Genetic structure of Sclerotinia sclerotiorum populations from sunflower and cabbage in West Azarbaijan province of Iran

Sclerotinia sclerotiorum is one of the most destructive fungal pathogens infecting a wide array of plant species worldwide. Management of this pathogen relies on the coordinated use of fungicides and resistant host cultivars with other control measures, but the effectiveness of these methods requires knowledge of the genetic variability and structure of the fungal populations. To provide insight into the genetic diversity and structure of this pathogen in West Azarbaijan province of Iran, a total of 136 isolates were collected from symptomatic sunflower and cabbage plants within fields in three regions and analysed using inter-simple sequence repeat (ISSR) markers and intergenic spacer (IGS) region of the rRNA gene sequences. A total of 83 ISSR multilocus genotypes (MLGs) were identified, some of which were shared among at least two regional or host populations but in a low frequency. High genotypic diversity, low levels of clonal fraction, and random association of ISSR loci in a region indicated a low level of clonal reproduction, and possibly a high level of sexually recombining life cycle for the pathogen in the province. Marker analyses revealed that the pathogen was spatially homogeneous among fields, and thus similar control measures, such as the choice of resistant cultivars and fungicides, may effectively manage S. sclerotiorum within the region. Four IGS haplotypes (IGS1-IGS4) were detected within populations with IGS3 being the most prevalent haplotype. The low IGS haplotype diversity, the absence of spatial structure, and shared MLGs among populations may suggest a single introduction and subsequent dispersal of S. sclerotiorum within West Azarbaijan province.

Evaluation of foliar fungus-mediated interactions with below and aboveground enemies of the invasive plant Ageratina adenophora

Plant-fungal associations are frequently key drivers of plant invasion success. Foliar fungi can benefit their invasive hosts by enhancing growth promotion, disease resistance and environmental stress tolerance. However, the roles of foliar fungi may vary when a given invasive plant faces different stresses. In this study, we designed three independent experiments to evaluate the effects of a foliar fungus, Colletotrichum sp., on the growth performance of the invasive plant Ageratina adenophora under different soil conditions, as well as the responses of A. adenophora to the foliar fungal pathogen Diaporthe helianthi and to herbivory. We found that the soil type was the most influential factor for the growth of A. adenophora. The role of the foliar fungus Colletotrichum sp. varied in the different soil types but generally adversely affected leaf development in A. adenophora. Colletotrichum sp. may be a weak latent foliar pathogen that can enhance the pathogenicity of D. helianthi on leaves of A. adenophora and marginally reduce signs of herbivory by natural insects in the wild on A. adenophora seedlings. In general, the benefits of the foliar fungus Colletotrichum to the fitness of A. adenophora are not significant in the context of this experimental design. However, our data highlight the need to consider both aboveground and belowground biota in different soil habitats when evaluating the effects of foliar fungi.

Genetic analysis reveals long-standing population differentiation and high diversity in the rust pathogen Melampsora lini

A priority for research on infectious disease is to understand how epidemiological and evolutionary processes interact to influence pathogen population dynamics and disease outcomes. However, little is understood about how population adaptation changes across time, how sexual vs. asexual reproduction contribute to the spread of pathogens in wild populations and how diversity measured with neutral and selectively important markers correlates across years. Here, we report results from a long-term study of epidemiological and genetic dynamics within several natural populations of the Linum marginale-Melampsora lini plant-pathogen interaction. Using pathogen isolates collected from three populations of wild flax (L. marginale) spanning 16 annual epidemics, we probe links between pathogen population dynamics, phenotypic variation for infectivity and genomic polymorphism. Pathogen genotyping was performed using 1567 genome-wide SNP loci and sequence data from two infectivity loci (AvrP123, AvrP4). Pathogen isolates were phenotyped for infectivity using a differential set. Patterns of epidemic development were assessed by conducting surveys of infection prevalence in one population (Kiandra) annually. Bayesian clustering analyses revealed host population and ecotype as key predictors of pathogen genetic structure. Despite strong fluctuations in pathogen population size and severe annual bottlenecks, analysis of molecular variance revealed that pathogen population differentiation was relatively stable over time. Annually, varying levels of clonal spread (0–44.8%) contributed to epidemics. However, within populations, temporal genetic composition was dynamic with rapid turnover of pathogen genotypes, despite the dominance of only four infectivity phenotypes across the entire study period. Furthermore, in the presence of strong fluctuations in population size and migration, spatial selection may maintain pathogen populations that, despite being phenotypically stable, are genetically highly dynamic.

Melampsora lini is a rust fungus that infects native flax, Linum marginale in south-eastern Australia where its epidemiology and evolution have been intensively studied since 1987. Over that time, substantial diversity in the pathotypic structure of M. lini has been demonstrated but an understanding of how genetic diversity in pathogen populations is maintained through space and time is lacking. Here we integrated phenotypic, genotypic and epidemiological datasets spanning 16 annual epidemics across three host populations to examine long-term pathogen genetic dynamics. The results show that host ecotype is the dominant selective force in the face of strong bottlenecks and annual patterns of genetic turnover. Results from previous studies indicate that in this geographic region, M. lini lacks the capacity to reproduce sexually–we thus expected to find limited genetic diversity and evidence for strong clonality influencing genetic dynamics within growing seasons. However, the breadth of genomic coverage provided by the SNP markers revealed high levels of genotypic variation within M. lini populations. This discovery contrasts with observed phenotypic dynamics as the epidemics of this pathogen were largely dominated by four pathotypes across the study period. Based on a detailed assessment and comparison of pathotypic and genotypic patterns, our study increases the understanding of how genetic diversity is generated and maintained through space and time within wild pathogen populations. The implications for the management of resistance to pathogens in agricultural or conservation contexts are significant: the appearance of clonality may be hiding high levels of pathogen diversity and recombination. Understanding how this diversity is generated could provide new and unique ways to mitigate or suppress the emergence of infectious strains, allowing to efficiently combat harmful diseases.

Population Structure and Aggressiveness of Sclerotinia sclerotiorum From Rapeseed (Brassica napus) in Chongqing City

Sclerotinia sclerotiorum is one of the most devastating fungal plant pathogens of oilseed Brassica and is distributed worldwide. In particular, Sclerotinia stem rot has always been a serious threat to rapeseed production in Chongqing City, China. In this study, simple sequence repeat (SSR) markers and mycelial compatibility groups (MCGs) were used to characterize the population structure of 90 geographic isolates of S. sclerotiorum collected from rapeseed in nine counties of Chongqing. A total of 52 microsatellite haplotypes were identified, and a few haplotypes were found with high frequency. Gene diversity ranged from 0.1570 to 0.4700 in nine populations. A constructed unweighted pair group with arithmetic mean dendrogram based on Nei genetic distance and a STRUCTURE analysis revealed that the genetic composition of the isolates collected in the five counties located in western Chongqing are different from those collected in the two eastern counties, suggesting that breed lines should be cultivated in both the western and eastern regions to effectively evaluate resistance levels. A total of 47 MCGs were identified, and 72% of the MCGs was represented by single isolates. Seven of 13 MCGs that included at least two isolates contained isolates from only one county. SSR haplotypes were not correlated with MCGs. A subset of 34 isolates were inoculated on rapeseed stems, and the aggressiveness showed variation. This research revealed the population genetic structure and aggressiveness of this pathogen in Chongqing, and the results will help to develop disease management and resistance screening strategies.

