Genetic diversity of the Chestnut blight fungus Cryphonectria parasitica in four French populations assessed by microsatellite markers

Microsatellite Analysis Revealing High Genetic Diversity of the Chestnut Blight Fungus in South Tyrol (Northern Italy)

Cryphonectria parasitica, which causes chestnut blight, is one of the most important pathogens of forest trees. In Europe, mycovirus-mediated biocontrol is the most efficient method to control the disease but can be impeded by the lack of information about the population structure of the fungus within a region. In particular, sexual reproduction and the new introduction of the pathogen can complicate biocontrol strategies. For this reason, this study aimed to determine the population structure of C. parasitica, which causes chestnut blight, in the northern Italian region of South Tyrol, using eleven multilocus microsatellite markers. Fifty-one haplotypes were found across South Tyrol, belonging to three divergent clusters. Recombinant genotypes demonstrated that sexual reproduction occurs across the different clusters. The most dominant genotypes in the region were also the most dominant in neighboring areas, such as Switzerland, northern Italy and France. All of the clusters from South Tyrol were related to the Italian genotype pool and are thought to have been introduced from northern Italian and other European populations due to naturally occurring gene flow or human-mediated introduction. At least three separate introduction events of C. parasitica might have happened in South Tyrol that could be separated by time. This study demonstrated a high genetic diversity of C. parasitica in South Tyrol and helped to shed light on the sexual reproduction and introduction events in the local populations.

Microsatellite Genotyping in the Chestnut Blight Fungus Cryphonectria parasitica

This chapter describes the use of polymorphic microsatellite (simple sequence repeats, SSR) markers for genotyping isolates of Cryphonectria parasitica, the causal agent of chestnut blight. The SSR presented are particularly useful to characterize the genetic population structure of this invasive fungal pathogen, including invasion history (e.g., possible source population, introduced genotypes) and reproduction mode (sexual vs. asexual). Microsatellite markers can also be used to track fungal strains in laboratory and field experiments.

Temporal and Spatial Genetic Population Structure of Cryphonectria parasitica and Its Associated Hypovirus Across an Invasive Range of Chestnut Blight in Europe

Chestnut blight has spread throughout Europe since the introduction of its causal agent, Cryphonectria parasitica, >70 years ago. In our study, we analyzed the diversity of vegetative compatibility (vc) and microsatellite genotypes of C. parasitica, as well as sequence diversity of Cryphonectria hypovirus 1 (CHV1) in six populations from Switzerland, Croatia, and North Macedonia. Resampling of local populations that were already investigated more than a decade ago allowed us to analyze the spatial and temporal population structure across an invasive range of the pathogen in Europe. Regardless of which genetic marker was used, the >60-year-old Swiss and Croatian populations had high population diversity, whereas more recent North Macedonian populations were mostly clonal. These diversity differences between the investigated populations remained stable over time. A high diversity of CHV1 was observed in all three countries, with North Macedonian strains forming a separate cluster from strains obtained in other countries. No correlation between vc diversity and CHV1 prevalence was observed, suggesting a well-established and maintained natural hypovirulence in all countries, further corroborated by an observed increase in genetic diversity of Croatian C. parasitica populations over time, without collapse of CHV1 prevalence.

Link between epigenetic diversity and invasive status of south-eastern European populations of phytopathogenic fungus Cryphonectria parasitica

Epigenetic modifications may play an important role in invasion and adaptation of clonal and invasive populations to different environments. The aim of this study was to analyse epigenetic diversity and structure within and among populations of invasive pathogenic fungus Cryphonectria parasitica from south-eastern Europe, where one haplotype S12 dominates. The highest level of epigenetic diversity was found in haplotype S1, followed by S2, while the lowest level of epigenetic diversity was found in haplotype S12. Similar pattern of epigenetic diversity was detected in the control, genetically diverse Croatian population where S1 haplotype dominates. In four south-eastern European populations, the highest level of epigenetic diversity was observed in the Italian population, the oldest population in the studied area, while the lowest diversity was found in most recently established Bulgarian population. This relationship between epigenetic diversity and population age implies the important role of epigenetic modifications on the process of invasion. Our data suggest that epigenetic differences might affect the success of expansion of certain haplotype into new regions. Understanding the role of epigenetic processes in expansion and (pre)adaptation of fungal plant pathogens, besides fundamental knowledge, can contribute to development of strategies for control of fungal spread and pathogenesis.

