Late blight, caused by oomycetes Phytophthora infestans is one of the most challenging fungal diseases to manage in tomato plants (Solanum lycopersicum L.). Toward managing the disease, conventional breeding has successfully introgressed genetic loci conferring disease resistance from various wild relatives of tomato into commercial varieties. The cataloging of disease-associated SNP markers and a deeper understanding of disease-resistance mechanisms are needed to keep up with the demand for commercial varieties resistant against emerging pathogen strains. To this end, we performed transcriptome sequencing to evaluate the gene expression dynamics of tomato varieties, resistant and susceptible to Phytophthora infection. Further integrating the transcriptome dataset with large-scale public genomic data of varieties with known disease phenotypes, a panel of single nucleotide polymorphism (SNP) markers correlated with disease resistance was identified. These SNPs were then validated on 31 lines with contrasting phenotypes for late blight. The identified SNPs are located on genes coding for a putative cysteine-rich transmembrane module (CYSTM), Solyc09g098310, and a nucleotide-binding site–leucine-rich repeat protein, Solyc09g098100, close to the well-studied Ph-3 resistance locus known to have a role in plant immunity against fungal infections. The panel of SNPs generated by this study using transcriptome sequencing showing correlation with disease resistance across a broad set of plant material can be used as markers for molecular screening in tomato breeding.

Soil fungi play a key role in nutrient cycling and soil organic matter turnover, yet the influence of pedological context on fungal communities across forest types remains insufficiently understood. Here, we combined soil chemical analyses, Fourier-transform infrared spectroscopy (FTIR), and ITS2 metabarcoding to investigate soil properties and fungal communities in temperate mountain beech (Fagus sylvatica L.) and Norway spruce (Picea abies (L.) H. Karst) forests in Italy developed on contrasting geological substrates. Soil horizons were sampled across seasons to characterize the main associations between fungal community structure, inferred functional diversity, and environmental context. Soil chemistry revealed site- and horizon-dependent patterns, particularly in pH, Ca, and P availability, whereas differences related to dominant tree species were comparatively limited. FTIR spectra showed clear variation in organic matter composition among sites, consistent with site- and stand-associated differences in organic matter composition. Fungal community composition was primarily associated with site and soil horizon. Functional guild patterns suggested ectomycorrhizal dominance in Ca-rich soils and greater prevalence of saprotrophs in more acidic soils. Overall, this multi-proxy approach suggests that pedological context was more closely associated with fungal community structure and ecological strategies than with vegetation type or season within the studied stands. These patterns should be interpreted as site-specific and hypothesis-generating because substrate types were not replicated across independent locations.