Fungal clones win the battle, but recombination wins the war

Clonal reproduction is common in fungi and fungal-like organisms during epidemics and invasion events. The success of clonal fungi shaped systems for their classification and some pathogens are tacitly treated as asexual. We argue that genetic recombination driven by sexual reproduction must be a starting hypothesis when dealing with fungi for two reasons: (1) Clones eventually crash because they lack adaptability; and (2) fungi find a way to exchange genetic material through recombination, whether sexual, parasexual, or hybridisation. Successful clones may prevail over space and time, but they are the product of recombination and the next successful clone will inevitably appear. Fungal pathogen populations are dynamic rather than static, and they need genetic recombination to adapt to a changing environment.

Evidence for Sexual Recombination in Didymella tanaceti Populations, and Their Evolution Over Spring Production in Australian Pyrethrum Fields

Tan spot, caused by Didymella tanaceti, is one of the most important foliar diseases affecting pyrethrum in Tasmania, Australia. Population dynamics, including mating-type ratios and genetic diversity of D. tanaceti, was characterized within four geographically separated fields in both late winter and spring 2012. A set of 10 microsatellite markers was developed and used to genotype 774 D. tanaceti isolates. Isolates were genotypically diverse, with 123 multilocus genotypes (MLG) identified across the four fields. Fifty-eight MLG contained single isolates and P_sex analysis estimated that, within many of the recurrent MLG, there were multiple clonal lineages derived from recombination. Isolates of both mating types were at a 1:1 ratio following clone correction in each field at each sampling period, which was suggestive of sexual recombination. No evidence of genetic divergence of isolates of each mating type was identified, indicating admixture within the population. Linkage equilibrium in two of the four field populations sampled in late winter could not be discounted following clone correction. Evaluation of temporal changes in gene and genotypic diversity identified that they were both similar for the two sampling periods despite an increased D. tanaceti isolation frequency in spring. Genetic differentiation was similar in populations sampled between the two sampling periods within fields or between fields. These results indicated that sexual reproduction may have contributed to tan spot epidemics within Australian pyrethrum fields and has contributed to a genetically diverse D. tanaceti population.

Sclerotinia sclerotiorum: An Evaluation of Virulence Theories

Oxalic acid production in Sclerotinia sclerotiorum has long been associated with virulence. Research involving UV-induced, genetically undefined mutants that concomitantly lost oxalate accumulation, sclerotial formation, and pathogenicity supported the conclusion that oxalate is an essential pathogenicity determinant of S. sclerotiorum. However, recent investigations showed that genetically defined mutants that lost oxalic acid production but accumulated fumaric acid could cause disease on many plants and substantiated the conclusion that acidic pH, not oxalic acid per se, is the necessary condition for disease development. Critical evaluation of available evidence showed that the UV-induced mutants harbored previously unrecognized confounding genetic defects in saprophytic growth and pH responsiveness, warranting reevaluation of the conclusions about virulence based on the UV-induced mutants. Furthermore, analyses of the evidence suggested a hypothesis for the existence of an unrecognized regulator responsive to acidic pH. Identifying the unknown pH regulator would offer a new avenue for investigating pH sensing/regulation in S. sclerotiorum and novel targets for intervention in disease control strategies.

Population structure and phenotypic variation of Sclerotinia sclerotiorum from dry bean (Phaseolus vulgaris) in the United States

The ascomycete pathogen Sclerotinia sclerotiorum is a necrotrophic pathogen on over 400 known host plants, and is the causal agent of white mold on dry bean. Currently, there are no known cultivars of dry bean with complete resistance to white mold. For more than 20 years, bean breeders have been using white mold screening nurseries (wmn) with natural populations of S. sclerotiorum to screen new cultivars for resistance. It is thus important to know if the genetic diversity in populations of S. sclerotiorum within these nurseries (a) reflect the genetic diversity of the populations in the surrounding region and (b) are stable over time. Furthermore, previous studies have investigated the correlation between mycelial compatibility groups (MCG) and multilocus haplotypes (MLH), but none have formally tested these patterns. We genotyped 366 isolates of S. sclerotiorum from producer fields and wmn surveyed over 10 years in 2003-2012 representing 11 states in the United States of America, Australia, France, and Mexico at 11 microsatellite loci resulting in 165 MLHs. Populations were loosely structured over space and time based on analysis of molecular variance and discriminant analysis of principal components, but not by cultivar, aggressiveness, or field source. Of all the regions tested, only Mexico (n = 18) shared no MLHs with any other region. Using a bipartite network-based approach, we found no evidence that the MCGs accurately represent MLHs. Our study suggests that breeders should continue to test dry bean lines in several wmn across the United States to account for both the phenotypic and genotypic variation that exists across regions.

PATTERNS OF DESCENT IN CLONAL LINEAGES AND THEIR MULTILOCUS FINGERPRINTS ARE RESOLVED WITH COMBINED GENE GENEALOGIES

Clonal lineages in the filamentous ascomycete (fungi) Sclerotinia sclerotiorum were determined by analysis of genealogies of four loci: the intergenic spacer of the nuclear ribosomal repeat (IGS; approximately 4 kb), the translation elongation factor (EF-1α; approximately 300 bp), an anonymous region (44.11; approximately 700 bp), and the calmodulin gene (CAL; approximately 400 bp). Three of the four loci are physically unlinked. The combined analysis of the four loci provided the best estimate of phylogeny, which is consistent with a pattern of some recombination among clonal lineages against a background of predominant clonality. Comparison of gene genealogies with a phylogeny inferred from DNA fingerprints and a combined phylogeny of the entire dataset identified convergent or parallel changes in fingerprints. Analysis of the entire data matrix allowed us to resolve patterns of descent among clonal lineages that could not be inferred from fingerprints alone and to discern recent episodes of divergence that were not detected in gene genealogies. Prerequisites for applying this approach to other systems are a haploid context for inferring multiple gene genealogies (such as the mitochondrial genome) that indicate limited recombination and another data matrix that identifies recently evolved genotypes.