What was old is new again: thermal adaptation within clonal lineages during range expansion in a fungal pathogen

Range-expanding species are expected to gain an increasing importance in the context of global change. They provide a great opportunity to study contemporary evolutionary changes and to unravel the mechanisms of evolution. Cryphonectria parasitica, the causal agent of chestnut blight, originating from Asia, has been spread since the beginning of the 20th century into different continents. We took advantage of the C. parasitica recent emergence in northern France to study the changes in population genetic structure and in phenotypic traits along this colonization and climatic gradient. Four hundred twenty-seven C. parasitica isolates were sampled in 47 chestnut sites in northern France. The C. parasitica outbreak in the north was found to be due to the expansion of five dominant clonal groups from southern France and to the emergence of a few rare recombined genotypes. The evolutionary changes during C. parasitica range expansion were studied by analysing phenotypic changes in isolates from the same clonal lineage, with or without a geographic shift. Growth rates were assessed in vitro, at four temperatures. The northern isolates grew faster at 12 and 15 °C and more slowly at 28 and 32 °C than the southern isolates. These results strongly suggest local adaptation to low temperatures in C. parasitica, with a trade-off of slower growth at high temperatures. They also reflect the high evolutionary potential of C. parasitica along a colonization gradient and show that clonal evolution is not a limitation for the rapid thermal adaptation of this invasive fungal species.

Multiple introductions and recombination in Cryphonectria hypovirus 1: perspective for a sustainable biological control of chestnut blight

Cryphonectria hypovirus 1 (CHV1) is a mycovirus which decreases the virulence of its fungal host Cryphonectria parasitica, the causal agent of chestnut blight recently introduced in Europe. The understanding of the evolutionary processes which have shaped CHV1 populations in Europe is required to develop a sustainable biocontrol strategy targeting chestnut blight and effective in European chestnut forests. To retrace the evolutionary history of CHV1, we analyzed sequences from two genomic regions on a collection of 55 CHV1 strains from France and northern Spain, two countries where multiple introductions of C. parasitica occurred. Several recombination events and variable selection pressures contributed to CHV1 evolution, agreeing with a non-clock-like diversification rate. These two mechanisms may be at the origin of CHV1 population diversity observed in western Europe. Considering the actual prevalence of CHV1 and its association with host genotypes, multiple introductions of CHV1 may have occurred in Europe, some of them directly from Asia and some of them through North America. Although some viral strains remained with low frequency in their introduction area, multiple infections might have allowed homologous recombination within parental sequences. Some of these recombinant lineages are associated with the spread of CHV1 in European regions.

Genetic diversification of the chestnut blight fungus Cryphonectria parasitica and its associated hypovirus in Germany

Chestnut blight in south-western Germany was first reported in 1992 and is since expanding in distribution. Here we investigated the invasion history of Cryphonectria parasitica and its associated hypovirus. For this, we characterized 284 isolates collected between 1992 and 2012 for hypovirulence, vegetative compatibility (vc), mating type, and microsatellite haplotype. A total of 27 haplotypes and 15 vc types were observed, although the C. parasitica population analyzed is currently dominated to 50 % by one haplotype and to 64 % by the vc type EU-2. Structure analysis indicated two divergent genetic pools. Over 66 % of the haplotypes belonged to a pool probably originating from northern Italy. Further diversification is expected due to ongoing sexual recombination, but also to new migration and additional introductions. Cryphonectria hypovirus 1 (CHV-1) was found in four of five C. parasitica populations from Baden-Württemberg. Genetic analysis of the 35 CHV-1 isolates obtained revealed that they all belong to the German subtype, although they have clearly diverged from the first German hypovirus isolated in 1992. Our study suggests that C. parasitica has been introduced into Germany several times from two different gene pools, whereas the hypovirus most probably has a single origin.

