Phytopathology®

Canada thistle (Cirsium arvense (L.) Scop., CT) is one of the worst weeds threatening temperate regions of the world. A host-specific rust fungus, Puccinia punctiformis (F. Strauss) Rohl., is known to cause systemic disease of CT, ultimately killing individuals and reducing stand densities. In 2013, it was demonstrated that fall inoculation of rosettes with coarsely ground leaves bearing P. punctiformis telia can successfully initiate epiphytotics. In the same year, a cooperative project between the Colorado Department of Agriculture and United States Department of Agriculture was initiated, in which CT patches across the state of Colorado (USA) were inoculated and tracked over subsequent years for changes in stem density. Here, we report our findings from 8 years (2014-2021) of monitoring effort. At most sites (N = 87), CT stem densities declined, from a mean ({+/-} SE) of 87.9 ({+/-} 6.5) stems to 44.7 ({+/-} 4.2). These declines however were spatially-autocorrelated, and likely attributable to local growing conditions, as mean annual daily maximum temperature and standard deviation of elevation, as well as climatic conditions around the times of both treatment and monitoring, were found to be important predictors of CT decline. Further, we observed that the amount of inoculum deployed, timing since last release, and method in which it was spread locally at a site were also associated with the magnitude of CT stem decline. These results are indicative of the value of P. punctiformis as a CT biological control agent. The name Cirsium arvense dieback (CADB) is proposed herein to describe the agriculturally important decline in CT stem densities attributable to this previously un-named systemic disease.

In South Asia, bacterial wilt pathogens in the Ralstonia solanacearum species complex (RSSC) impose major constraints on eggplant, tomato, and pepper production. To improve the efficacy of bacterial wilt management, the goals of this study were to (1) conduct a survey of RSSC pathogens in Bangladesh and Nepal, (2) characterize the genetic diversity of these isolates, and (3) screen 37 tomato, eggplant, and pepper accessions for resistance to six representative isolates from South Asia. We isolated 99 isolates from Bangladesh and 20 isolates from Nepal and determined that all are phylotype I isolates of the Ralstonia pseudosolanacearum species. We sequenced and assembled draft genomes for 25 isolates. Phylogenomic analyses suggest that there is a wide diversity of endemic phylotype I isolates in South Asia, and possible introductions of two clonal phylotype I lineages into Bangladesh and Nepal. We contextualize our newly described isolates based on prior reports of RSSC diversity in South Asia and global reports of RSSC pathogens on eggplant and pepper. Greenhouse trials revealed multiple tomato, eggplant, and pepper accessions that exhibit promising levels of resistance to six phylotype I isolates from South Asia.

Oat is a minor forage crop grown in Taiwan. Only a few historical records of oat rust disease have been reported in the country, therefore the pathogen population remains poorly characterized. A rust-like disease outbreak was detected at the Experimental Farm of National Taiwan University in 2019, which caused significant damage to the field experiments. To determine the identity of the pathogen responsible for this disease outbreak, we collected infected foliar material. Disease signs suggested infection by the oat crown rust fungus. Hence, common procedures in rust pathology were applied to confirm the identity of the pathogen with phenotypic and molecular diagnostic techniques. A total of 50 field samples from infected oat cultivars were collected in 2019 and five rust isolates were purified in 2020 and 2021. Phylogenetic analysis based on ITS sequences indicated that the pathogen was likely Puccinia coronata f. sp. avenae (Pca), which was further supported by the placement of Taiwanese isolate NTU-01 with other Pca representatives in a phylogenetic tree of Basidiomycete fungi. Phenotyping assays across 36 oat differential lines demonstrated that Taiwanese isolates are phenotypically similar with relatively limited virulence. This study presents the first molecular confirmation of Pca in Taiwan and reports the virulence profiles of Taiwanese Pca population.