Population Structure of Sclerotinia subarctica and Sclerotinia sclerotiorum in England, Scotland and Norway

Sclerotinia species are important fungal pathogens of a wide range of crops and wild host plants. While the biology and population structure of Sclerotinia sclerotiorum has been well-studied, little information is available for the related species S. subarctica. In this study, Sclerotinia isolates were collected from different crop plants and the wild host Ranuculus ficaria (meadow buttercup) in England, Scotland, and Norway to determine the incidence of Sclerotinia subarctica and examine the population structure of this pathogen for the first time. Incidence was very low in England, comprising only 4.3% of isolates while moderate and high incidence of S. subarctica was identified in Scotland and Norway, comprising 18.3 and 48.0% of isolates respectively. Characterization with eight microsatellite markers identified 75 haplotypes within a total of 157 isolates over the three countries with a few haplotypes in Scotland and Norway sampled at a higher frequency than the rest across multiple locations and host plants. In total, eight microsatellite haplotypes were shared between Scotland and Norway while none were shared with England. Bayesian and principal component analyses revealed common ancestry and clustering of Scottish and Norwegian S. subarctica isolates while English isolates were assigned to a separate population cluster and exhibited low diversity indicative of isolation. Population structure was also examined for S. sclerotiorum isolates from England, Scotland, Norway, and Australia using microsatellite data, including some from a previous study in England. In total, 484 haplotypes were identified within 800 S. sclerotiorum isolates with just 15 shared between England and Scotland and none shared between any other countries. Bayesian and principal component analyses revealed a common ancestry and clustering of the English and Scottish isolates while Norwegian and Australian isolates were assigned to separate clusters. Furthermore, sequencing part of the intergenic spacer (IGS) region of the rRNA gene resulted in 26 IGS haplotypes within 870 S. sclerotiorum isolates, nine of which had not been previously identified and two of which were also widely distributed across different countries. S. subarctica therefore has a multiclonal population structure similar to S. sclerotiorum, but has a different ancestry and distribution across England, Scotland, and Norway.

Population genetic analysis reveals cryptic sex in the phytopathogenic fungus Alternaria alternata

Reproductive mode can impact population genetic dynamics and evolutionary landscape of plant pathogens as well as on disease epidemiology and management. In this study, we monitored the spatial dynamics and mating type idiomorphs in ~700 Alternaria alternata isolates sampled from the main potato production areas in China to infer the mating system of potato early blight. Consistent with the expectation of asexual species, identical genotypes were recovered from different locations separated by hundreds of kilometers of geographic distance and spanned across many years. However, high genotype diversity, equal MAT1-1 and MAT1-2 frequencies within and among populations, no genetic differentiation and phylogenetic association between two mating types, combined with random association amongst neutral markers in some field populations, suggested that sexual reproduction may also play an important role in the epidemics and evolution of the pathogen in at least half of the populations assayed despite the fact that no teleomorphs have been observed yet naturally or artificially. Our results indicated that A. alternata may adopt an epidemic mode of reproduction by combining many cycles of asexual propagation with fewer cycles of sexual reproduction, facilitating its adaptation to changing environments and making the disease management on potato fields even more difficult.

Recombination between clonal lineages of the asexual fungus Verticillium dahliae detected by genotyping by sequencing

Most asexual species of fungi have either lost sexuality recently, or they experience recombination by cryptic sexual reproduction. Verticillium dahliae is a plant-pathogenic, ascomycete fungus with no known sexual stage, even though related genera have well-described sexual reproduction. V. dahliae reproduces mitotically and its population structure is highly clonal. However, previously described discrepancies in phylogenetic relationships among clonal lineages may be explained more parsimoniously by recombination than mutation; therefore, we looked for evidence of recombination within and between clonal lineages. Genotyping by sequencing was performed on 141 V. dahliae isolates from diverse geographic and host origins, resulting in 26,748 single-nucleotide polymorphisms (SNPs). We found a strongly clonal population structure with the same lineages as described previously by vegetative compatibility groups (VCGs) and molecular markers. We detected 443 recombination events, evenly distributed throughout the genome. Most recombination events detected were between clonal lineages, with relatively few recombinant haplotypes detected within lineages. The only three isolates with mating type MAT1-1 had recombinant SNP haplotypes; all other isolates had mating type MAT1-2. We found homologs of eight meiosis-specific genes in the V. dahliae genome, all with conserved or partially conserved protein domains. The extent of recombination and molecular signs of sex in (mating-type and meiosis-specific genes) suggest that V. dahliae clonal lineages arose by recombination, even though the current population structure is markedly clonal. Moreover, the detection of new lineages may be evidence that sexual reproduction has occurred recently and may potentially occur under some circumstances. We speculate that the current clonal population structure, despite the sexual origin of lineages, has arisen, in part, as a consequence of agriculture and selection for adaptation to agricultural cropping systems.

Recent introduction and recombination in Colletotrichum acutatum populations associated with citrus postbloom fruit drop epidemics in São Paulo, Brazil

Citrus crops in São Paulo State, Brazil, have been severely affected by postbloom fruit drop disease (PFD), which is caused by Colletotrichum acutatum. This disease leads to the drop of up to 100% of young fruits. Previous studies have assumed that this pathogen exhibits a clonal reproductive mode, although no population genetic studies have been conducted so far. Thus, the genetic structure of six C. acutatum populations from sweet orange orchards showing PFD symptoms was determined using nine microsatellite markers, enabling inference on predominant mode of reproduction. C. acutatum populations exhibit a nearly panmictic genetic structure and a high degree of admixture, indicating either ongoing contemporary gene flow at a regional scale or a recent introduction from a common source, since this pathogen was introduced in Brazil only very recently. Sharing haplotypes among orchards separated by 400 km suggests the natural dispersal of fungal propagules, with the possible involvement of pollinators. A significant population expansion was detected, which was consistent with an increase in host density associated with crop expansion toward new areas across the state. Findings of moderate to high levels of haplotypic diversity and gametic equilibrium suggest that recombination might play an important role in these pathogen populations, possibly via parasexual reproduction or a cryptic sexual cycle. This study provides additional tools for epidemiological studies of C. acutatum to improve prevention and management strategies for this disease.

Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatellite alleles, high mutation rates confound the estimates of recombination. To distinguish high mutation rates from recombination to infer outcrossing, 8 population samples comprising 268 S. sclerotiorum isolates from widely distributed agricultural fields were genotyped for 12 microsatellite markers, resulting in multiple polymorphic markers on three chromosomes. Each isolate was homokaryotic for the 12 loci. Pairwise LD was estimated using three methods: Fisher's exact test, index of association (IA) and Hedrick's D'. For most of the populations, pairwise LD decayed with increasing physical distance between loci in two of the three chromosomes. Therefore, the observed recombination of alleles cannot be simply attributed to mutation alone. Different recombination rates in various DNA regions (recombination hot/cold spots) and different evolutionary histories of the populations could explain the observed differences in rates of LD decay among the chromosomes and among populations. The majority of the isolates exhibited mycelial incompatibility, minimizing the possibility of heterokaryon formation and mitotic recombination. Thus, the observed high intrachromosomal recombination is due to meiotic recombination, suggesting frequent outcrossing in these populations, supporting the view that homothallism favors universal compatibility of gametes instead of traditionally believed haploid selfing in S. sclerotiorum. Frequent outcrossing facilitates emergence and spread of new traits such as fungicide resistance, increasing difficulties in managing Sclerotinia diseases.

Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen

BACKGROUND

Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used; however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Species boundaries were estimated using several approaches including those that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common.

RESULTS

Coalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage sorting and recombination. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported at most loci. A consensus of species tree estimation methods supported two species of Alternaria causing citrus brown spot worldwide. Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2 and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the human-mediated movement of citrus and associated pathogens out of SE Asia.

CONCLUSIONS

The number of Alternaria species identified as causing brown spot of citrus worldwide using morphological criteria has been overestimated. Little support was found for most of these morphospecies using quantitative species recognition approaches. Correct species delimitation of plant-pathogenic fungi is critical for understanding the evolution of pathogenicity, introductions of pathogens to new areas, and for regulating the movement of pathogens to enforce quarantines. This research shows that multilocus phylogenetic methods that allow for recombination and incomplete lineage sorting can be useful for the quantitative delimitation of asexual species that are morphologically indistinguishable. Two phylogenetic species of Alternaria were identified as causing citrus brown spot worldwide. Further research is needed to determine how these species were introduced worldwide, how they differ phenotypically and how these species are maintained.

The dispersal process of asexual propagules and the contribution to population persistence in Marchantia (Marchantiaceae)

PREMISE OF THE STUDY

The dispersal process involves emigration from a focal source, dispersal through the landscape, and immigration into a new population or habitat. Despite the fact that dispersal is vital for the long-term persistence of a species, key stages of the process are unknown or understudied for many species, including the importance and contribution of asexual reproduction. Focusing only on a single stage in the dispersal process may give an incomplete and potentially flawed picture of the effects of asexual reproduction on metapopulation dynamics in plant species.

METHODS

Using a multifaceted approach that combines laboratory experiments, field studies, and mathematical models, we quantify the production, dispersal, and survival of immigrants of water-dispersed asexual offspring (gemmae) of the clonal liverwort Marchantia inflexa.

KEY RESULTS

Compared to female plants, male plants of Marchantia inflexa produce gemmae more quickly and in higher numbers, but due to desiccation have lower gemmae survival rates. Gemmae move up to 20 cm per minute in light rain, suggesting they can leave the source population. Long distance dispersal of gemmae is supported by the mathematical analysis of unisexual metapopulations. Upon reaching the new habitat, gemmae survival is high if they stay moist.

CONCLUSIONS

By integrating multiple experiments to quantify the effects of gemmae on metapopulation dynamics, we found that different stages of dispersal can lead to different conclusions on which sex has an advantage. Gemmae are critical for the maintenance of both sexes, the persistence of single-sex metapopulations and species, and the invasibility of clonal organisms.

Experimental measures of pathogen competition and relative fitness

Competition among pathogen strains for limited host resources can have a profound effect on pathogen evolution. A better understanding of the principles and consequences of competition can be useful in designing more sustainable disease management strategies. The competitive ability and relative fitness of a pathogen strain are determined by its intrinsic biological properties, the resistance and heterogeneity of the corresponding host population, the population density and genetic relatedness of the competing strains, and the physical environment. Competitive ability can be inferred indirectly from fitness components, such as basic reproduction rate or transmission rate. However, pathogen strains that exhibit higher fitness components when they infect a host alone may not exhibit a competitive advantage when they co-infect the same host. The most comprehensive measures of competitive ability and relative fitness come from calculating selection coefficients in a mixed infection in a field setting. Mark-release-recapture experiments can be used to estimate fitness costs associated with unnecessary virulence and fungicide resistance.

Variation in Sclerotinia sclerotiorum Bean Isolates from Multisite Resistance Screening Locations

There is no complete resistance to Sclerotinia sclerotiorum, cause of white mold in dry bean (Phaseolus vulgaris). Variable resistance expression is one problem in screening for improved white mold resistance. With no previous information in the literature, pathogen variation in multisite screening nurseries was evaluated as one cause of diverse resistance expression. In all, 10 isolates of S. sclerotiorum used in greenhouse screening and 146 isolates collected from nine white mold field screening nurseries in major bean production areas in the United States were compared using mycelial compatibility groupings (MCGs) and an aggressiveness test. These 10 greenhouse screening isolates formed six MCGs. Among 156 field and greenhouse isolates, 64 MCGs were identified and 36 of those were each composed of a single unique isolate. Significant differences in isolate aggressiveness were found between some isolates in different MCGs but the isolates within an MCG did not differ in aggressiveness. High isolate variation found within and between field locations could influence the disease phenotype of putative white mold resistant germplasm. We next compared genotype and phenotype of isolates from screening nurseries and those from producer fields. Variability found in and among screening locations did reflect variability found in the four producer fields sampled. White mold resistance screening can be improved by knowledge of isolate genotypic and phenotypic characteristics.

Sexual reproduction and gene flow in the pine pathogen Dothistroma septosporum in British Columbia

Dothistroma septosporum has caused a serious needle blight epidemic in the lodgepole pine forests in northwest British Columbia over the past several years. Although ascocarps had been observed in British Columbia, nothing was known about the contribution of sexual reproduction, gene flow and long-distance dispersal to the epidemic. Amplified fragment length polymorphism and mating-type markers in 19 sites were used to generate population and reproductive data. Overall, evidence suggests a mixed mode of reproduction. Haplotypic diversity was high, with 79 unique and 56 shared haplotypes (possible clones) identified from 192 fungal isolates. Overall, mating-type segregation did not differ significantly from 1:1; however, random mating was rejected in most populations in the index of association and parsimony tree-length permutation analyses using the full data set and, when using clone-corrected data sets, more of the smaller populations showed random mating. Two of the smaller populations consistently showed random mating for both tests using both clone-corrected and noncorrected data. High gene flow is suggested by no differentiation between 14 of the 19 sites, several of which came from young plantations where the pathogen was not likely present prior to the current outbreak. The remaining five sites showed some level of divergence, possibly due to historic separation and endemic pathogen populations. Results indicate a high evolutionary potential and long-distance dispersal in this pathogen, important to consider in future forest management.