Discovery of a new gene pool and a high genetic diversity of the chestnut blight fungus Cryphonectria parasitica in Caucasian Georgia

In this study, we investigated the population genetic structure and possible origins of the plant pathogen Cryphonectria parasitica in Caucasian Georgia, a region within the centre of origin of the host species Castanea sativa. A total of 427 C. parasitica isolates from nine populations were genotyped at 10 microsatellite loci. A high genetic diversity was detected, but the overall Georgian population was dominated by three haplotypes which were present in most individual populations. Two of them have not been previously found in Europe. Bayesian clustering analysis and principal component analysis could not identify their source population, neither in Asia nor in North America. On the other hand, one haplotype is frequent in Central Europe and probably naturally invaded Caucasian Georgia from neighbouring Turkey. Seventy-three haplotypes were unique to specific populations, and 66 of them were represented by a single isolate. Allele patterns suggest that most of these haplotypes emerged locally through sexual recombination between haplotypes of the Georgian and the central European gene pool. Due to the high incidence of haplotypes not otherwise present in Europe, Caucasian Georgia represents an additional source of diversity for the European C. parasitica population.

Evidence for multiple introductions and clonality in Spanish populations of Fusarium circinatum

Fusarium circinatum is thought to have been moved around the world with pine planting stock consisting, most probably, of infected seed. In this effort, we investigate the genetic structure of F. circinatum in Spain and globally. In total, 223 isolates were studied from five regions in northern Spain and eight countries. Eight microsatellite markers revealed 66 multilocus genotypes (MLGs). Minimum spanning network analysis of MLGs by region within Spain as well as globally, discriminant analysis of principal components, and analysis of molecular variance revealed that Spanish populations are significantly differentiated and structured into two distinct groups, each one including one of the dominant genotypes observed. This result suggests that two independent introductions occurred into Spain that subsequently underwent clonal divergence and admixture. This result is further supported by the linkage disequilibrium and clonality observed for F. circinatum populations in northern Spain. The maintenance of differentiation between the clusters could result from the lack of or rare sexual reproduction in Spain. Possible introduction pathways from other countries and subsequent routes of dispersion of F. circinatum in Spain are discussed.

Mycovirus transmission revisited by in situ pairings of vegetatively incompatible isolates of Cryphonectria parasitica

In disease ecology, parasite transmission is a key parameter important at both epidemiological and evolutionary scales. Mycoviruses can be transmitted both horizontally and vertically. Their horizontal transmission is strongly restricted by the host vegetative compatibility system, which controls the outcome of somatic fusion in fungi, and by the same way, may limit mycovirus transmission. However, most of current knowledge and predictive capabilities regarding these host/pathogen systems are derived from studies pairing fungal mycelia on artificial medium. An original bioassay method, using infected mycelia as well as asexual spores, had been developed to assess in situ transmission of Cryphonectria Hypovirus-1 (CHV1), a mycovirus of Cryphonectria parasitica that causes chestnut blight. For every pair of different vegetative compatibility types tested, rates of CHV1 transmission were always superior in situ than in vitro. This study supports the hypothesis that the natural ability of CHV1 to migrate within a fungal population composed of different vegetative compatible types may have been underestimated by in vitro essays. This result offers opportunities for a biological control of fungal diseases with mycoviruses.