The wheat curl mite (WCM)-transmissible wheat streak disease complex is the most serious disease of wheat in the U.S. Great Plains. In the current study, we determined the genetic variability in WCM and mite-transmitted viruses in Colorado and identified sources of resistance in Colorado wheat germplasm to wheat streak disease complex. We identified two distinct genotypes of WCM, Type 1 and Type 2 based on the ribosomal ITS1 region. Both genotypes were found to co-exist throughout the wheat producing regions of Colorado. Analysis of the whole genome and partial coat protein sequences revealed rich diversity of wheat streak mosaic virus (WSMV) and High Plains wheat mosaic virus (HPWMoV) isolates collected from Colorado, whereas triticum mosaic virus (TriMV) showed low sequence variability. Analysis of WSMV isolates revealed two novel isolates and one that was 100% similar to a new variant of WSMV from Kansas. Interestingly, between 2-4 genotypes of all 8 RNA segments of HPWMoV were identified, which suggests new variants of emaraviruses and co-occurrence of multiple strains within host populations. Several novel viruses including mycoviruses were identified for the first time in Colorado. We found variation in WSMV resistance among wheat varieties; however a variety that harbored dual resistance to mite and WSMV had lower virus titer compared to varieties that contained single resistance gene. This suggests that pyramiding genes will ensure improved and durable resistance. Future research may be aimed at elucidating the dynamics, diversity, and distribution of the new WSMV and HPWMoV isolates and their responses to wheat genotypes.

In bacteria, plasmids can confer the ability to cause disease. Although they can potentially vary in copy number, little has been reported on the dynamics of plasmids in plant pathogenic bacteria. Pathogenicity of the bacterium Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff), which causes foliar disease on leguminous crops, including mung bean (Vigna radiata), has previously been linked to a plasmid. This study explored the variation in plasmid copy number among a genetically diverse collection of 25 Cff isolates using purposely designed quantitative PCR assays for chromosomal and plasmid DNA targets. Pathogenicity and virulence of six Cff isolates, including one plasmid-free isolate, were assessed on the susceptible mung bean cultivar Opal-AU using visual symptoms, trifoliate dry weights and Cff DNA quantities following stem inoculation. Plasmid copy numbers varied significantly (p <0.001) among plasmid-carrying isolates, ranging from 1.37 to 2.74. For subsequent quantification in planta, the single-copy chromosomal PCR target gene, gyrase b, was selected. Mung beans inoculated with plasmid-carrying isolates exhibited significant variation in visual symptoms (p <0.001), while trifoliate dry weights and Cff DNA quantities did not significantly differ. The treatment using a plasmid-free isolate was not significantly different from the negative control for each of the disease traits. Knowledge of plasmid dynamics in Cff populations lays a foundation for improved understanding of the inheritance and impact of plasmid-related traits. The quantification assays will be useful for monitoring Cff populations and the demonstrated variation in pathogenicity and virulence can assist efforts to breed host plant germplasm with reduced susceptibility to Cff.

Late blight caused by Phytophthora infestans poses a significant global threat to potato and tomato cultivation with profound historical and ongoing impacts on food security. In Central America, particularly in Guatemala and Honduras, the disease has intensified over the last decade, possibly due to favorable climatic conditions and changes in local pathogen populations. This study identified four distinct clonal lineages of the A2 mating type, US7A2, US8A2, and 13A2, and a newly identified lineage exhibiting genetic variation. Mitochondrial haplotype analysis confirmed that the patterns aligned with those reported in previous studies, thereby reflecting the diverse genetic composition of this pathogen. The genetic variability of P. infestans, including its reduced sensitivity to fungicides such as metalaxyl, and its ability to overcome host resistance, underscores the importance of understanding its population dynamics. Approximately 61% of the genetic variation was observed between lineages, likely because of the introduction of genetically distinct propagules into infected seeds. These findings underscore the urgent need for region-specific disease management strategies guided by local genetic data to effectively mitigate the impact of late blight and suggest the need to strengthen local seed production to minimize the import of new genotypes.