Relatedness of Macrophomina phaseolina isolates from tallgrass prairie, maize, soybean and sorghum

Agricultural and wild ecosystems may interact through shared pathogens such as Macrophomina phaseolina, a generalist clonal fungus with more than 284 plant hosts that is likely to become more important under climate change scenarios of increased heat and drought stress. To evaluate the degree of subdivision in populations of M. phaseolina in Kansas agriculture and wildlands, we compared 143 isolates from maize fields adjacent to tallgrass prairie, nearby sorghum fields, widely dispersed soybean fields and isolates from eight plant species in tallgrass prairie. Isolate growth phenotypes were evaluated on a medium containing chlorate. Genetic characteristics were analysed based on amplified fragment length polymorphisms and the sequence of the rDNA-internal transcribed spacer (ITS) region. The average genetic similarity was 58% among isolates in the tallgrass prairie, 71% in the maize fields, 75% in the sorghum fields and 80% in the dispersed soybean fields. The isolates were divided into four clusters: one containing most of the isolates from maize and soybean, two others containing isolates from wild plants and sorghum, and a fourth containing a single isolate recovered from Solidago canadensis in the tallgrass prairie. Most of the sorghum isolates had the dense phenotype on media containing chlorate, while those from other hosts had either feathery or restricted phenotypes. These results suggest that the tallgrass prairie supports a more diverse population of M. phaseolina per area than do any of the crop species. Subpopulations show incomplete specialization by host. These results also suggest that inoculum produced in agriculture may influence tallgrass prairie communities, and conversely that different pathogen subpopulations in tallgrass prairie can interact there to generate 'hybrids' with novel genetic profiles and pathogenic capabilities.

Population structure and diversity in sexual and asexual populations of the pathogenic fungus Melampsora lini

Many pathogens undergo both sexual and asexual reproduction to varying degrees, yet the ecological, genetic and evolutionary consequences of different reproductive strategies remain poorly understood. Here we investigate the population genetic structure of wild populations of the plant pathogen Melampsora lini on its host Linum marginale, using amplified fragment length polymorphism (AFLP) markers, two genes underlying pathogen virulence, and phenotypic variation in virulence. In Australia, M. lini occurs as two genetically and geographically divergent lineages (AA and AB), one of which is completely asexual (AB), and the other able to reproduce both clonally and sexually (AA). To quantify the genetic and evolutionary consequences of these different life histories, we sampled five populations in each of two biogeographical regions. Analysis of AFLP data obtained for 275 isolates revealed largely disjunct geographical distributions for the two different lineages, low genetic diversity within lineages, and strong genetic structure among populations within each region. We also detected significant divergence among populations for both Avr genes and virulence phenotypes, although generally these values were lower than those obtained with AFLP markers. Furthermore, isolates belonging to lineage AA collectively harboured significantly higher genotypic and phenotypic diversity than lineage AB isolates. Together these results illustrate the important roles of reproductive modes and geographical structure in the generation and maintenance of virulence diversity in populations of M. lini.

Community structure of Phialocephala fortinii s. lat. in European tree nurseries, and assessment of the potential of the seedlings as dissemination vehicles

Patterns of colonization of conifer roots by dark septate endopyhtes of the Phialocephala fortinii s. lat. species complex in nurseries in Switzerland and Lithuania were studied. The potential for man-mediated genotype flow was estimated for two Swiss nurseries based on customers' addresses and the number of delivered plants. Two hundred and forty-nine strains from three Swiss and five Lithuanian nurseries and an afforestation site were characterized using a combination of inter-simple sequence repeat-anchored PCR (ISSR-PCR), single-copy RFLP analysis, and sequence analysis. P. fortinii s. lat. was abundant in nursery seedlings, but the frequency of seedlings colonized varied considerably among and within nurseries. Ten cryptic species (CSP) of P. fortinii s. lat. were identified, including four hitherto undiscovered CSP. P. helvetica was the dominant species in Swiss nurseries, whereas P. fortinii s. str. was the most abundant species in Lithuanian nurseries and the afforestation site. Swiss nurseries deliver plants over distances of more than 200km indicating the high potential for man-mediated genotype flow in P. fortinii s. lat.

Diversity of fungal isolates from three Hawaiian marine sponges

Sponges harbor diverse prokaryotic and eukaryotic microbes. However, the nature of sponge-fungal association and diversity of sponge-derived fungi have barely been addressed. In this study, the cultivation-dependent approach was applied to study fungal diversity in the Hawaiian sponges Gelliodes fibrosa, Haliclona caerulea, and Mycale armata. The cultivated fungal isolates were representatives of 8 taxonomic orders, belonging to at least 25 genera of Ascomycota and 1 of Basidiomycota. A portion of these isolates (n=15, 17%) were closely affiliated with fungal isolates isolated from other marine habitats; the rest of the isolates had affiliation with terrestrial fungal strains. Cultivated fungal isolates were classified into 3 groups: 'sponge-generalists'-found in all sponge species, 'sponge-associates'-found in more than one sponge species, and 'sponge-specialists'-found only in one sponge species. Individuals of G. fibrosa collected at two different locations shared the same group of 'sponge-specialists'. Also, representatives of 15 genera were identified for the first time in marine sponges. Large-scale phylogenetic analysis of sponge-derived fungi may provide critical information to distinguish between 'resident fungi' and 'transient fungi' in sponges as it has been done in other marine microbial groups. This is the first report of the host specificity analysis of culturable fungal communities in marine sponges.

Phylogenetic diversity of culturable fungi associated with the Hawaiian Sponges Suberites zeteki and Gelliodes fibrosa

Sponges are well documented to harbor large amounts of microbes. Both culture-dependent and molecular approaches have revealed remarkable bacterial diversity in marine sponges. Fungi are commonly isolated from marine sponges, yet no reports on phylogenetic diversity of sponge-inhabiting fungi exist. In this report, we investigated the phylogenetic diversity of culturable fungi from the Hawaiian alien marine sponges Suberites zeteki and Gelliodes fibrosa. A total of 44 independent isolates were recovered from these two sponge species, representing 7 orders and 22 genera of Ascomycota. The majority (58%) of fungal isolates from S. zeteki resided in the Pleosporales group, while the predominant isolates (52%) from G. fibrosa were members of the Hypocreales group. Though differing in fungal species composition and structure, culturable communities of these two sponges displayed similar phylogenetic diversity. At the genus level, only two genera Penicillium and Trichoderma in the Eurotiales and Hypocreales orders, respectively, were present in both sponge species. The other genera of the fungal isolates were associated with either S. zeteki or G. fibrosa. Some of these fungal genera had been isolated from sponges collected in other marine habitats, but more than half of these genera were identified for the first time in these two marine sponges. Overall, the diversity of culturable fungal communities from these two sponge species is much higher than that observed in studies of marine sponges from other areas. This is the first report of phylogenetic diversity of marine sponge-associated fungi and adds one more dimension to our current understanding of the phylogenetic diversity of sponge-symbiotic microbes.

New Populations of Sclerotinia sclerotiorum from Lettuce in California and Peas and Lentils in Washington

ABSTRACT Four populations of Sclerotinia sclerotiorum in North America were inferred previously, based on analyses of both rapidly evolving markers (DNA fingerprint and mycelial compatiblity), and multilocus DNA sequence spanning the range between fast and slow evolution. Each population was defined as an interbreeding unit of conspecific individuals sharing a common recent ancestor and arising in a unique evolutionary event. The present study applies this standard to extend characterization of S. sclerotiorum populations to the Western United States. Isolates of S. sclerotiorum (N = 294) were determined to represent three genetically differentiated populations: California (CA, lettuce), Washington (WA, pea/lentil), and Ontario (ON, lettuce). CA was the most diverse population yet sampled in North America. Clonality was detected in ON and WA. No DNA fingerprints were common among the populations. The index of association (I(A)), based on fingerprint, was closer to zero (0) for CA than it was for the other populations. High diversity and lack of association of markers in California are consistent either with genetic exchange and recombination, or with large population size and high standing genetic variation. Intra- and interlocus conflict among three DNA sequence loci was consistent with recombination. The coalescent IGS genealogy confirmed subdivision and showed CA to be older than WA or ON. The Nearest Neighbor statistic on combined data confirmed subdivision among all present and previously defined populations. All isolates had both MAT1-1 and MAT1-2, consistent with uniform homothallism.

