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

Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva

Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.

Going with the flow: Intraspecific variation may act as a natural ally to counterbalance the impacts of global change for the riparian species Populus deltoides

The speed and magnitude of global change will have major impacts on riparian ecosystems, thereby leading to greater forest vulnerability. Assessing species' adaptive capacities to provide relevant information for vulnerability assessments remains challenging, especially for nonmodel species like the North American Populus deltoides W. Bartram ex Marshall. The objective of this study was to understand how genomic diversity of this foundation species was shaped by its environment (climate, soil, and biotic interactions) to gauge its adaptive capacity. We used two complementary approaches to get a full portrait of P. deltoides genetic diversity at both the species and whole-genome ranges. First, we used a set of 93 nuclear and three chloroplastic SNP markers in 946 individuals covering most of the species' natural distribution. Then, to measure the degree of intraspecific divergence at the whole-genome level and to support the outlier and genomic-environment association analyses, we used a sequence capture approach on DNA pools. Three distinct lineages for P. deltoides were detected, and their current distribution was associated with abiotic and biotic variations. The comparison between both cpDNA and ncDNA patterns showed that gene flow between the lineages is unbalanced. The southern and northeastern populations may benefit from the input, through river flow, of novel alleles located upstream to their local gene pools. These alleles could migrate from populations that are already adapted to conditions that fit the predicted climates in the receiving local populations, hotter at the northeastern limit and drier in the Central United States. These "preadapted" incoming alleles may help to cope with maladaptation in populations facing changing conditions.

Phylogeography and Population Structure Analysis Reveal Diversity by Gene Flow and Mutation in Ustilago segetum (Pers.) Roussel tritici Causing Loose Smut of Wheat

Ustilago segetum (Pers.) Roussel tritici (UST) causes loose smut of wheat account for considerable grain yield losses globally. For effective management, knowledge of its genetic variability and population structure is a prerequisite. In this study, UST isolates sampled from four different wheat growing zones of India were analyzed using the second largest subunit of the RNA polymerase II (RPB2) and a set of sixteen neutral simple sequence repeats (SSRs) markers. Among the 112 UST isolates genotyped, 98 haplotypes were identified. All the isolates were categorized into two groups (K = 2), each consisting of isolates from different sampling sites, on the basis of unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure. The positive and significant index of association (I_A = 1.169) and standardized index of association (rBar_D = 0.075) indicate population is of non-random mating type. Analysis of molecular variance showed that the highest variance component is among isolates (91%), with significantly low genetic differentiation variation among regions (8%) (F_st = 0.012). Recombination (R_m = 0) was not detected. The results showed that UST isolates have a clonal genetic structure with limited genetic differentiation and human arbitrated gene flow and mutations are the prime evolutionary processes determining its genetic structure. These findings will be helpful in devising management strategy especially for selection and breeding of resistant wheat cultivars.

Pest categorisation of Sphaerulina musiva

Following a request from the European Commission, the EFSA Plant Health Panel performed a pest categorisation of Sphaerulina musiva, a well‐defined and distinguishable fungal species of the family Mycosphaerellaceae. Following a recent phylogenetic analysis of the genus Septoria and other closely related genera, a new name (S. musiva) was introduced for the species. The former species name Mycosphaerella populorum is used in the Council Directive 2000/29/EC. The pathogen is regulated in Annex IAI as a harmful organism whose introduction into the EU is banned. S. musiva is reported from North and South America and not known to occur in the EU. S. musiva causes Septoria leaf spots and cankers of poplar (Populus spp.). Of the poplars native to Europe, Populus nigra is reported as susceptible and Populus tremula as susceptible when planted in North America. The hybrid Populus x canadensis (arising from a cross of P. nigra and the North American Populus deltoides), widely grown in the EU, is also susceptible. The pest could enter the EU on plants for planting, cut branches, isolated bark and wood with and without bark. S. musiva could establish in the EU, as hosts are common and favourable climatic conditions are widespread, and could spread following establishment by natural dispersal and movement of infected plants for planting, cut branches, isolated bark and wood with or without bark. The pest introduction would have impacts in woodlands, plantations and nurseries. The pathogen is considered the most serious disease affecting hybrid poplar production in North America. Selection, breeding and planting of resistant species and clones are the main methods used to control the damage caused by the pathogen. There is some uncertainty on the geographical distribution of the pest in the Caucasus, the Crimean Peninsula and South America and on the level of susceptibility among Populus species native to Europe as well as Salix spp. The criteria assessed by the Panel for consideration as a potential quarantine pest are met. For regulated non‐quarantine pests, the criterion on the pest presence in the EU is not met.

