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

A pathogen's spatial range is not constrained by geographical features in the flax rust pathosystem

Climate change and shifting environmental conditions can allow pathogens to spread into previously unburdened areas. For plant pathogens, this dynamic has the potential to disrupt natural ecosystem equilibria and human agriculture, making predicting plant pathogen range shifts increasingly important. Although such predictions will hinge on an accurate understanding of the determinants of pathogen range-namely the environmental, geographical, and host range characteristics that modulate local pathogen habitation-few studies to date have probed these in natural plant populations. Here, we characterize range determinants for the model system of Lewis flax (Linum lewisii) and its pathogen, flax rust (Melampsora lini), in the Rocky Mountains. Transect surveys were performed to assess three relationships: (i) the effect of geographical features-elevation, slope aspect, slope grade, and land cover-on flax presence and density, (ii) the effect of geographical features on flax rust presence and prevalence, and (iii) the effects of flax's local population density and metapopulation structure on flax rust presence and prevalence. We found that flax population density, but not host metapopulation structure, influences the distribution of flax rust. Additionally, we showed that, while the distribution of flax was broadly constrained to a relatively narrow range of geographical and resulting environmental features, flax rust was evenly distributed across the full range of settings measured. These results indicate that a warming environment, which is expected to modulate such features, may restrict the optimal range of the plant more than that of its pathogen. Importantly, our results also suggest that even if flax shifts its spatial range to escape increasing climatic pressures, flax rust will not face any significant barriers to track this movement.

The Melampsora americana Population on Salix purpurea in the Great Lakes Region Is Highly Diverse with a Contributory Influence of Clonality

Shrub willows (Salix spp.) are emerging as a viable lignocellulosic, second-generation bioenergy crop with many growth characteristics favorable for marginal lands in New York State and surrounding areas. Willow rust, caused by members of the genus Melampsora, is the most limiting disease of shrub willow in this region and remains extremely understudied. In this study, genetic diversity, genetic structure, and pathogen clonality were examined in Melampsora americana over two growing seasons via genotyping-by-sequencing to identify single-nucleotide polymorphism markers. In conjunction with this project, a reference genome of rust isolate R15-033-03 was generated to aid in variant discovery. Sampling between years allowed regional and site-specific investigation into population dynamics, in the context of both wild and cultivated hosts within high-density plantings. This work revealed that this pathogen is largely panmictic over the sampled areas, with few sites showing moderate genetic differentiation. These data support the hypothesis of sexual recombination between growing seasons because no genotype persisted across the two years of sampling. Additionally, clonality was determined as a driver of pathogen populations within cultivated fields and single shrubs; however, there is also evidence of high genetic diversity of rust isolates in all settings. This work provides a framework for M. americana population structure in the Great Lakes region, providing crucial information that can aid in future resistance breeding efforts.

Genetic Analysis of Plant Pathogens Natural Populations

Population genetics allow to address fundamental questions about the biology of plant pathogens. By testing specific hypotheses, population genetics provide insights into the population genetic variability of pathogens across different geographical areas, time, and associated plant hosts, as well as on the structure and differentiation of populations, and on the possibility that a population is introduced and from where it has originated. In this chapter, basic concepts of population genetics are introduced, as well as the five evolutionary factors affecting populations, that is, mutations, recombination, variation in population size, gene flow, and natural selection. A step-by-step workflow, from sampling to data analysis, on how to perform a genetic analysis of natural populations of plant pathogens is discussed. Increased knowledge of the population biology of pathogens is pivotal to improve management strategies of diseases in agricultural and forest ecosystems.

Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici

Pathogens cause significant challenges to global food security. On annual crops, pathogens must re-infect from environmental sources in every growing season. Fungal pathogens have evolved mixed reproductive strategies to cope with the distinct challenges of colonizing growing plants. However, how pathogen diversity evolves during growing seasons remains largely unknown. Here, we performed a deep hierarchical sampling in a single experimental wheat field infected by the major fungal pathogen Zymoseptoria tritici. We analysed whole genome sequences of 177 isolates collected from 12 distinct cultivars replicated in space at three time points of the growing season to maximize capture of genetic diversity. The field population was highly diverse with 37 SNPs per kilobase, a linkage disequilibrium decay within 200-700 bp and a high effective population size. Using experimental infections, we tested a subset of the collected isolates on the dominant cultivar planted in the field. However, we found no significant difference in virulence of isolates collected from the same cultivar compared to isolates collected on other cultivars. About 20 % of the isolate genotypes were grouped into 15 clonal groups. Pairs of clones were disproportionally found at short distances (<5 m), consistent with experimental estimates for per-generation dispersal distances performed in the same field. This confirms predominant leaf-to-leaf transmission during the growing season. Surprisingly, levels of clonality did not increase over time in the field although reproduction is thought to be exclusively asexual during the growing season. Our study shows that the pathogen establishes vast and stable gene pools in single fields. Monitoring short-term evolutionary changes in crop pathogens will inform more durable strategies to contain diseases.

Battling the biotypes of balsam: the biological control of Impatiens glandulifera using the rust fungus Puccinia komarovii var. glanduliferae in GB

Impatiens glandulifera, or Himalayan balsam, is a prolific invader of riverine habitats. Introduced from the Himalayas for ornamental purposes in 1839, this annual species has naturalised across Great Britain (GB) forming dense monocultures with negative affects across whole ecosystems. In 2006 a programme exploring biocontrol as an alternative control method was initiated and to date, two strains of the rust fungus Puccinia komarovii var. glanduliferae have been released. To better understand the observed differences in susceptibility of GB Himalayan balsam stands to the two rust strains, inoculation studies were conducted using urediniospores and basidiospores. Experiments revealed large variation in the susceptibility of stands to urediniospores of the two rust strains, with some resistant to both. Furthermore, the infectivity of basidiospores was found to differ, with some stands fully susceptible to the urediniospore stage, being immune to basidiospore infection. Therefore, before further rust releases at new sites, it is necessary to ensure complete compatibility of the invasive stands with both urediniospores and basidiospores. However, for successful control across GB it is essential that plant biotypes are matched to the most virulent rust strains. This will involve additional strains from the native range to tackle those biotypes resistant to the strains currently released.