Bacterial leaf spot caused by Xanthomonas was reported in 2014 as a new disease of crape myrtle. Unfortunately, this foundational strain was lost, preventing further experimentation, sequencing of the genome, and phylogenetic analysis. This work describes a collection of Xanthomonas strains isolated from angular leaf spot lesions on crape myrtle in North Carolina from 2014 to 2023. This study includes full reference genomes, as well as re-fulfillment of Kochs postulates. Genomes were obtained with hybrid whole genome sequencing using Illumina and Nanopore and assembled to develop robust genomic resources for these disease-causing strains. The completed genomes support inclusion of the strains in the X. citri species group; however, both phylogenetic analysis and the identification of a novel plant host suggest the creation of the new pathovar Xanthomonas citri pv. lagerstroemium.

The continuous changes in the lineage proportions of populations in the clonal plant pathogen Phytophthora infestans on potato and tomato crops have been perplexing to researchers and disease managers. Sudden outbreaks of newly emergent genotypes are often associated with these rapid composition changes. Modelling can predict the persistence and displacement of pathogen genotypes with differential fitness among hosts. Building upon previous models, we combined analytical and simulation methods to model the outcome of interactions between competing lineages on multiple hosts. Model inputs include pathogenesis parameters, and the outputs are fitness and lineage proportions within each host. Analytical solutions yielding complete displacement, partial coexistence-displacement, and complete coexistence were described. In a retrospective study, the lesion growth rate and sporulation density of P. infestans lineages on potato and tomato from pathogenicity trials were used as inputs. Output lineage frequencies were compared with historical epidemiological situations to check model accuracy. The results showed that pathogenesis traits measured from empirical trials could simulate lineage constituents on potato and tomato, and estimate genotypic fitness with reasonable accuracy. The model also showed promise in predicting ongoing lineage displacements in the subsequent year or few years, even when the displaced lineage was still highly prevalent during the time of isolation. However, large uncertainties remain at temporal-spatial scales owing to complex meta-population dynamics in some regions and adaptation to local environmental factors. This simulation model provides a new tool for forecasting pathogen compositions, and can be used to identify potentially problematic genotypes based on pathogen life-history traits.

Cassava witches broom disease (CWBD) has emerged as a significant threat to cassava production in the Oiapoque region of Amapa, Brazil. Diseased plants exhibit stunted growth, vascular necrosis, abnormal shoot proliferation, and distinctive broom-like appearance. This study aimed to characterize the disease and identify its causal agent(s). The assessment by high-throughput sequencing of total nucleic acids (DNA and RNA) from affected cassava tissues revealed Rhizoctonia theobromae (syn. Ceratobasidium theobromae) associated with CWBD. PCR-based detection using species-specific primers confirmed the presence of R. theobromae in 74% of symptomatic samples. Genetic diversity analysis based on the Ca2+/calmodulin-dependent protein kinase gene showed low variability among Brazilian isolates compared with Asian populations, suggesting their recent introduction. This first report of R. theobromae causing CWBD in Brazil follows a recent report of the disease from French Guiana and highlights the urgent need for effective measures to prevent the further spread of this emerging pathogen, which poses a deadly threat to cassava cultivation in the rainforest, a significant risk to cassava production in Brazil, and regions with similar eco-climatic conditions.

Phytopathogens are a continuous threat for global food production and security. Emergence or re-emergence of plant pathogens is highly dependent on the environmental conditions affecting pathogen spread and survival. Under climate change, a geographic expansion of pathogen distribution poleward has been observed, potentially resulting in disease outbreaks on crops and wild plants. Therefore, estimating the adaptive potential of plants to novel epidemics and describing its underlying genetic architecture, is a primary need to propose agricultural management strategies reducing pathogen outbreaks and to breed novel plant cultivars adapted to pathogens that might spread in novel habitats under climate change. To address this challenge, we inoculated Pseudomonas syringae strains isolated from Arabidopsis thaliana populations located in south-west of France on the highly genetically polymorphic TOU-A A. thaliana population located east-central France. While no adaptive potential was identified in response to most P. syringae strains, the TOU-A population displays a variable disease response to the P. syringae strain JACO-CL belonging to the phylogroup 7 (PG7). This strain carried a reduced T3SS characteristic of the PG7 as well as flexible genomic traits and potential novel effectors. GWA mapping on 192 TOU-A accessions inoculated with JACO-CL revealed a polygenic architecture. The main QTL region encompasses two R genes and the AT5G18310 gene encoding for ubiquitin hydrolase, a target of the AvrRpt2 P. syringae effector. Altogether, our results pave the way for a better understanding of the genetic and molecular basis of the adaptive potential in an ecologically relevant A. thaliana - P. syringae pathosystem.