Analyses of Lettuce Drop Incidence and Population Structure of Sclerotinia sclerotiorum and S. minor

ABSTRACT To understand the geographical distribution of lettuce drop incidence and the structure of Sclerotinia minor and S. sclerotiorum populations, commercial lettuce fields were surveyed in the Salinas, San Joaquin, and Santa Maria Valleys in California. Lettuce drop incidence, pathogen species, and mycelial compatibility groups (MCGs) were determined and analyzed using geostatistic and geographical information system tools. Lettuce drop incidence was lowest in the San Joaquin Valley, and not significantly different between the other two valleys. Semivariogram analysis revealed that lettuce drop incidence was not spatially correlated between different fields in the Salinas Valley, suggesting negligible field-to-field spread or influence of inoculum in one field on other fields. Lettuce drop incidence was significantly lower in fields with a surface drip system than in fields with furrow or sprinkler irrigation systems, suggesting that the surface drip system can be a potential management measure for reducing lettuce drop. In the San Joaquin Valley, S. sclerotiorum was the prevalent species, causing drop in 63.5% of the fields, whereas S. minor also was identified in 25.4% of the fields. In contrast, in the Salinas Valley, S. minor was the dominant species (76.1%) whereas S sclerotiorum only observed in only 13.6% fields, in which only a few plants were infected by S. sclerotiorum. In the Santa Maria Valley, both species frequently were identified, with S. minor being slightly more common. Although many MCGs were identified in S. minor, most of them consisted of only one or two isolates. In all, approximately 91.4% of the isolates belonged to four MCGs. Among them, MCG-1 was the most prevalent group in all three valleys, accounting for 49.8% of total isolates. It was distributed all over the surveyed areas, whereas other MCGs were distributed more or less locally. Populations of S. sclerotiorum exhibited greater diversity, with 89 isolates collected from the Salinas and San Joaquin Valleys belonging to 37 different MCGs. Among them, the most recurrent MCG-A contained 16 isolates, and 30 MCGs contained only 1 isolate each. Many MCGs occurred within only one or a part of the two valleys. Potential reasons for this abundant diversity are discussed.

Population genetic analysis of Phialocephala fortinii s.l. and Acephala applanata in two undisturbed forests in Switzerland and evidence for new cryptic species

The genetic structure of the root endophytes Phialocephala fortinii s.l. and Acephala applanata was analyzed in two undisturbed forests. A total of 606 strains isolated from surface-sterilized, fine roots of Picea abies and Vaccinium myrtillus were examined. Two new cryptic species of P. fortinii were recognized and host specialization of A. applanata was confirmed. This species was almost exclusively isolated from roots of P. abies. The index of association did not deviate significantly from zero within any population, suggesting that recombination occurs or had occurred. Significant gene but no genotype flow was detected among study sites for P. fortinii s.l. In contrast, several isolates of A. applanata with both identical multi-locus haplotype and identical ISSR fingerprint were found in both study sites indicating genotype flow or a recent common history.

Sclerotinia sclerotiorum (Lib.) de Bary: biology and molecular traits of a cosmopolitan pathogen

SUMMARY Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic fungal pathogen causing disease in a wide range of plants. This review summarizes current knowledge of mechanisms employed by the fungus to parasitize its host with emphasis on biology, physiology and molecular aspects of pathogenicity. In addition, current tools for research and strategies to combat S. sclerotiorum are discussed.

TAXONOMY

Sclerotinia sclerotiorum (Lib.) de Bary: kingdom Fungi, phylum Ascomycota, class Discomycetes, order Helotiales, family Sclerotiniaceae, genus Sclerotinia.

IDENTIFICATION

Hyphae are hyaline, septate, branched and multinucleate. Mycelium may appear white to tan in culture and in planta. No asexual conidia are produced. Long-term survival is mediated through the sclerotium; a pigmented, multi-hyphal structure that can remain viable over long periods of time under unfavourable conditions for growth. Sclerotia can germinate to produce mycelia or apothecia depending on environmental conditions. Apothecia produce ascospores, which are the primary means of infection in most host plants.

HOST RANGE

S. sclerotiorum is capable of colonizing over 400 plant species found worldwide. The majority of these species are dicotyledonous, although a number of agriculturally significant monocotyledonous plants are also hosts. Disease symptoms: Leaves usually have water-soaked lesions that expand rapidly and move down the petiole into the stem. Infected stems of some species will first develop dark lesions whereas the initial indication in other hosts is the appearance of water-soaked stem lesions. Lesions usually develop into necrotic tissues that subsequently develop patches of fluffy white mycelium, often with sclerotia, which is the most obvious sign of plants infected with S. sclerotiorum.

USEFUL WEBSITES

http://www.whitemoldresearch.com; http://www.broad.mit.edu/annotation/fungi/sclerotinia_sclerotiorum.

Monitoring the spatial and temporal dynamics of a community of the tree-root endophyte Phialocephala fortinii s.l

Phialocephala fortinii sensu lato was isolated from Picea abies roots that had been collected from the same 3 x 3-m forest plot in 2001 and 2004, to examine the spatial and temporal dynamics of this fungal community. RFLP analysis was used to define the multilocus haplotype (MLH) of each isolate. Pielou's measure of association and chi(2) tests of independence were employed to examine the randomness of patterns of spatial distribution of MLH observed in 2001 and 2004. Population differentiation between the two samplings was tested using the G(ST) statistic. In 2001, 144 strains of 28 MLH were isolated; in 2004, 139 strains of 29 MLH. Abundant MLH in 2001 also prevailed in 2004, and the same two cryptic species were dominant in both collections. The probability of being isolated in both years increased with increasing frequency of an MLH. The patterns of spatial distribution of most MLH did not differ between years. The G(ST) values indicated identity of the two collections. Communities of P. fortinii sensu lato remain spatially and genetically stable for at least 3 yr.

