蛛Pardosa astrigera、甘肃平腹蛛Gnaphosa kansuensis和白斑隐蛛Nurscia albofasciata。2种邻作模式下,苜蓿田地表蜘蛛群落多样性、丰富度、均匀度及优势度指数同间作模式下的各指标均有显著差异,且多样性指数最大值出现时间分别为5月7日和5月18日,均早于间作模式下的7月3日。Gaussian函数拟合结果表明,苜蓿-小麦邻作模式下苜蓿田地表蜘蛛种群高峰期持续时间最长,为121.92 d,苜蓿-玉米邻作模式下2次种群高峰间隔时间最短,为49.2 d。苜蓿-小麦邻作模式下苜蓿田地表蜘蛛群落的个体数量最大值出现在5月上旬,其它2种模式下均出现在5月中旬。