Xanthomonas wilt (XW) of banana caused by Xanthomonas vasicola pv. musacearum (Xvm) does not spread to all plants physically interconnected through the rhizome when one or a few are diseased. However, the factors behind this incomplete systemic spread of Xvm are not fully known yet could inform XW management. This study explored the effect of Xvm inoculum amounts, number and size of suckers, sucker positioning on mother plant corms and other mother plant corm attributes on sucker colonization. A shorter (p <0.05) incubation period (17.9 vs 21.1 days) and higher (p<.001) cumulative number of symptomatic leaves (5.2 vs 1.6 leaves) was observed when all (high inoculum) compared to two leaves (low inoculum) were inoculated. Xvm was recovered in corms at 29 days post inoculation (dpi) in both treatments with no differences (p >0.05) in proportions of corms with Xvm between the treatments. However, Xvm was recovered earlier and at a higher frequency in suckers when all leaves were inoculated. Lower Xvm recoveries occurred in the lower corm sections to which most suckers were attached relative to the middle and upper corm sections. Xvm incidence in corms increased with the number of attached maiden suckers, and the dpi while it declined with increasing mother plant and corm height. Thus, Xvm spread within mats is influenced by the amount of inoculum and the physiological stage (e.g., height) of the plant and attached suckers. The position of suckers, predominantly at the bottom of corms also protects them from infection. Measures that reduce Xvm inoculum build-up in mats are thus crucial for minimizing within mat XW spread.

Bacterial canker, caused the Pseudomonas syringae species complex, is a major constraint on sweet cherry production worldwide. However, the influence of agronomic practices on pathogen ecology, dispersal and evolution under field conditions remains poorly understood. Here, we combined a factorial-design field experiment with whole-genome sequencing to investigate the effects of polytunnel covering and nitrogen fertigation on phyllosphere populations and the dynamics of a key pathogen, P. syringae pathovar syringae 9644 (Pss9644) in young cherry trees. Epiphytic P. syringae populations initially resembled those in surrounding woodland environments. Over time, pathogenic phylogroup 2d lineages became dominant, particularly on uncovered trees. Diversity of P. syringae populations was higher in uncovered treatments. Polytunnel covering markedly altered community composition and limited rain-splash dispersal of Pss9644 from stem cankers to leaves, thereby interrupting a key stage of the disease cycle. By contrast, nitrogen fertigation had no detectable effect on phyllosphere community structure, but enhanced plant growth and reduced lesion expansion following inoculation. Whole-genome sequencing of re-isolated Pss9644 strains revealed limited short-term genomic diversification, with single-nucleotide polymorphisms detected in 22 re-isolates. In total, 36 mutations were identified across the chromosome although no mutation affected virulence or motility. Taken together, our results show that agronomic practices influence both pathogen ecology and disease outcomes through distinct mechanisms: polytunnel covering primarily limits pathogen dispersal and reshapes phyllosphere communities, while nitrogen fertigation enhances plant growth and reduces disease severity. These findings highlight the potential to integrate canopy management and nutrient strategies to mitigate bacterial canker risk in commercial cherry production.