The Correlation Between Septoria Leaf Spot and Stem Canker Resistance in Hybrid Poplar

Sphaerulina musiva is an important fungal pathogen that causes a leaf spot and stem canker disease of hybrid poplar. Stem cankers are widely regarded as the greatest threat to hybrid poplar plantations because of their ability to cause tree mortality; thus, the efforts of breeding programs have been focused on stem canker resistance. To explore the relationship between resistance to leaf spot and stem canker in Populus nigra × P. deltoides hybrids, two experiments were conducted. Initially, comparisons among leaves of different ages indicated that younger leaves were more susceptible to leaf spot infection than older leaves. Correlations between leaf spot severity and stem canker severity for both individual leaves and all leaves averaged together indicated that, in 10 of 11 comparisons, there were no significant correlations. The lack of correlation suggests that deploying genotypes resistant to stem canker may not affect the pathogen population causing leaf spot disease. To our knowledge, this is the first study specifically designed to test the correlation between stem canker resistance and leaf spot resistance by inoculating whole trees with a spore suspension in a controlled environment.

Variation in Resistance of Populus nigra to Sphaerulina musiva in the North-Central United States

Populus nigra, commonly used in hybrid poplar breeding programs in the north-central United States, is susceptible to Septoria stem canker, caused by Sphaerulina musiva. In this study, two experiments were conducted to (i) characterize the variation in resistance of 47 genotypes of P. nigra collected from seven locations in Europe in terms of cankers per centimeter and disease severity score; (ii) determine whether location, isolate, genotype, or their interactions significantly affect cankers per centimeter and disease severity score; and (iii) examine the correlation of disease severity score between single-isolate and bulk-isolate inoculations. The majority of the variation in resistance for cankers per centimeter was explained by location (72%; P < 0.001) followed by genotype(location) (28%; P < 0.001). In contrast, the majority of the variation in disease severity score was explained by genotype-location (51%; P < 0.001) followed by location (26%; P = 0.025). The disease severity score model also indicated the presence of a significant isolate effect (P = 0.034) and genotype(location) × isolate interaction (P = 0.004). The correlation coefficients for disease severity score indicated a significant range of correlations (r = 0.871 to r = 0.952) when correlating single-isolate to bulk-isolate inoculations.

A Nonwounding Greenhouse Screening Protocol for Prediction of Field Resistance of Hybrid Poplar to Septoria Canker

Populus spp. and their hybrids are short-rotation woody crops which supply fiber to a diversity of industries in North America. The potential of hybrid poplar trees has been limited by the fungal pathogen Septoria musiva, the cause of leaf spot and stem canker of Populus spp. An inoculation protocol that does not rely on stem wounding to achieve infection was recently developed to screen poplar clones for resistance to Septoria canker. Prior to this study, the relationship between results obtained using this inoculation protocol and long-term field resistance of clones was unknown. Young ramets of 14 clones of hybrid poplar that were previously assigned to long-term canker damage categories (low, intermediate, and high) were inoculated with a conidial suspension of three isolates of S. musiva under greenhouse conditions. Three weeks post inoculation, lesion number, lesions per centimeter of stem length, area of stem that was necrotic, and proportion of stem area that was necrotic were measured. Logistic regression with lesion number and proportion necrotic area correctly predicted long-term disease damage categories for 11 of 14 clones tested, including the most resistant (NM6) and the most susceptible (NC11505) clones, demonstrating that this screening protocol is a promising method for prediction of long-term disease impact of the most resistant clones.

Micro- and macrospatial scale analyses illustrates mixed mating strategies and extensive geneflow in populations of an invasive haploid pathogen

Sexual reproduction in fungi involves either a single individual (selfing) or two individuals (outcrossing). To investigate the roles that these two strategies play in the establishment of an invasive alien pathogen, the Eucalyptus leaf-infecting fungus, Teratosphaeria (Mycosphaerella) nubilosa was studied. Specifically, the genetic diversity of the pathogen was investigated at micro and macrospatial scales. Interestingly, while data obtained at microspatial scales show clearly that selfing is the main reproductive strategy, at macrospatial scales the population genetic structure was consistent with a genetically outcrossing organism. Additional analyses were performed to explore these apparently discordant results at different spatial scales and to quantify the contribution of selfing vs. outcrossing to the genotypic diversity. The results clearly show that the fungus has a mixed mating strategy. While selfing is the predominant form of mating, outcrosses must have occurred in the pathogen that increased the genotypic diversity of the fungus over time. This mating strategy, coupled with the high levels of geneflow between distant populations of the pathogen, has created an even distribution of maximum diversity from the smallest (leaf) to largest scales (>500 km), which will make breeding for resistance difficult. These data illustrate the evolutionary potential and danger of the introduction of multiple genotypes of a potentially outcrossing pathogen, especially when it has a high dispersal potential.