Invasion history and demographic pattern of Cryphonectria hypovirus 1 across European populations of the chestnut blight fungus

We reconstructed the invasion history of the fungal virus Cryphonectria hypovirus 1 (CHV-1) in Europe, which infects the chestnut blight fungus Cryphonectria parasitica. The pattern of virus evolution was inferred based on nucleotide sequence variation from isolates sampled across a wide area in Europe at different points in time. Phylogeny and time estimates suggested that CHV-1 was introduced together with its fungal host to Europe and that it rapidly colonized the central range along the south facing slopes of the Alps and the north-east facing slopes of the Dinaric Alps. These central populations were the source for two waves of simultaneous invasions toward the southern Balkans and Turkey, as indicated by migration rates. Our results showed that the evolutionary scenarios for CHV-1 and C. parasitica were spatially congruent. As infection with CHV-1 reduces the pathogenicity of C. parasitica toward the chestnut tree, CHV-1 invasions of the newly established C. parasitica populations probably prevented the development of devastating chestnut blight epidemics in Europe. We propose that in this, and supposedly in other pathosystems, geographic, vegetation-related, demographic, economic, and political factors may help explain the correlated invasion pattern of a parasite and its host.

The chestnut blight fungus world tour: successive introduction events from diverse origins in an invasive plant fungal pathogen

Clonal expansion has been observed in several invasive fungal plant pathogens colonizing new areas, raising the question of the origin of clonal lineages. Using microsatellite markers, we retraced the evolutionary history of introduction of the chestnut blight fungus, Cryphonectria parasitica, in North America and western Europe. Combining discriminant analysis of principal components and approximate Bayesian computation analysis, we showed that several introduction events from genetically differentiated source populations have occurred in both invaded areas. In addition, a low signal of genetic recombination among different source populations was suggested in North America. Finally, two genetic lineages were present in both invaded areas as well as in the native areas, suggesting the existence of genetic lineages with a high capacity to establish in diverse environments and host species. This study confirmed the importance of multiple introductions, but questioned the role of genetic admixture in the success of introduction of a fungal plant pathogen.

Invasion genetics of the chestnut blight fungus Cryphonectria parasitica in Switzerland

Cryphonectria parasitica is the best-known example of an invasive forest pathogen in Europe. In southern Switzerland, chestnut blight was first reported in 1948 whereas, north of the Alps, it did not appear until the 1980s. Between 1995 and 2008, we sampled 640 C. parasitica isolates from nine populations south of the Alps and nine north of the Alps. Twelve historical isolates, collected between 1950 and 1972 in the south, were obtained from our collection. All 652 isolates were screened at 10 microsatellite loci to test for the existence of divergent genetic pools and to infer possible origins of haplotypes. In total, 52 haplotypes were identified. Structure software analysis indicated that 43 haplotypes (including all historical haplotypes) belonged to a main cluster, 6 haplotypes belonged to a different cluster, and 3 haplotypes had an intermediate allele pattern. All newly founded populations in northern Switzerland were initiated by one or just a few haplotypes from the main cluster, which probably came directly from the populations south of the Alps. Subsequently, genetic diversity increased through mutations, sexual reproduction, or new migrations. The highest increase in diversity was observed in populations where haplotypes from different genetic pools were encountered.

Temperature-dependent genotype-by-genotype interaction between a pathogenic fungus and its hyperparasitic virus

The outcome of host-parasite interactions may depend not only on the genotypes of the species involved but also on environmental factors. We used the fungus Cryphonectria parasitica, the causal agent of chestnut blight, and its hyperparasitic virus, Cryphonectria hypovirus-1 (CHV1), to test for genotype-by-genotype-by-environment interactions in a host-parasite system. In C. parasitica, infection with CHV1 induces a hypovirulent phenotype with reduced virulence toward the chestnut tree (Castanea spp.) and thus controls chestnut blight in many European regions. In contrast, uninfected virulent C. parasitica have nearly eradicated the American chestnut in North America. We applied a full factorial design and assessed the fungal growth and sporulation of four C. parasitica strains, uninfected and infected with each of the four known CHV1 subtypes, at 12°, 18°, 24°, and 30°C. We found a significant (P ≤ .00001) genotype-by-genotype-by-environment interaction, demonstrating the potential for a selection mosaic. As a consequence, different host and parasite genotypes would be selected under different climatic conditions, affecting the coevolutionary dynamics of the host-parasite interaction and the course of chestnut blight epidemics. Genotype-by-genotype-by-environment interactions are essential to take into account when designing biological control strategies.