Fusarium wilt, caused by Fusarium oxysporum f. sp. vasinfectum (Fov), is one of the most destructive early-season cotton diseases worldwide. The recent emergence of the highly virulent Fov race 4 (Fov4) and its aggressiveness have raised significant concerns for the U.S. cotton industry. Unlike predominant Fov races in US cotton production, which require root-knot nematodes to cause damage, Fov4 is known to infect cotton independent of nematodes. However, molecular mechanisms of Fov4 virulence in cotton are not clearly understood. Secondary metabolites are often identified as the culprits in pathogen virulence toward plant hosts. To investigate these factors in Fov4, we analyzed the genomes of Fov1 and Fov4 using Fungal antiSMASH and identified a Fov4-specific nonribosomal peptide synthetase (NRPS) gene FNP1. To investigate its function, we generated FNP1 knock-out mutant using CRISPR-Cas9 approach. Growth assays revealed that the mutants exhibit significantly attenuated hyphal production on media containing cotton roots as the sole carbon source, increased sensitivity to cell stress agents, as well as lagged spore germination. Furthermore, the mutant exhibited defect in cotton root rot virulence and significant decrease in Fusaric acid production. Microscopic observation of GFP-labeled FNP1 deletion mutant showed impeded infection progression in cotton roots compared to the wild type (WT), which further explained the impeded virulence in FNP1 mutant. Gene complementation restored the observed defects, confirming that FNP1 is critical for Fov4 virulence, hyphal development, Fusaric acid production, and stress responses. HighlightsComparative genomic analysis between Fov1 and Fov4 identified FNP1 as a gene specific to Fov4. CRISPR/Cas9 system was employed in Fov4 to generate gene deletion mutants and GFP labeling. FNP1 plays a critical role in Fov4 hyphal development, virulence, fusaric acid production, and stress responses. This study is the first report to identify and functionally characterize a virulence gene in Fusarium oxysporum f. sp. vasinfectum (Fov) race 4 (Fov4) in cotton wilt pathogenesis.

Assessment of the severity of Fusarium wilt disease in cowpea and other crops relies mainly on visual rating scales which are prone to errors, which can compromise the reproducibility of the data. Furthermore, the rating scales require considerable practical training and routine experience for reliable assessment. Two objective metrics, stem vascular discoloration length (%VDL) and number of Fusarium necrotic vessels (NFNV), for quantitative measurement of vascular damage incited by Fusarium oxysporum f. sp. tracheiphilum race 4 (Fot4) of cowpea, were compared and their utility as a measure of disease severity and potential usefulness in other crop pathosystems is proposed. The metrics were tested in seven F2 populations and one F2:3 population, segregating for wilt response, and inoculated with race Fot4 at the seedling stage. %VDL and NFNV were highly correlated with plant wilting for all populations (r = 0.51 - 0.93 and 0.52 - 0.94, respectively). Furthermore, the relationships between the variables were linear in all populations (R2 = 0.81 to 0.87 and 0.71 to 0.91), indicating that they can provide accurate and reliable measurement of severity of Fusarium wilt disease. Also, %VDL and NFNV were strongly correlated (r = 0.88 - 0.97) and demonstrated a linear relationship (R2 = 0.69 - 0.94). Analysis of goodness-of-fit in two F2 populations revealed that errors in measurement of vascular discoloration length can result in higher segregation distortion when compared to enumeration of necrotic vessels. However, both metrics were highly effective in accounting for the severity of vascular damage caused by Fusarium wilt disease.

Most Ralstonia solanacearum species complex strains cause bacterial wilts in tropical or subtropical zones, but the group known as Race 3 biovar 2 (R3bv2) is cool virulent and causes potato brown rot at lower temperatures. R3bv2 has invaded potato-growing regions around the world but is not established in the United States. Phylogenetically, R3bv2 corresponds to a subset of the R. solanacearum phylotype IIB clade, but little is known about the distribution of the cool virulence phenotype within phylotype IIB. Therefore, genomes of 76 potentially cool virulent phylotype IIB strains and 30 public genomes were phylogenetically analyzed. A single clonal lineage within the sequevar 1 subclade of phylotype IIB that originated in South America has caused nearly all brown rot outbreaks worldwide. To correlate genotypes with relevant phenotypes, we quantified virulence of ten Ralstonia strains on tomato and potato at both 22{degrees}C and 28{degrees}C. Cool virulence on tomato did not predict cool virulence on potato. We found that cool virulence is a quantitative trait. Strains in the sequevar 1 pandemic clonal lineage caused the most disease, while other R3bv2 strains were only moderately cool virulent. However, some non-R3bv2 strains were highly cool virulent and aggressively colonized potato tubers. Thus, cool virulence is not consistently correlated with strains historically classified as R3bv2 group. To aid detection of sequevar 1 strains, this group was genomically delimited in the LINbase web server and a sequevar 1 diagnostic primer pair was developed and validated. We discuss implications of these results for the R3bv2 definition.

