Transcriptome sequencing of phytophthora infestans (late blight) resistant and susceptible tomato lines .

Late Blight caused by oomycetes Phytophthora infestans has been one of the most challenging fungal diseases to manage in tomatoes (Solanum lycopersicum L). For managing the disease, breeding programs to produce disease resistance have successfully incorporated many genetic loci from various wild relatives of tomatoes into commercial varieties. However, more understanding of disease and efficient breeding strategy is required to keep up with the demand for resistant commercial varieties with broad-spectrum resistance against emerging pathogen strains. In this study, we performed transcriptome sequencing to understand the gene expression dynamics in resistant and susceptible tomato varieties upon infection. Further, incorporating the transcriptome with large-scale public genomic data of varieties with known phenotypes, we report a set of single nucleotide polymorphism (SNP) markers correlating with resistance, which can support marker-assisted breeding programs. The identified SNPs were located on a putative cysteine-rich transmembrane module (CYSTM) gene and a nucleotide-binding site–leucine-rich repeat protein close to well-studied Ph-3 resistance locus and known to have a role in plant immunity against fungal infections. Finally, the identified SNPs were validated using rhAmp SNP assays on a large set of breeding varieties contrasting for resistance against late blight.