Genetic discontinuities and disequilibria in recently established populations of the plant pathogenic fungus Mycosphaerella fijiensis

Dispersal processes of fungal plant pathogens can be inferred from analysis of spatial genetic structures resulting from recent range expansion. The relative importance of long-distance dispersal (LDD) events vs. gradual dispersal in shaping population structures depends on the geographical scale considered. The fungus Mycosphaerella fijiensis, pathogenic on banana, is an example of a recent worldwide epidemic. Founder effects in this species were detected at both global and continental scale, suggesting stochastic spread of the disease through LDD events. In this study, we analysed the structure of M. fijiensis populations in two recently (∼1979-1980) colonized areas in Costa Rica and Cameroon. Isolates collected in 10-15 sites distributed along a ∼250- to 300- km-long transect in each country were analysed using 19 microsatellite markers. We detected low-to-moderate genetic differentiation among populations in both countries and isolation by distance in Cameroon. Combined with historical data, these observations suggest continuous range expansion at the scale of banana-production area through gradual dispersal of spores. However, both countries displayed specific additional signatures of colonization: a sharp discontinuity in gene frequencies was observed along the Cameroon transect, while the Costa Rican populations seemed not yet to have reached genetic equilibrium. These differences in the genetic characteristics of M. fijiensis populations in two recently colonized areas are discussed in the light of historical data on disease spread and ecological data on landscape features.

Microsatellite Diversity in Natural Populations of Ascomycetous Fungus, Emericella Nidulans, from Different Climatic-Edaphic Conditions in Israel

The genetic divergence of Israeli populations of the soil ascomycetous fungusEmericella nidulanswas studied on regional and local scales using fifteen microsatellite (SSR) markers. The study was performed in the framework of the "Evolution Canyon" research program at the Institute of Evolution, University of Haifa, in three "Evolution Canyons" (ECs): EC I (Mt. Carmel), EC II (western Upper Galilee), and EC III (the southern Negev desert). The first two canyons (EC I and EC II) are located in the northern part of Israel at a distance of 38 km apart; EC III is located southward at a distance of nearly 350 km from the northern ECs. In each canyon,E. nidulansstrains were isolated from opposite slopes and, in EC III, from the valley bottom. All three EC populations ofE. nidulanswere found to be genetically distinct. The estimated genetic divergences correspond to geographical distances and ecological differences between the three studied canyons. On a regional scale, simple sequence repeat (SSR) polymorphism tends to increase with severity of ecological conditions. In general, both environmental parameters (soil moisture and temperature) and genetic factors (predicted number of repeats in SSR markers, distance from marker to centromere, codon evolutionary chronologies, and hydrophobic vs. hydrophilic character of encoded amino acid) influenced genetic diversity ofE. nidulanspopulations.

Multiple introductions of divergent genetic lineages in an invasive fungal pathogen, Cryphonectria parasitica, in France

The occurrence of multiple introductions may be a crucial factor in the successful establishment of invasive species, but few studies focus on the introduction of fungal pathogens, despite their significant effect on invaded habitats. Although Cryphonectria parasitica, the chestnut blight fungus introduced in North America and Europe from Asia during the 20th century, caused dramatic changes in its new range, the history of its introduction is not well retraced in Europe. Using 10 microsatellite loci, we investigated the genetic diversity of 583 isolates in France, where several introductions have been hypothesized. Our analyses showed that the seven most frequent multilocus genotypes belonged to three genetic lineages, which had a different and geographically limited distribution. These results suggest that different introduction events occurred in France. Genetic recombination was low among these lineages, despite the presence of the two mating types in each chestnut stand analysed. The spatial distribution of lineages suggests that the history of introductions in France associated with the slow expansion of the disease has contributed to the low observed rate of recombination among the divergent lineages. However, we discuss the possibility that environmental conditions or viral interactions could locally reduce recombination among genotypes.