Small-spored Alternaria species such as A. alternata and A. arborescens are frequently isolated from diseased potato and tomato plants. However, their respective host ranges and pathogenic behaviours remain poorly resolved, and it is unclear whether their occurrence across hosts reflects true specialisation or ecological opportunism. Limited genetic differentiation among these closely related taxa further complicates their classification as primary necrotrophs or secondary colonisers. In this study, we analysed natural populations of small-spored Alternaria from Germany, Poland, and Serbia using molecular phylogenetics, morphological characterisation, and controlled infection assays to clarify species identity, host associations, and pathogenic potential. Both A. alternata and A. arborescens were detected across all regions and hosts, indicating broad distribution and ecological overlap. The two species were consistently isolated from foliar lesions and were each capable of causing characteristic Alternaria Brown-Spot (ABS) symptoms, thereby fulfilling Kochs postulates. Phylogenetic analyses based on Alt A1 and RPB2 loci resolved two well-supported species clades and revealed extensive haplotype sharing across more than 1300 km, multiple hosts, and diverse climates, suggesting high gene flow and limited population structure. The consistent co-occurrence and comparable pathogenicity of A. alternata and A. arborescens underscore their equal ecological relevance and redefine their roles in ABS epidemiology. These findings indicate that perceived differences in host specialisation may be overstated and that both species contribute equally to Alternaria Brown-Spot epidemics in solanaceous crops.

Wheat blast, caused by Pyricularia oryzae Triticum (PoT), is an emergent threat to wheat production. Current understanding of the evolution and population biology of the pathogen and epidemiology of the disease has been based on phylogenomic studies that compared the wheat blast pathogen with isolates collected from grasses that were invasive to Brazilian wheat fields. Genetic similarity between isolates from wheat and grasses lead to the conclusion that significant cross-infection occurs, especially on signalgrass (Urochloa spp.); and this in turn prompted speculation that its widespread use as forage is a key driver of the diseases epidemiology. We reanalyzed data from those studies and found that all but one of the isolates from non-wheat hosts were members of PoT and the related Lolium-adapted lineage (PoL1), which meant that the Pyricularia populations typically found on endemic grasses had not yet been sampled. To address this shortcoming, we performed a comprehensive sampling of blast lesions in wheat crops and endemic grasses found in and away from wheat fields in Minas Gerais. A total 1,368 diseased samples were collected (976 leaves of wheat and grasses and 392 wheat heads) which yielded a working collection of 564 Pyricularia isolates. We show that, contrary to earlier implications, PoT was rarely found on endemic grasses and, conversely, members of grass-adapted populations were rarely found on wheat. Instead, most populations were host-specialized with constituent isolates usually grouping according to their host-of-origin. With regard to the dominant role proposed for signalgrass in wheat blast epidemiology, we found only one PoT member in 67 isolates collected from signalgrass grown away from wheat fields, and only three members of Urochloa-adapted populations among hundreds of isolates from wheat. Cross-inoculation assays on wheat and a signalgrass used in pastures (U. brizantha) suggested that the limited cross-infection observed in the field may be due to innate compatibility differences. Whether or not the observed level of cross-infection would be sufficient to provide an inoculum reservoir, or serve as a bridge between wheat growing regions, is questionable and, therefore, deserves further investigation.