Genetic Diversity Among Alternaria solani Isolates from Potatoes in South Africa

Genetic diversity among isolates of Alternaria solani, the causal agent of early blight of potato, from various potato-growing regions in South Africa (SA), was determined using virulence assays, vegetative compatibility (VC) tests, and random amplified microsatellite (RAMS) primers. The virulence assays showed low virulence levels for the largest part of the population, but failed to otherwise characterize the population diversity. The VC tests revealed 19 VC groups (VCGs), indicating a relatively high level of diversity among the isolates. There was little correlation between geographic origin of isolates and VCGs. Analysis of RAMS profiles revealed 27% genetic diversity among 46 isolates. This value is relatively high for an asexually reproducing fungus, but is similar to values obtained previously by authors studying A. solani. Distance analysis of the RAMS profiles also provided no evidence for geographical clustering of isolates. VCG and RAMS profiles indicated that isolates are randomly spread across SA. This fact, together with the high diversity of A. solani in SA, indicates that the fungus has a high potential to adapt to resistant cultivars or fungicides. This information can aid in the breeding and deployment of A. solani-resistant potato varieties, and in early blight disease management in SA.

Genetic Interactions Between Glycine max and Sclerotinia sclerotiorumUsing a Straw Inoculation Method

Genetic interactions for disease response between cultivars of Glycine max and isolates of Scle-rotinia sclerotiorum were evaluated in controlled-environment inoculations of five soybean cultivars with four genetically unique isolates of S. sclerotiorum. The objective of this study was to identify host-pathogen interactions using isolates of the pathogen which had different geographical and crop-wise distribution as well as a different DNA-based fingerprint. To do so, 4-week-old soybean plants were inoculated with individual isolates of S. sclerotiorum using a straw inoculation method. Inoculated plants were incubated for 48 h in continuous leaf wetness and rated for disease severity 1 and 2 weeks after inoculation. Significant differences in disease severity were detected among the soybean cultivars, and NK S08-80 consistently had the lowest disease severity among the five cultivars tested. No significant differences in disease severity were observed among pathogen isolates and no significant interactions were detected between soybean cultivars and pathogen isolates. These results suggest the following interpretations: (i) either the clonal genotype of the four pathogen isolates as determined by mycelial compatibility and DNA fingerprint was not associated with level of virulence on the five soybean cultivars or (ii) the soybean cultivars themselves were not capable of revealing any differences in virulence among isolates that would be related to their genetic fingerprint or regional distribution. The results of this study are consistent with the practice of considering different isolates of S. scle-rotiorum sampled from soybean in the same geographical region as equivalent for the evaluation of soybean cultivars for resistance to Sclerotinia stem rot.

High genetic diversity, phenotypic uniformity, and evidence of outcrossing in sclerotinia sclerotiorum in the columbia basin of washington state

ABSTRACT Sclerotinia sclerotiorum, the causal agent of potato stem rot, is prevalent and poorly managed on potatoes in the Columbia Basin of Washington. Because of the ubiquitous nature of the fungus and high crop diversity within the Columbia Basin, understanding the population structure and the potential for outcrossing of the pathogen would be helpful in developing disease management strategies. The population structure of S. sclerotiorum in the Columbia Basin from potato was examined using microsatellite markers and mycelial compatibility. Analysis of molecular variance revealed that 92% of the variability among 167 isolates was found within subpopulations, with limited, yet statistically significant impact of the collection date, but not the year or location of collection. Linkage disequilibrium and index of association analyses noted a potential for outcrossing in two locations, which was substantiated by the discovery of recombinant ascospores in three field-generated apothecia from the 12 apothecia examined. Microsatellite haplotypes were not correlated with mycelial compatibility groups. This high haplotypic diversity did not seem to impact pathologically important phenotypes. Greenhouse inoculations of potato plants exhibited no significant differences in aggressiveness on potato stems. Moreover, in vitro studies of response to fungicides and temperature stimuli yielded no significant differences among studied isolates. These findings illustrate the potential for outcrossing in warm temperate regions of North America, where a diversity of crops are planted simultaneously and in neighboring fields. This study also indicates that the unsatisfactory management of potato stem rot is likely not directly attributable to genetic factors, but to gaps in agricultural practices.

Mycelial Compatibility Grouping and Aggressiveness of Sclerotinia sclerotiorum

Population variability of Sclerotinia sclerotiorum, the causal organism of Sclerotinia stem rot of soybean, was determined by mycelial compatibility grouping (MCG) and isolate aggressiveness comparisons. MCG and aggressiveness of S. sclerotiorum isolates from diverse hosts and geographic locations (Diverse Set, 24 isolates), from a soybean field in Argentina (Argentine Set, 21 isolates), and from soybean fields in DeKalb and Watseka, Illinois (DeKalb Set, 124 isolates, and Watseka Set, 130 isolates) were assessed. Among 299 isolates tested, 42 MCGs were identified, and 61% were represented by single isolates observed at single locations. Within the Diverse Set, 17 MCGs were identified; 1 MCG consisted of six isolates, and 16 MCGs consisted of one isolate each. Nine MCGs were identified within the Argentine field with two MCGs composed of either five or six isolates, two MCGs composed of two isolates, and the remaining composed of one isolate each. Each Illinois field was a mosaic of MCGs, but MCG frequencies differed between the two fields. Common MCGs were identified among the Diverse, DeKalb, and Watseka Sets, but no MCGs within the Argentine Set were observed with other sets. MCG 8 was the most frequently sampled and widely dispersed MCG and occurred at a frequency of 29, 36, and 62% in the Diverse, DeKalb, and Watseka Sets, respectively. Variation in isolate aggressiveness was assessed using a limited-term, plug inoculation technique. Isolate aggressiveness varied (P = 0.001) within the Diverse, Argentine, DeKalb, and Watseka Sets. Within widely dispersed MCGs, isolate aggressiveness varied (P ≤ 0.10); however, within locally observed MCGs detected only in single fields, isolate aggressiveness did not vary. Additionally, individual MCGs within the DeKalb and Watseka Sets differed in isolate aggressiveness. Using six soybean cultivars and six S. sclerotiorum isolates, no cultivar-isolate interaction was detected, but resistant and susceptible cultivars performed similarly when inoculated with either less or highly aggressive isolates. Pathogen population structure and variability in isolate aggressiveness may be important considerations in disease management systems.

Multilocus population structure of Tapesia yallundae in Washington State

Population genetic structure of the fungal wheat pathogen Tapesia yallundae in Washington State was determined using genetically characterized amplified fragment length polymorphic (AFLP) markers and mating-type (MAT1-1 or MAT1-2). Segregation and linkage relationships among 164 AFLP markers and MAT were analysed using 59 progeny derived from an in vitro cross. Alleles at 158 AFLP loci and the mating-type locus segregated in a 1:1 ratio. Ten unlinked markers were chosen to determine genetic and genotypic diversity and to test the hypothesis of random mating and population differentiation among five subpopulations of T. yallundae representative of the geographical distribution of wheat production in eastern Washington. Among 228 isolates collected, overall gene diversity was high (h = 0.425) and a total of 91 unique multilocus genotypes (MLG) were identified, with 32 MLG occurring at least twice. The overall population genetic structure was consistent with random mating based on the segregation of mating-type, index of association (IA), parsimony tree length permutation test (PTLPT) and genotypic diversity analyses. However, clonal genotypes were found within each subpopulation and were also distributed among the five subpopulations. No significant differences in allele frequencies were found among the five subpopulations for all 10 loci based on contingency table analysis (G2) and Wier & Cockerham's population differentiation statistic theta (theta = -0.008, P = 0.722). T. yallundae appears to consist of a large homogeneous population throughout eastern Washington with both sexual and asexual reproduction contributing to the observed population genetic structure despite no report of sexual fruiting bodies of T. yallundae occurring under natural field conditions.