Clonal population structure of the chestnut blight fungus in expanding ranges in southeastern Europe

Expanding populations are often less genetically diverse at their margins than at the centre of a species' range. Established, older populations of the chestnut blight fungus, Cryphonectria parasitica, are more variable for vegetative compatibility (vc) types than in expanding populations in southeastern Europe where C. parasitica has colonized relatively recently. To test whether vc types represent clones, we genotyped 373 isolates of C. parasitica from southern Italy, Romania, Bulgaria, Macedonia, Greece and Turkey using 11 sequence-characterized amplified region (SCAR) markers. Ten SCAR loci and six vegetative incompatibility (vic) loci were polymorphic in these samples. These populations are clonal by all criteria tested: (i) among 373 isolates, we found only eight multilocus haplotypes, and the same haplotypes were found in multiple countries, sometimes separated in time by as much as 12 years; (ii) the number of haplotypes observed was significantly less than expected under random mating; (iii) populations are in linkage disequilibrium; (iv) the two sets of independent markers, SCARs and vc types, are highly correlated; and (v) sexual structures of C. parasitica were found only in Bulgaria and Romania. One mating type (MAT-1) was found in 98% of the isolates sampled. In contrast, a population in northern Italy, in the central part of the range in Europe, had 12 multilocus haplotypes among 19 isolates. The spread of a few clones could be the result either of founder effect and restricted migration, or these clones have greater fitness than others and spread because they are better adapted to conditions in southeastern Europe.

Challenges of microsatellite isolation in fungi

Although they represent powerful genetic markers in many fields of biology, microsatellites have been isolated in few fungal species. The aim of this study was to assess whether obtaining microsatellite markers with an acceptable level of polymorphism is generally harder from fungi than in other organisms. We therefore surveyed the number, nature and polymorphism level of published microsatellite markers in fungi from the literature and from our own data on seventeen fungal microsatellite-enriched libraries, and in five other phylogroups (angiosperms, insects, fishes, birds and mammals). Fungal microsatellites indeed appeared both harder to isolate and to exhibit lower polymorphism than in other organisms. This appeared to be due, at least in part, to genomic specificities, such as scarcity and shortness of fungal microsatellite loci. A correlation was observed between mean repeat number and mean allele number in the published fungal microsatellite loci. The cross-species transferability of fungal microsatellites also appeared lower than in other phylogroups. However, microsatellites have been useful in some fungal species. Thus, the considerable advantages of these markers make their development worthwhile, and this study provides some guidelines for their isolation.

Cultivation-independent analysis of fungal genotypes in soil by using simple sequence repeat markers

Cultivation-independent analyses of fungi are used for community profiling as well as identification of specific strains in environmental samples. The objective of the present study was to adapt genotyping based on simple sequence repeat (SSR) marker detection for use in cultivation-independent monitoring of fungal species or strains in bulk soil DNA. As a model system, a fungal biocontrol agent (BCA) based on Beauveria brongniartii, for which six SSR markers have been developed, was used. Species specificity of SSR detection was verified with 15 fungal species. Real-time PCR was used to adjust for different detection sensitivities of the six SSR markers as well as for different template quantities. The limit for reliable detection per PCR assay was below 2 pg target DNA, corresponding to an estimated 45 genome copies of B. brongniartii. The cultivation-independent approach was compared to cultivation-dependent SSR analysis with soil samples from a B. brongniartii BCA-treated field plot. Results of the cultivation-independent method were consistent with cultivation-dependent genotyping and allowed for unambiguous identification and differentiation of the applied as well as indigenous strains in the samples. Due to the larger quantities of soil used for cultivation-dependent analysis, its sensitivity was higher, but cultivation-independent SSR genotyping was much faster. Therefore, cultivation-independent monitoring of B. brongniartii based on multiple SSR markers represents a rapid and strain-specific approach. This strategy may also be applicable to other fungal species or strains for which SSR markers have been developed.