The characterization of virulence frequencies has to be regularly updated to identify which genes are currently efficient and use this information to advise gene deployment by choosing varieties depending on the current composition of local pathogen population. In L. maculans on Brassica napus, because different genes were characterized by different teams, because new interactions are continuously identified and seed of differentials are difficult to obtain, we today still lack isolates characterized on all current resistance genes. On the one hand, we assembled a set of 12 isolates characterized on 13 of the 17 described resistance genes, having clearly compatible and clearly incompatible isolates for each interaction. This set can be used to characterize the L. maculans - B. napus interaction at cotyledon stage. Expanding the set of isolates with clearly virulent ones allowed us to detect inconsistent behaviour or intermediate (avirulent) phenotypes. On the other hand, we used this set of isolates as controls to identify virulence frequencies in a current French L. maculans population sampled in 2018 at Le Rheu. We provide the current status for 13 avirulence frequencies, including LepR1, LepR2 and LepR3 available in near isogenic lines of spring canola but not yet documented in France. Avirulence frequencies on the genes Rlm1, Rlm2, Rlm3, Rlm4, Rlm7, Rlm9 and LepR3 were low, indicating the lack of efficacy of these genes against the current population. In the opposite, all or most of isolates were avirulent for the genes Rlm5, Rlm6, Rlm10, Rlm11, LepR1 and LepR2. An optimistic point of view could conclude that there are ample resources for oilseed rape breeding. However, as compared to previous studies, so far all the resistance genes used on significant acreage without additional management practices have lost efficacy and only avirulences corresponding to resistance genes not deployed in France retain efficacy. While the call to wisely manage the available host resistance genes is not recent, it is still relevant. Adding, management practices to the deployment of resistance genes in order to reduce inoculum carry-over from one growing season to the next and to lower population sizes is key to maintain their efficacy over time.

Phyllachora maydis Maubl, the causal pathogen of tar spot of corn (Zea mays L.), has emerged recently in the United States and Canada. Studies related to its genetic diversity and population structure are limited and are necessary to improve our understanding of this pathogens biology, ecology, epidemiology, and evolutionary potential within this region. This study developed and used 13 microsatellites (SSR markers) to assess the genetic population structure, diversity, gene flow and reproductive mode of 181 P. maydis samples across five states in the Midwest U.S. The polymorphic information content (PIC) of loci ranged from 0.32 to 0.72 per locus, indicating their high utility for assessing the dynamics of P. maydis populations. Analysis of molecular variance (AMOVA) detected a significantly low, but statistically significant genetic differentiation (FST = 0.15) among populations, where 85% of the variance resided within populations. P. maydis populations were highly diverse (He = 0.55), with moderate gene flow (Nm = 2.80), and showed evidence of sexual recombination ([r]d; p = > 0.001). Structure analysis showed the samples were not geographically structured but rather grouped into two genetic clusters (k =2) of severe genetic admixture suggesting possible long-distance dispersal of aerial spores or infected corn materials among the five Midwest states. Both principal coordinate analysis (PCoA) and discriminate analysis of principal component (DAPC) supported the STRUCTURE analysis of the two clusters. These 13 highly polymorphic molecular markers could be used for future investigations of this pathogens population dynamics within the U.S., and possibly populations outside.

Tomato (Solanum lycopersicum) is one of the most economically important vegetables in the world. Root-knot nematodes (RKN) form a complex of species that can cause severe losses in tomatoes. Since symptoms and damage depend on the particular nematode species, accurate species identification is critical for implementing potential control measures. Detailed surveys of plant parasitic nematodes in Nepal have not been conducted. Therefore, there is no information on which RKN species occur in key tomato-growing areas. We conducted an initial survey to assess the occurrence and importance of RKN. Nine different districts of Nepal were included: Bhaktapur, Chitwan, Dhading, Dolakha, Kaski, Kathmandu, Kavrepalanchok, Lalitpur, and Lamjung. In the first approach, 70 farmers were interviewed about their awareness and knowledge of RKN. More than 60% of the farmers surveyed knew of RKN and the main signs and symptoms. 40% had limited or no knowledge about it. In a second approach, we conducted a survey of RKN occurrence in tomato fields in the same nine districts. Soil sampling and subsequent analysis in the Kathmandu district revealed RKN infestation at very high levels. Except for Kaski and Chitwan, RKN prevalence was found to be 100% in the districts sampled. The overall prevalence of Meloidogyne species was also 100% in most districts. To identify the species, samples with RKN-infected galls were collected and determined morphologically using perineal patterns and molecularly using specific PCR analyses. Both methods showed that Meloidogyne incognita was the most abundant in the tomato fields, followed by M. arenaria and M. javanica. Our results confirm the importance of RKN in Nepal and suggest that it would be highly beneficial economically to increase farmer awareness of nematode problems and possible control measures.