Susceptibility of Populus balsamifera to Septoria musiva: A Field Study and Greenhouse Experiment

A greenhouse inoculation experiment and field study were conducted to determine the cause of an outbreak of Septoria musiva cankers on Populus balsamifera in a northern Alberta plantation. Four clones of P. balsamifera, five clones of putatively resistant P. deltoides, and one susceptible hybrid poplar clone, Northwest, were inoculated with seven isolates identified as S. musiva. Four of the isolates were from P. balsamifera in Alberta and the others were from P. deltoides in Quebec. Results indicated that disease severity was similar for Alberta and Quebec isolates (P = 0.243) and that P. balsamifera had the greatest mean disease severity (x-bar = 4.20), P. deltoides had the lowest (x-bar = 2.76), and Northwest was intermediate (x-bar = 3.45). A genetic analysis comparing six polymorphic polymerase chain reaction restriction fragment length polymorphism loci and the mitochondrial small subunit ribosomal DNA sequences of the seven isolates indicated that the Alberta population was made up of at least three distinct genotypes. Canker incidence and age on Northwest and 56 different clones of P. balsamifera in a plantation were recorded. Canker incidence (P = 0.726) and the canker age distributions (P = 0.994) were similar for the two species. In conclusion, contrary to what has been reported in the literature, P. balsamifera appears to be quite susceptible to Septoria canker.

Microsatellite markers for the Eucalyptus stem canker fungal pathogen Kirramyces gauchensis

Ten microsatellite markers were developed for the fungus Kirramyces gauchensis, which causes an important stem canker disease of Eucalyptus trees in plantations. Primers for 21 microsatellite regions were designed from cloned fragments. Fourteen of the primer pairs provided single amplicons and 10 of these were polymorphic for K. gauchensis. Allelic diversity ranged from 0.21 to 0.76 with a total of 30 alleles. None of the markers was able to amplify in the phylogenetically distinct but morphologically similar species Kirramyces zuluensis. The 10 characterized polymorphic microsatellite regions will be studied to determine the population structure of K. gauchensis in plantations of different countries.

Genetic structure of Phaeosphaeria nodorum populations in the north-central and midwestern United States

Stagonospora nodorum blotch, caused by Phaeosphaeria nodorum, is considered one of the most destructive foliar diseases of wheat in the United States. However, relatively little is known about the population biology of this fungus in the major wheat-growing regions of the central United States. To rectify this situation, 308 single-spore isolates of P. nodorum were analyzed from 12 populations, five from hard red spring wheat cultivars in Minnesota and North Dakota and seven from soft red winter wheat in Indiana and Ohio. The genetic structure of the sampled populations was determined by analyzing polymorphisms at five microsatellite or simple-sequence repeat (SSR) loci and the mating type locus. Although a few clones were identified, most P. nodorum populations had high levels of gene (H(S) = 0.175 to 0.519) and genotype (D = 0.600 to 0.972) diversity. Gene diversity was higher among isolates collected from spring wheat cultivars in North Dakota and Minnesota (mean H(S) = 0.503) than in those from winter wheat cultivars in Indiana and Ohio (H(S) = 0.269). Analyses of clone-corrected data sets showed equal frequencies of both mating types in both regional and local populations, indicating that sexual recombination may occur regularly. However, significant gametic disequilibrium occurred in three of the four populations from North Dakota, and there was genetic differentiation both within and among locations. Genetic differentiation between the hard red spring and soft red winter wheat production regions was moderate (F(ST) = 0.168), but whether this is due to differences in wheat production or to geographical variation cannot be determined. These results suggest that sexual reproduction occurs in P. nodorum populations in the major wheat-growing regions of the central United States, and that geographically separated populations can be genetically differentiated, reflecting either restrictions on gene flow or selection.

Specific and sensitive PCR-based detection of Septoria musiva, S. populicola and S. populi, the causes of leaf spot and stem canker on poplars

The development of a PCR assay for the detection of the poplar pathogenic fungi Septoria musiva (teleomorph Mycosphaerella populorum), S. populicola (M. populicola) and S. populi (M. populi) is described. Three pairs of species-specific PCR primers were designed using interspecific polymorphisms in the internal transcribed spacer (ITS) of nuclear ribosomal RNA gene (rDNA) repeats. The specificity of the three primer pairs was successfully tested on a collection of 40 S. musiva, 39 S. populicola and six S. populi isolates. Using stringent PCR conditions, no cross-reaction was observed with any of the isolates tested. The specificity of the PCR assay was further confirmed with DNA extracted from 12 additional Septoria species and 17 other fungal species obtained from stems or leaves of poplars. Specific amplification of the fragments for S. musiva and S. populicola was sensitive relatively to the technique used, detecting as low as 1 pg template DNA, and 10 pg of DNA of the target species in a background of 1 ng of DNA of the other species. Moreover, using DNA purified directly from disrupted conidia, it was possible to detect with a probability of 90%, using one unique PCR assay, the DNA equivalent of 166 conidia per microl of S. musiva and 156 conidia per microl of S. populicola. The procedures developed in this work can thus be applied for rapid and accurate detection and identification of Septoria species from poplars.