Establishing causes of eradication failure based on genetics: case study of ship rat eradication in Ste. Anne archipelago

Determining the causes of a failed eradication of a pest species is important because it enables an argued adjustment of the methodologies used and the improvement of the protocols for future attempts. We examined how molecular monitoring can help distinguish between the two main reasons for an eradication failure (i.e., survival of some individuals vs. recolonization after eradication). We investigated genetic variation in seven microsatellite loci in ship rat (Rattus rattus) populations from four islets off the Martinique coast (French Caribbean). In 1999 an eradication attempt was conducted on the four islets. Three years later rats were observed again on two of them. We compared the genetic signatures of the populations before and after the eradication attempt. On one of the islands, the new rat population was likely a subset of the pre-eradication population. A weak genetic differentiation was found between them, with almost no new alleles observed in the new population and moderate F(ST) values (0.15). Moreover, assignment procedures clustered the two populations together. In contrast, on the other islet, many new alleles were observed after the eradication attempt, resulting in an increase in genetic diversity (from 2.57 to 3.57 mean number of alleles per locus) and strong F(ST) values (0.39). Moreover, genetic clustering clearly separated the two samples (i.e., before and after the eradication attempt) in two different populations. Thus, to achieve long-term eradication on these islets, it seems necessary to redevelop the eradication procedure to avoid individuals surviving and to prevent reinvasion, probably from the mainland, by installing permanent trapping and poisoning devices and conducting regular monitoring. We strongly encourage wildlife managers conducting eradication campaigns to integrate molecular biological tools in their protocols, which can be done easily for most common invasive species.

Genetic diversity and population differentiation of chestnut blight fungus, Cryphonectria parasitica, in China as revealed by RAPD

Seventeen Cryphonectria parasitica populations sampled from six regions in China were investigated using RAPD. Across all 169 isolates from the 17 populations evaluated, 52 of the 71 markers (73%) were polymorphic, total genetic diversity (h) was 0.1463, and Shannon's index was 0.2312. Diversity within populations accounted for 74% of total genetic diversity, and genetic differentiation among populations was 0.26 (G (ST) = 0.26). Gene flow was 1.4 among the populations; higher gene flow was found among populations within regions and among regions [N (m) (G (SR)) = 2.8 and N (m) (G (RT)) = 3.5]. The unweighted pair group mean analysis (UPGMA) dendrogram revealed two distinct clusters: the northern China group and the southern China group. The spatial autocorrelation analysis revealed that the variation at most loci was randomly distributed and lacked spatial structure, but several loci and closer distances were spatially structured. Human activity and habitat could also be important factors affecting genetic structure among C. parasitica populations in China. Genetic diversity was highest in Southwest China, descending in an orderly fashion to Northeast China. This pattern indicated that Southwest China might be the center of origin of C. parasitica in China. The present study provides useful information for understanding the origin and spread of chestnut blight fungus in China and valuable data for formulating relevant strategies for controlling the disease in China.

Identification and genetic mapping of highly polymorphic microsatellite loci from an EST database of the septoria tritici blotch pathogen Mycosphaerella graminicola

A database of 30,137 EST sequences from Mycosphaerella graminicola, the septoria tritici blotch fungus of wheat, was scanned with a custom software pipeline for di- and trinucleotide units repeated tandemly six or more times. The bioinformatics analysis identified 109 putative SSR loci, and for 99 of them, flanking primers were developed successfully and tested for amplification and polymorphism by PCR on five field isolates of diverse origin, including the parents of the standard M. graminicola mapping population. Seventy-seven of the 99 primer pairs generated an easily scored banding pattern and 51 were polymorphic, with up to four alleles per locus, among the isolates tested. Among these 51 loci, 23 were polymorphic between the parents of the mapping population. Twenty-one of these as well as two previously published microsatellite loci were positioned on the existing genetic linkage map of M. graminicola on 13 of the 24 linkage groups. Most (66%) of the primer pairs also amplified bands in the closely related barley pathogen Septoria passerinii, but only six were polymorphic among four isolates tested. A subset of the primer pairs also revealed polymorphisms when tested with DNA from the related banana black leaf streak (Black Sigatoka) pathogen, M. fijiensis. The EST database provided an excellent source of new, highly polymorphic microsatellite markers that can be multiplexed for high-throughput genetic analyses of M. graminicola and related species.