Telomere and microsatellite primers reveal diversity among Sclerotinia sclerotiorum isolates from Brazil

Sclerotinia sclerotiorum, the causal agent of white mold, is a problem of winter bean (Phaseolus vulgaris) production in Brazil under center-pivot irrigation. Isolates of S. sclerotiorum were obtained from a center-pivot-irrigated field near Guaíra-SP, Brazil. Mycelial compatibility group (MCG) studies revealed the presence of only two MCG. PCR/RFLP analysis of the ITS1-5.8S-ITS2 ribosomal subunit regions of these field isolates of S. sclerotiorum failed to show any genetic differences between these two MCGs. DNA amplification with a chromosomal telomere sequence-based primer and one microsatellite primer revealed genetic polymorphisms among isolates within the same MCG. Isolates taken from beans and two other crops from another region of Brazil showed the same two MCG and had identical banding patterns for the telomere and microsatellite primers. These findings support the use of telomere sequence-based primers for revealing genotypic differences among S. sclerotiorum isolates.

Pathogen population genetics, evolutionary potential, and durable resistance

We hypothesize that the evolutionary potential of a pathogen population is reflected in its population genetic structure. Pathogen populations with a high evolutionary potential are more likely to overcome genetic resistance than pathogen populations with a low evolutionary potential. We propose a flexible framework to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure. According to this framework, pathogens that pose the greatest risk of breaking down resistance genes have a mixed reproduction system, a high potential for genotype flow, large effective population sizes, and high mutation rates. The lowest risk pathogens are those with strict asexual reproduction, low potential for gene flow, small effective population sizes, and low mutation rates. We present examples of high-risk and low-risk pathogens. We propose general guidelines for a rational approach to breed durable resistance according to the evolutionary potential of the pathogen.

Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine-scale, ongoing genetic divergence in a wild microbial metapopulation

Nested haplotype networks for three loci in a haploid, fungal plant pathogen, Sclerotinia sclerotiorum, in two natural, Norwegian populations of the woodland buttercup, Ranunculus ficaria, were extended with DNA fingerprints to determine fine-scale population divergence. To preserve the cladistic structure in the network for both nonrecombinant and postrecombinant haplotypes in highly recombinant clades, recombinant events were not removed ('peeled off'), but instead were examined in alternative (marginal) networks. Fungi from both sampling locations share a common origin with subsequent genetic divergence, consistent with expectations for metapopulation structure. Evidence for divergence includes (i) lack of shared fingerprints between the two locations, (ii) evolution of new fingerprints, via transposition and recombination, within 2 years on a fine spatial scale within one sampling location, and (iii) increase in the size of the intergenic spacer (IGS) in both sampling locations. Sites of microsatellite repeat expansion and of an insertion were consistent with the boundaries of two recombination blocks in the IGS. Both alternative networks based on the recombination blocks were essential to finding all associations of DNA fingerprints with IGS size, sampling site, sampling year and mycelial compatibility group. Variation in the elongation factor 1alpha and calmodulin loci supported the topologies and the recurrent, ongoing polarity of change in fingerprints and IGS size inferred from the IGS.

Population structure and dynamics of Magnaporthe grisea in the Indian Himalayas

The population genetics of Magnaporthe grisea, the rice blast pathogen, were analyzed in a center of rice diversity (the Uttar Pradesh hills of the Indian Himalayas) using multilocus and single-, or low-copy, DNA markers. Based on DNA fingerprinting with the multilocus probe MGR586 and single-locus probes, 157 haplotypes clustered into 56 lineages (at >/=70% MGR586 band similarity, each with unique single-locus profiles) and high diversity indices were detected among 458 isolates collected from 29 sites during 1992-1995. Most valleys sampled had distinct populations (73% of the lineages were site specific) with some containing one or a few lineages, confirming the importance of clonal propagation, and others were very diverse. Widely distributed lineages suggested that migration occurs across the region and into the Indo-Gangetic plains. Repeated sampling at one site, Matli, (170 isolates, 1992-1995) yielded 19 lineages and diversity significantly greater than that reported from similar samples from Colombia and the Philippines. Analysis of allelic associations using pairwise comparisons and multilocus variance analysis failed to reject the hypothesis of gametic phase equilibrium. The Matli population shifted from highly diverse in 1992 to almost complete dominance by one lineage in 1995. Such population dynamics are consistent with recombination followed by differential survival of clonal descendants of recombinant progeny. At another site, Ranichauri, population (n = 84) composition changed from 2 to 11 lineages over 2 yr and yielded additional evidence for equilibrium. Sexually fertile and hermaphrodite isolates of both mating types were recovered from rice in both Matli and Ranichauri. We demonstrate that Himalayan M. grisea populations are diverse and dynamic and conclude that the structure of some populations may be affected to some extent by sexual recombination.

THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification

Phylogenetic and population genetic methods that compare nucleic acid variation are being used to identify species and populations of pathogenic fungi and determine how they reproduce in nature. These studies show that asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior, and that fungi with all types of reproductive morphologies and behaviors can be accommodated by a phylogenetic species concept. Although approximately one fifth of described fungi have been thought to be asexual and clonal, recent studies have shown that they are also recombining. Whether a particular pathogen reproduces clonally or by recombination depends on factors relating to its biology and its distribution in space and time. Knowing the identity of species and populations and their reproductive modes, while taking a broad view of pathogen behavior in space and time, should enhance the ability of pathologists to control pathogens and even predict their behavior.

Random association among alleles in clonal populations of Sclerotinia sclerotiorum

Multiple loci identified in DNA fingerprints were used to test for random association in two agricultural populations of S. sclerotiorum. In linkage disequilibrium tests among pairs of loci with frequencies between 0.1 and 0.9, 44.5 and 80.5% of pairs of loci were consistent with random association in the clone-corrected samples of the Canadian canola and the North Carolina cabbage populations, respectively. In estimates of corrected (Bonferroni) P value, 70.66 and 98.89% of pairs of loci were in random association. All four possible genotypes for each pair of loci were observed in the Canadian canola sample, consistent with random association among loci. In multilocus association tests across all loci, however, significant association was observed in both populations. In the Canadian canola population, 40 possible heterokaryons were identified. Our data suggest that populations of S. sclerotiorum are predominantly clonal and that occasional genetic exchange and recombination, and not mutation alone, may be a source of new genotypes.